spaCy/spacy/pipeline/_parser_internals/arc_eager.pyx

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# cython: profile=True, cdivision=True, infer_types=True
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
from cymem.cymem cimport Pool, Address
from libc.stdint cimport int32_t
from libcpp.vector cimport vector
from collections import defaultdict, Counter
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from ...typedefs cimport hash_t, attr_t
from ...strings cimport hash_string
from ...structs cimport TokenC
from ...tokens.doc cimport Doc, set_children_from_heads
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from ...tokens.token cimport MISSING_DEP
from ...training import split_bilu_label
from ...training.example cimport Example
from .stateclass cimport StateClass
from ._state cimport StateC, ArcC
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from ...errors import Errors
from .search cimport Beam
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cdef weight_t MIN_SCORE = -90000
cdef attr_t SUBTOK_LABEL = hash_string('subtok')
DEF NON_MONOTONIC = True
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cdef enum:
SHIFT
REDUCE
LEFT
RIGHT
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BREAK
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N_MOVES
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MOVE_NAMES = [None] * N_MOVES
MOVE_NAMES[SHIFT] = 'S'
MOVE_NAMES[REDUCE] = 'D'
MOVE_NAMES[LEFT] = 'L'
MOVE_NAMES[RIGHT] = 'R'
MOVE_NAMES[BREAK] = 'B'
2015-01-27 19:18:43 +03:00
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef enum:
HEAD_IN_STACK = 0
HEAD_IN_BUFFER
HEAD_UNKNOWN
IS_SENT_START
SENT_START_UNKNOWN
cdef struct GoldParseStateC:
char* state_bits
int32_t* n_kids_in_buffer
int32_t* n_kids_in_stack
int32_t* heads
attr_t* labels
int32_t** kids
int32_t* n_kids
int32_t length
int32_t stride
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
weight_t push_cost
weight_t pop_cost
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef GoldParseStateC create_gold_state(Pool mem, const StateC* state,
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
heads, labels, sent_starts) except *:
cdef GoldParseStateC gs
gs.length = len(heads)
gs.stride = 1
assert gs.length > 0
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gs.labels = <attr_t*>mem.alloc(gs.length, sizeof(gs.labels[0]))
gs.heads = <int32_t*>mem.alloc(gs.length, sizeof(gs.heads[0]))
gs.n_kids = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids[0]))
gs.state_bits = <char*>mem.alloc(gs.length, sizeof(gs.state_bits[0]))
gs.n_kids_in_buffer = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids_in_buffer[0]))
gs.n_kids_in_stack = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids_in_stack[0]))
for i, is_sent_start in enumerate(sent_starts):
if is_sent_start == True:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
1
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
0
)
2020-10-04 12:16:31 +03:00
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
elif is_sent_start is None:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
1
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
0
)
else:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
0
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
0
)
2020-10-04 12:16:31 +03:00
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for i, (head, label) in enumerate(zip(heads, labels)):
if head is not None:
gs.heads[i] = head
gs.labels[i] = label
if i != head:
gs.n_kids[head] += 1
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_UNKNOWN,
0
)
else:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_UNKNOWN,
1
)
# Make an array of pointers, pointing into the gs_kids_flat array.
assert gs.length > 0
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gs.kids = <int32_t**>mem.alloc(gs.length, sizeof(int32_t*))
for i in range(gs.length):
if gs.n_kids[i] != 0:
gs.kids[i] = <int32_t*>mem.alloc(gs.n_kids[i], sizeof(int32_t))
# This is a temporary buffer
js_addr = Address(gs.length, sizeof(int32_t))
js = <int32_t*>js_addr.ptr
for i in range(gs.length):
if not is_head_unknown(&gs, i):
head = gs.heads[i]
if head != i:
gs.kids[head][js[head]] = i
js[head] += 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
gs.push_cost = push_cost(state, &gs)
gs.pop_cost = pop_cost(state, &gs)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
return gs
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef void update_gold_state(GoldParseStateC* gs, const StateC* s) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for i in range(gs.length):
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_IN_BUFFER,
0
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_IN_STACK,
0
)
gs.n_kids_in_stack[i] = 0
gs.n_kids_in_buffer[i] = 0
2020-10-04 12:16:31 +03:00
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
for i in range(s.stack_depth()):
s_i = s.S(i)
if not is_head_unknown(gs, s_i) and gs.heads[s_i] != s_i:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gs.n_kids_in_stack[gs.heads[s_i]] += 1
for kid in gs.kids[s_i][:gs.n_kids[s_i]]:
gs.state_bits[kid] = set_state_flag(
gs.state_bits[kid],
HEAD_IN_STACK,
1
)
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
for i in range(s.buffer_length()):
b_i = s.B(i)
if s.is_sent_start(b_i):
break
if not is_head_unknown(gs, b_i) and gs.heads[b_i] != b_i:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gs.n_kids_in_buffer[gs.heads[b_i]] += 1
for kid in gs.kids[b_i][:gs.n_kids[b_i]]:
gs.state_bits[kid] = set_state_flag(
gs.state_bits[kid],
HEAD_IN_BUFFER,
1
)
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
gs.push_cost = push_cost(s, gs)
gs.pop_cost = pop_cost(s, gs)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef class ArcEagerGold:
cdef GoldParseStateC c
cdef Pool mem
def __init__(self, ArcEager moves, StateClass stcls, Example example):
self.mem = Pool()
heads, labels = example.get_aligned_parse(projectivize=True)
2021-01-13 16:20:05 +03:00
labels = [example.x.vocab.strings.add(label) if label is not None else MISSING_DEP for label in labels]
2021-01-16 05:44:11 +03:00
sent_starts = _get_aligned_sent_starts(example)
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
assert len(heads) == len(labels) == len(sent_starts), (len(heads), len(labels), len(sent_starts))
self.c = create_gold_state(self.mem, stcls.c, heads, labels, sent_starts)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def update(self, StateClass stcls):
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
update_gold_state(&self.c, stcls.c)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def _get_aligned_sent_starts(example):
"""Get list of SENT_START attributes aligned to the predicted tokenization.
If the reference has not sentence starts, return a list of None values.
This function is slightly different from the one on Example, because we also
check whether the reference sentences align across multiple sentences,
and return missing values if they do. This prevents a problem where you have
the start of a sentence merged onto a token that belongs to two sentences.
"""
if example.y.has_annotation("SENT_START"):
align = example.alignment.y2x
sent_starts = [False] * len(example.x)
seen_words = set()
for y_sent in example.y.sents:
x_indices = list(align[y_sent.start : y_sent.end])
if any(x_idx in seen_words for x_idx in x_indices):
# If there are any tokens in X that align across two sentences,
# regard the sentence annotations as missing, as we can't
# reliably use them.
return [None] * len(example.x)
seen_words.update(x_indices)
sent_starts[x_indices[0]] = True
return sent_starts
else:
return [None] * len(example.x)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef int check_state_gold(char state_bits, char flag) nogil:
cdef char one = 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
return 1 if (state_bits & (one << flag)) else 0
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef int set_state_flag(char state_bits, char flag, int value) nogil:
cdef char one = 1
if value:
return state_bits | (one << flag)
else:
return state_bits & ~(one << flag)
cdef int is_head_in_stack(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_IN_STACK)
cdef int is_head_in_buffer(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_IN_BUFFER)
cdef int is_head_unknown(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_UNKNOWN)
cdef int is_sent_start(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], IS_SENT_START)
cdef int is_sent_start_unknown(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], SENT_START_UNKNOWN)
# Helper functions for the arc-eager oracle
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t push_cost(const StateC* state, const GoldParseStateC* gold) nogil:
cdef weight_t cost = 0
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
b0 = state.B(0)
if b0 < 0:
return 9000
if is_head_in_stack(gold, b0):
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cost += 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cost += gold.n_kids_in_stack[b0]
if Break.is_valid(state, 0) and is_sent_start(gold, state.B(1)):
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cost += 1
return cost
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t pop_cost(const StateC* state, const GoldParseStateC* gold) nogil:
cdef weight_t cost = 0
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
s0 = state.S(0)
if s0 < 0:
return 9000
if is_head_in_buffer(gold, s0):
cost += 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cost += gold.n_kids_in_buffer[s0]
return cost
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef bint arc_is_gold(const GoldParseStateC* gold, int head, int child) nogil:
if is_head_unknown(gold, child):
return True
elif gold.heads[child] == head:
return True
else:
return False
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef bint label_is_gold(const GoldParseStateC* gold, int child, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
if is_head_unknown(gold, child):
return True
2017-05-30 21:37:24 +03:00
elif label == 0:
return True
elif gold.labels[child] == label:
return True
else:
return False
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef bint _is_gold_root(const GoldParseStateC* gold, int word) nogil:
return gold.heads[word] == word or is_head_unknown(gold, word)
cdef class Shift:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
"""Move the first word of the buffer onto the stack and mark it as "shifted"
Validity:
* If stack is empty
* At least two words in sentence
* Word has not been shifted before
Cost: push_cost
Action:
* Mark B[0] as 'shifted'
* Push stack
* Advance buffer
"""
@staticmethod
2017-05-28 15:06:40 +03:00
cdef bint is_valid(const StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.stack_depth() == 0:
return 1
elif st.buffer_length() < 2:
return 0
elif st.is_sent_start(st.B(0)):
return 0
elif st.is_unshiftable(st.B(0)):
return 0
else:
return 1
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef int transition(StateC* st, attr_t label) nogil:
st.push()
2014-12-16 14:44:43 +03:00
@staticmethod
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t cost(const StateC* state, const void* _gold, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gold = <const GoldParseStateC*>_gold
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
return gold.push_cost
cdef class Reduce:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
"""
Pop from the stack. If it has no head and the stack isn't empty, place
it back on the buffer.
Validity:
* Stack not empty
* Buffer nt empty
* Stack depth 1 and cannot sent start l_edge(st.B(0))
Cost:
* If B[0] is the start of a sentence, cost is 0
* Arcs between stack and buffer
* If arc has no head, we're saving arcs between S[0] and S[1:], so decrement
cost by those arcs.
"""
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef bint is_valid(const StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.stack_depth() == 0:
return False
elif st.buffer_length() == 0:
return True
elif st.stack_depth() == 1 and st.cannot_sent_start(st.l_edge(st.B(0))):
return False
else:
return True
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef int transition(StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.has_head(st.S(0)) or st.stack_depth() == 1:
st.pop()
else:
st.unshift()
@staticmethod
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t cost(const StateC* state, const void* _gold, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gold = <const GoldParseStateC*>_gold
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if state.is_sent_start(state.B(0)):
return 0
s0 = state.S(0)
cost = gold.pop_cost
if not state.has_head(s0):
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
# Decrement cost for the arcs we save, as we'll be putting this
# back to the buffer
if is_head_in_stack(gold, s0):
cost -= 1
cost -= gold.n_kids_in_stack[s0]
return cost
cdef class LeftArc:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
"""Add an arc between B[0] and S[0], replacing the previous head of S[0] if
one is set. Pop S[0] from the stack.
Validity:
* len(S) >= 1
* len(B) >= 1
* not is_sent_start(B[0])
Cost:
pop_cost - Arc(B[0], S[0], label) + (Arc(S[1], S[0]) if H(S[0]) else Arcs(S, S[0]))
"""
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef bint is_valid(const StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.stack_depth() == 0:
return 0
elif st.buffer_length() == 0:
2018-04-08 15:50:21 +03:00
return 0
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
elif st.is_sent_start(st.B(0)):
return 0
elif label == SUBTOK_LABEL and st.S(0) != (st.B(0)-1):
return 0
else:
return 1
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef int transition(StateC* st, attr_t label) nogil:
st.add_arc(st.B(0), st.S(0), label)
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
# If we change the stack, it's okay to remove the shifted mark, as
# we can't get in an infinite loop this way.
st.set_reshiftable(st.B(0))
st.pop()
@staticmethod
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef inline weight_t cost(const StateC* state, const void* _gold, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gold = <const GoldParseStateC*>_gold
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t cost = gold.pop_cost
s0 = state.S(0)
s1 = state.S(1)
b0 = state.B(0)
if state.has_head(s0):
# Increment cost if we're clobbering a correct arc
cost += gold.heads[s0] == s1
else:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
# If there's no head, we're losing arcs between S0 and S[1:].
cost += is_head_in_stack(gold, s0)
cost += gold.n_kids_in_stack[s0]
if b0 != -1 and s0 != -1 and gold.heads[s0] == b0:
cost -= 1
cost += not label_is_gold(gold, s0, label)
return cost
cdef class RightArc:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
"""
Add an arc from S[0] to B[0]. Push B[0].
Validity:
* len(S) >= 1
* len(B) >= 1
* not is_sent_start(B[0])
Cost:
push_cost + (not shifted[b0] and Arc(B[1:], B[0])) - Arc(S[0], B[0], label)
"""
@staticmethod
2017-05-28 15:06:40 +03:00
cdef bint is_valid(const StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.stack_depth() == 0:
return 0
elif st.buffer_length() == 0:
return 0
elif st.is_sent_start(st.B(0)):
return 0
elif label == SUBTOK_LABEL and st.S(0) != (st.B(0)-1):
# If there's (perhaps partial) parse pre-set, don't allow cycle.
2018-04-08 15:50:21 +03:00
return 0
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
else:
return 1
2020-10-04 12:16:31 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef int transition(StateC* st, attr_t label) nogil:
st.add_arc(st.S(0), st.B(0), label)
st.push()
@staticmethod
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef inline weight_t cost(const StateC* state, const void* _gold, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gold = <const GoldParseStateC*>_gold
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cost = gold.push_cost
s0 = state.S(0)
b0 = state.B(0)
if s0 != -1 and b0 != -1 and gold.heads[b0] == s0:
cost -= 1
cost += not label_is_gold(gold, b0, label)
elif is_head_in_buffer(gold, b0) and not state.is_unshiftable(b0):
cost += 1
return cost
cdef class Break:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
"""Mark the second word of the buffer as the start of a
sentence.
Validity:
* len(buffer) >= 2
* B[1] == B[0] + 1
* not is_sent_start(B[1])
* not cannot_sent_start(B[1])
Action:
* mark_sent_start(B[1])
Cost:
* not is_sent_start(B[1])
* Arcs between B[0] and B[1:]
* Arcs between S and B[1]
"""
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef bint is_valid(const StateC* st, attr_t label) nogil:
2015-06-09 02:41:09 +03:00
cdef int i
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if st.buffer_length() < 2:
2015-06-09 02:41:09 +03:00
return False
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
elif st.B(1) != st.B(0) + 1:
2015-06-09 02:41:09 +03:00
return False
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
elif st.is_sent_start(st.B(1)):
return False
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
elif st.cannot_sent_start(st.B(1)):
2017-10-09 01:02:45 +03:00
return False
2015-06-09 02:41:09 +03:00
else:
2017-08-26 03:50:55 +03:00
return True
2015-06-09 02:41:09 +03:00
@staticmethod
2017-05-28 15:06:40 +03:00
cdef int transition(StateC* st, attr_t label) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
st.set_sent_start(st.B(1), 1)
@staticmethod
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef weight_t cost(const StateC* state, const void* _gold, attr_t label) nogil:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
gold = <const GoldParseStateC*>_gold
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef int b0 = state.B(0)
cdef int cost = 0
cdef int si
for i in range(state.stack_depth()):
si = state.S(i)
if is_head_in_buffer(gold, si):
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cost += 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cost += gold.n_kids_in_buffer[si]
# We need to score into B[1:], so subtract deps that are at b0
if gold.heads[b0] == si:
cost -= 1
if gold.heads[si] == b0:
cost -= 1
if not is_sent_start(gold, state.B(1)) \
and not is_sent_start_unknown(gold, state.B(1)):
cost += 1
return cost
2015-08-09 00:31:54 +03:00
2017-03-11 20:12:01 +03:00
cdef void* _init_state(Pool mem, int length, void* tokens) except NULL:
2017-11-14 04:11:40 +03:00
st = new StateC(<const TokenC*>tokens, length)
2017-03-11 20:12:01 +03:00
return <void*>st
cdef int _del_state(Pool mem, void* state, void* x) except -1:
cdef StateC* st = <StateC*>state
del st
cdef class ArcEager(TransitionSystem):
2017-03-11 20:12:01 +03:00
def __init__(self, *args, **kwargs):
TransitionSystem.__init__(self, *args, **kwargs)
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
self.init_beam_state = _init_state
self.del_beam_state = _del_state
2017-03-11 20:12:01 +03:00
@classmethod
def get_actions(cls, **kwargs):
min_freq = kwargs.get('min_freq', None)
actions = defaultdict(lambda: Counter())
actions[SHIFT][''] = 1
actions[REDUCE][''] = 1
for label in kwargs.get('left_labels', []):
actions[LEFT][label] = 1
actions[SHIFT][label] = 1
for label in kwargs.get('right_labels', []):
actions[RIGHT][label] = 1
actions[REDUCE][label] = 1
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for example in kwargs.get('examples', []):
# use heads and labels from the reference parse (without regard to
# misalignments between the predicted and reference)
example_gold_preproc = Example(example.reference, example.reference)
heads, labels = example_gold_preproc.get_aligned_parse(projectivize=True)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for child, (head, label) in enumerate(zip(heads, labels)):
if head is None or label is None:
continue
Restructure Example with merged sents as default (#4632) * Switch to train_dataset() function in train CLI * Fixes for pipe() methods in pipeline components * Don't clobber `examples` variable with `as_example` in pipe() methods * Remove unnecessary traversals of `examples` * Update Parser.pipe() for Examples * Add `as_examples` kwarg to `pipe()` with implementation to return `Example`s * Accept `Doc` or `Example` in `pipe()` with `_get_doc()` (copied from `Pipe`) * Fixes to Example implementation in spacy.gold * Move `make_projective` from an attribute of Example to an argument of `Example.get_gold_parses()` * Head of 0 are not treated as unset * Unset heads are set to self rather than `None` (which causes problems while projectivizing) * Check for `Doc` (not just not `None`) when creating GoldParses for pre-merged example * Don't clobber `examples` variable in `iter_gold_docs()` * Add/modify gold tests for handling projectivity * In JSON roundtrip compare results from `dev_dataset` rather than `train_dataset` to avoid projectivization (and other potential modifications) * Add test for projective train vs. nonprojective dev versions of the same `Doc` * Handle ignore_misaligned as arg rather than attr Move `ignore_misaligned` from an attribute of `Example` to an argument to `Example.get_gold_parses()`, which makes it parallel to `make_projective`. Add test with old and new align that checks whether `ignore_misaligned` errors are raised as expected (only for new align). * Remove unused attrs from gold.pxd Remove `ignore_misaligned` and `make_projective` from `gold.pxd` * Restructure Example with merged sents as default An `Example` now includes a single `TokenAnnotation` that includes all the information from one `Doc` (=JSON `paragraph`). If required, the individual sentences can be returned as a list of examples with `Example.split_sents()` with no raw text available. * Input/output a single `Example.token_annotation` * Add `sent_starts` to `TokenAnnotation` to handle sentence boundaries * Replace `Example.merge_sents()` with `Example.split_sents()` * Modify components to use a single `Example.token_annotation` * Pipeline components * conllu2json converter * Rework/rename `add_token_annotation()` and `add_doc_annotation()` to `set_token_annotation()` and `set_doc_annotation()`, functions that set rather then appending/extending. * Rename `morphology` to `morphs` in `TokenAnnotation` and `GoldParse` * Add getters to `TokenAnnotation` to supply default values when a given attribute is not available * `Example.get_gold_parses()` in `spacy.gold._make_golds()` is only applied on single examples, so the `GoldParse` is returned saved in the provided `Example` rather than creating a new `Example` with no other internal annotation * Update tests for API changes and `merge_sents()` vs. `split_sents()` * Refer to Example.goldparse in iter_gold_docs() Use `Example.goldparse` in `iter_gold_docs()` instead of `Example.gold` because a `None` `GoldParse` is generated with ignore_misaligned and generating it on-the-fly can raise an unwanted AlignmentError * Fix make_orth_variants() Fix bug in make_orth_variants() related to conversion from multiple to one TokenAnnotation per Example. * Add basic test for make_orth_variants() * Replace try/except with conditionals * Replace default morph value with set
2019-11-25 18:03:28 +03:00
if label.upper() == 'ROOT' :
label = 'ROOT'
if head == child:
actions[BREAK][label] += 1
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if head < child:
Restructure Example with merged sents as default (#4632) * Switch to train_dataset() function in train CLI * Fixes for pipe() methods in pipeline components * Don't clobber `examples` variable with `as_example` in pipe() methods * Remove unnecessary traversals of `examples` * Update Parser.pipe() for Examples * Add `as_examples` kwarg to `pipe()` with implementation to return `Example`s * Accept `Doc` or `Example` in `pipe()` with `_get_doc()` (copied from `Pipe`) * Fixes to Example implementation in spacy.gold * Move `make_projective` from an attribute of Example to an argument of `Example.get_gold_parses()` * Head of 0 are not treated as unset * Unset heads are set to self rather than `None` (which causes problems while projectivizing) * Check for `Doc` (not just not `None`) when creating GoldParses for pre-merged example * Don't clobber `examples` variable in `iter_gold_docs()` * Add/modify gold tests for handling projectivity * In JSON roundtrip compare results from `dev_dataset` rather than `train_dataset` to avoid projectivization (and other potential modifications) * Add test for projective train vs. nonprojective dev versions of the same `Doc` * Handle ignore_misaligned as arg rather than attr Move `ignore_misaligned` from an attribute of `Example` to an argument to `Example.get_gold_parses()`, which makes it parallel to `make_projective`. Add test with old and new align that checks whether `ignore_misaligned` errors are raised as expected (only for new align). * Remove unused attrs from gold.pxd Remove `ignore_misaligned` and `make_projective` from `gold.pxd` * Restructure Example with merged sents as default An `Example` now includes a single `TokenAnnotation` that includes all the information from one `Doc` (=JSON `paragraph`). If required, the individual sentences can be returned as a list of examples with `Example.split_sents()` with no raw text available. * Input/output a single `Example.token_annotation` * Add `sent_starts` to `TokenAnnotation` to handle sentence boundaries * Replace `Example.merge_sents()` with `Example.split_sents()` * Modify components to use a single `Example.token_annotation` * Pipeline components * conllu2json converter * Rework/rename `add_token_annotation()` and `add_doc_annotation()` to `set_token_annotation()` and `set_doc_annotation()`, functions that set rather then appending/extending. * Rename `morphology` to `morphs` in `TokenAnnotation` and `GoldParse` * Add getters to `TokenAnnotation` to supply default values when a given attribute is not available * `Example.get_gold_parses()` in `spacy.gold._make_golds()` is only applied on single examples, so the `GoldParse` is returned saved in the provided `Example` rather than creating a new `Example` with no other internal annotation * Update tests for API changes and `merge_sents()` vs. `split_sents()` * Refer to Example.goldparse in iter_gold_docs() Use `Example.goldparse` in `iter_gold_docs()` instead of `Example.gold` because a `None` `GoldParse` is generated with ignore_misaligned and generating it on-the-fly can raise an unwanted AlignmentError * Fix make_orth_variants() Fix bug in make_orth_variants() related to conversion from multiple to one TokenAnnotation per Example. * Add basic test for make_orth_variants() * Replace try/except with conditionals * Replace default morph value with set
2019-11-25 18:03:28 +03:00
actions[RIGHT][label] += 1
actions[REDUCE][''] += 1
elif head > child:
actions[LEFT][label] += 1
actions[SHIFT][''] += 1
if min_freq is not None:
for action, label_freqs in actions.items():
for label, freq in label_freqs.copy().items():
if freq < min_freq:
label_freqs.pop(label)
# Ensure these actions are present
actions[BREAK].setdefault('ROOT', 0)
if kwargs.get("learn_tokens") is True:
actions[RIGHT].setdefault('subtok', 0)
actions[LEFT].setdefault('subtok', 0)
# Used for backoff
actions[RIGHT].setdefault('dep', 0)
actions[LEFT].setdefault('dep', 0)
return actions
@property
def builtin_labels(self):
return ["ROOT", "dep"]
@property
def action_types(self):
return (SHIFT, REDUCE, LEFT, RIGHT, BREAK)
def get_doc_labels(self, doc):
"""Get the labels required for a given Doc."""
labels = set(self.builtin_labels)
for token in doc:
if token.dep_:
labels.add(token.dep_)
return labels
def transition(self, StateClass state, action):
cdef Transition t = self.lookup_transition(action)
t.do(state.c, t.label)
return state
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
def is_gold_parse(self, StateClass state, ArcEagerGold gold):
for i in range(state.c.length):
token = state.c.safe_get(i)
if not arc_is_gold(&gold.c, i, i+token.head):
return False
elif not label_is_gold(&gold.c, i, token.dep):
return False
return True
2017-05-26 19:31:23 +03:00
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def init_gold(self, StateClass state, Example example):
gold = ArcEagerGold(self, state, example)
self._replace_unseen_labels(gold)
return gold
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def init_gold_batch(self, examples):
# TODO: Projectivity?
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
all_states = self.init_batch([eg.predicted for eg in examples])
golds = []
states = []
for state, eg in zip(all_states, examples):
if self.has_gold(eg) and not state.is_final():
golds.append(self.init_gold(state, eg))
states.append(state)
n_steps = sum([len(s.queue) for s in states])
return states, golds, n_steps
def _replace_unseen_labels(self, ArcEagerGold gold):
backoff_label = self.strings["dep"]
root_label = self.strings["ROOT"]
left_labels = self.labels[LEFT]
right_labels = self.labels[RIGHT]
break_labels = self.labels[BREAK]
for i in range(gold.c.length):
if not is_head_unknown(&gold.c, i):
head = gold.c.heads[i]
label = self.strings[gold.c.labels[i]]
if head > i and label not in left_labels:
gold.c.labels[i] = backoff_label
elif head < i and label not in right_labels:
gold.c.labels[i] = backoff_label
elif head == i and label not in break_labels:
gold.c.labels[i] = root_label
return gold
cdef Transition lookup_transition(self, object name_or_id) except *:
if isinstance(name_or_id, int):
return self.c[name_or_id]
name = name_or_id
if '-' in name:
move_str, label_str = split_bilu_label(name)
2015-08-09 00:31:54 +03:00
label = self.strings[label_str]
else:
2015-08-09 00:31:54 +03:00
move_str = name
label = 0
move = MOVE_NAMES.index(move_str)
for i in range(self.n_moves):
if self.c[i].move == move and self.c[i].label == label:
return self.c[i]
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
raise KeyError(f"Unknown transition: {name}")
2017-05-28 15:06:40 +03:00
def move_name(self, int move, attr_t label):
label_str = self.strings[label]
if label_str:
return MOVE_NAMES[move] + '-' + label_str
else:
return MOVE_NAMES[move]
def class_name(self, int i):
return self.move_name(self.c[i].move, self.c[i].label)
2017-05-28 15:06:40 +03:00
cdef Transition init_transition(self, int clas, int move, attr_t label) except *:
# TODO: Apparent Cython bug here when we try to use the Transition()
# constructor with the function pointers
cdef Transition t
t.score = 0
t.clas = clas
t.move = move
t.label = label
if move == SHIFT:
t.is_valid = Shift.is_valid
t.do = Shift.transition
t.get_cost = Shift.cost
elif move == REDUCE:
t.is_valid = Reduce.is_valid
t.do = Reduce.transition
t.get_cost = Reduce.cost
elif move == LEFT:
t.is_valid = LeftArc.is_valid
t.do = LeftArc.transition
t.get_cost = LeftArc.cost
elif move == RIGHT:
t.is_valid = RightArc.is_valid
t.do = RightArc.transition
t.get_cost = RightArc.cost
elif move == BREAK:
t.is_valid = Break.is_valid
t.do = Break.transition
t.get_cost = Break.cost
else:
raise ValueError(Errors.E019.format(action=move, src='arc_eager'))
return t
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
def set_annotations(self, StateClass state, Doc doc):
for arc in state.arcs:
doc.c[arc["child"]].head = arc["head"] - arc["child"]
doc.c[arc["child"]].dep = arc["label"]
for i in range(doc.length):
if doc.c[i].head == 0:
doc.c[i].dep = self.root_label
set_children_from_heads(doc.c, 0, doc.length)
def get_beam_parses(self, Beam beam):
parses = []
probs = beam.probs
for i in range(beam.size):
state = <StateC*>beam.at(i)
if state.is_final():
prob = probs[i]
parse = []
arcs = self.get_arcs(state)
if arcs:
for arc in arcs:
dep = arc["label"]
label = self.strings[dep]
parse.append((arc["head"], arc["child"], label))
parses.append((prob, parse))
return parses
cdef get_arcs(self, StateC* state):
cdef vector[ArcC] arcs
state.get_arcs(&arcs)
return list(arcs)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def has_gold(self, Example eg, start=0, end=None):
Merge the parser refactor into `v4` (#10940) * Try to fix doc.copy * Set dev version * Make vocab always own lexemes * Change version * Add SpanGroups.copy method * Fix set_annotations during Parser.update * Fix dict proxy copy * Upd version * Fix copying SpanGroups * Fix set_annotations in parser.update * Fix parser set_annotations during update * Revert "Fix parser set_annotations during update" This reverts commit eb138c89edb306608826dca50619ea8a60de2b14. * Revert "Fix set_annotations in parser.update" This reverts commit c6df0eafd0046179c1c9fb7840074edf04e4721d. * Fix set_annotations during parser update * Inc version * Handle final states in get_oracle_sequence * Inc version * Try to fix parser training * Inc version * Fix * Inc version * Fix parser oracle * Inc version * Inc version * Fix transition has_gold * Inc version * Try to use real histories, not oracle * Inc version * Upd parser * Inc version * WIP on rewrite parser * WIP refactor parser * New progress on parser model refactor * Prepare to remove parser_model.pyx * Convert parser from cdef class * Delete spacy.ml.parser_model * Delete _precomputable_affine module * Wire up tb_framework to new parser model * Wire up parser model * Uncython ner.pyx and dep_parser.pyx * Uncython * Work on parser model * Support unseen_classes in parser model * Support unseen classes in parser * Cleaner handling of unseen classes * Work through tests * Keep working through errors * Keep working through errors * Work on parser. 15 tests failing * Xfail beam stuff. 9 failures * More xfail. 7 failures * Xfail. 6 failures * cleanup * formatting * fixes * pass nO through * Fix empty doc in update * Hackishly fix resizing. 3 failures * Fix redundant test. 2 failures * Add reference version * black formatting * Get tests passing with reference implementation * Fix missing prints * Add missing file * Improve indexing on reference implementation * Get non-reference forward func working * Start rigging beam back up * removing redundant tests, cf #8106 * black formatting * temporarily xfailing issue 4314 * make flake8 happy again * mypy fixes * ensure labels are added upon predict * cleanup remnants from merge conflicts * Improve unseen label masking Two changes to speed up masking by ~10%: - Use a bool array rather than an array of float32. - Let the mask indicate whether a label was seen, rather than unseen. The mask is most frequently used to index scores for seen labels. However, since the mask marked unseen labels, this required computing an intermittent flipped mask. * Write moves costs directly into numpy array (#10163) This avoids elementwise indexing and the allocation of an additional array. Gives a ~15% speed improvement when using batch_by_sequence with size 32. * Temporarily disable ner and rehearse tests Until rehearse is implemented again in the refactored parser. * Fix loss serialization issue (#10600) * Fix loss serialization issue Serialization of a model fails with: TypeError: array(738.3855, dtype=float32) is not JSON serializable Fix this using float conversion. * Disable CI steps that require spacy.TransitionBasedParser.v2 After finishing the refactor, TransitionBasedParser.v2 should be provided for backwards compat. * Add back support for beam parsing to the refactored parser (#10633) * Add back support for beam parsing Beam parsing was already implemented as part of the `BeamBatch` class. This change makes its counterpart `GreedyBatch`. Both classes are hooked up in `TransitionModel`, selecting `GreedyBatch` when the beam size is one, or `BeamBatch` otherwise. * Use kwarg for beam width Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Avoid implicit default for beam_width and beam_density * Parser.{beam,greedy}_parse: ensure labels are added * Remove 'deprecated' comments Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Parser `StateC` optimizations (#10746) * `StateC`: Optimizations Avoid GIL acquisition in `__init__` Increase default buffer capacities on init Reduce C++ exception overhead * Fix typo * Replace `set::count` with `set::find` * Add exception attribute to c'tor * Remove unused import * Use a power-of-two value for initial capacity Use default-insert to init `_heads` and `_unshiftable` * Merge `cdef` variable declarations and assignments * Vectorize `example.get_aligned_parses` (#10789) * `example`: Vectorize `get_aligned_parse` Rename `numpy` import * Convert aligned array to lists before returning * Revert import renaming * Elide slice arguments when selecting the entire range * Tagger/morphologizer alignment performance optimizations (#10798) * `example`: Unwrap `numpy` scalar arrays before passing them to `StringStore.__getitem__` * `AlignmentArray`: Use native list as staging buffer for offset calculation * `example`: Vectorize `get_aligned` * Hoist inner functions out of `get_aligned` * Replace inline `if..else` clause in assignment statement * `AlignmentArray`: Use raw indexing into offset and data `numpy` arrays * `example`: Replace array unique value check with `groupby` * `example`: Correctly exclude tokens with no alignment in `_get_aligned_vectorized` Simplify `_get_aligned_non_vectorized` * `util`: Update `all_equal` docstring * Explicitly use `int32_t*` * Restore C CPU inference in the refactored parser (#10747) * Bring back the C parsing model The C parsing model is used for CPU inference and is still faster for CPU inference than the forward pass of the Thinc model. * Use C sgemm provided by the Ops implementation * Make tb_framework module Cython, merge in C forward implementation * TransitionModel: raise in backprop returned from forward_cpu * Re-enable greedy parse test * Return transition scores when forward_cpu is used * Apply suggestions from code review Import `Model` from `thinc.api` Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Use relative imports in tb_framework * Don't assume a default for beam_width * We don't have a direct dependency on BLIS anymore * Rename forwards to _forward_{fallback,greedy_cpu} * Require thinc >=8.1.0,<8.2.0 * tb_framework: clean up imports * Fix return type of _get_seen_mask * Move up _forward_greedy_cpu * Style fixes. * Lower thinc lowerbound to 8.1.0.dev0 * Formatting fix Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Reimplement parser rehearsal function (#10878) * Reimplement parser rehearsal function Before the parser refactor, rehearsal was driven by a loop in the `rehearse` method itself. For each parsing step, the loops would: 1. Get the predictions of the teacher. 2. Get the predictions and backprop function of the student. 3. Compute the loss and backprop into the student. 4. Move the teacher and student forward with the predictions of the student. In the refactored parser, we cannot perform search stepwise rehearsal anymore, since the model now predicts all parsing steps at once. Therefore, rehearsal is performed in the following steps: 1. Get the predictions of all parsing steps from the student, along with its backprop function. 2. Get the predictions from the teacher, but use the predictions of the student to advance the parser while doing so. 3. Compute the loss and backprop into the student. To support the second step a new method, `advance_with_actions` is added to `GreedyBatch`, which performs the provided parsing steps. * tb_framework: wrap upper_W and upper_b in Linear Thinc's Optimizer cannot handle resizing of existing parameters. Until it does, we work around this by wrapping the weights/biases of the upper layer of the parser model in Linear. When the upper layer is resized, we copy over the existing parameters into a new Linear instance. This does not trigger an error in Optimizer, because it sees the resized layer as a new set of parameters. * Add test for TransitionSystem.apply_actions * Better FIXME marker Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> * Fixes from Madeesh * Apply suggestions from Sofie Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Remove useless assignment Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Rename some identifiers in the parser refactor (#10935) * Rename _parseC to _parse_batch * tb_framework: prefix many auxiliary functions with underscore To clearly state the intent that they are private. * Rename `lower` to `hidden`, `upper` to `output` * Parser slow test fixup We don't have TransitionBasedParser.{v1,v2} until we bring it back as a legacy option. * Remove last vestiges of PrecomputableAffine This does not exist anymore as a separate layer. * ner: re-enable sentence boundary checks * Re-enable test that works now. * test_ner: make loss test more strict again * Remove commented line * Re-enable some more beam parser tests * Remove unused _forward_reference function * Update for CBlas changes in Thinc 8.1.0.dev2 Bump thinc dependency to 8.1.0.dev3. * Remove references to spacy.TransitionBasedParser.{v1,v2} Since they will not be offered starting with spaCy v4. * `tb_framework`: Replace references to `thinc.backends.linalg` with `CBlas` * dont use get_array_module (#11056) (#11293) Co-authored-by: kadarakos <kadar.akos@gmail.com> * Move `thinc.extra.search` to `spacy.pipeline._parser_internals` (#11317) * `search`: Move from `thinc.extra.search` Fix NPE in `Beam.__dealloc__` * `pytest`: Add support for executing Cython tests Move `search` tests from thinc and patch them to run with `pytest` * `mypy` fix * Update comment * `conftest`: Expose `register_cython_tests` * Remove unused import * Move `argmax` impls to new `_parser_utils` Cython module (#11410) * Parser does not have to be a cdef class anymore This also fixes validation of the initialization schema. * Add back spacy.TransitionBasedParser.v2 * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Remove module from setup.py that got added during the merge * Bring back support for `update_with_oracle_cut_size` (#12086) * Bring back support for `update_with_oracle_cut_size` This option was available in the pre-refactor parser, but was never implemented in the refactored parser. This option cuts transition sequences that are longer than `update_with_oracle_cut` size into separate sequences that have at most `update_with_oracle_cut` transitions. The oracle (gold standard) transition sequence is used to determine the cuts and the initial states for the additional sequences. Applying this cut makes the batches more homogeneous in the transition sequence lengths, making forward passes (and as a consequence training) much faster. Training time 1000 steps on de_core_news_lg: - Before this change: 149s - After this change: 68s - Pre-refactor parser: 81s * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Apply suggestions from @shadeMe * Use chained conditional * Test with update_with_oracle_cut_size={0, 1, 5, 100} And fix a git that occurs with a cut size of 1. * Fix up some merge fall out * Update parser distillation for the refactor In the old parser, we'd iterate over the transitions in the distill function and compute the loss/gradients on the go. In the refactored parser, we first let the student model parse the inputs. Then we'll let the teacher compute the transition probabilities of the states in the student's transition sequence. We can then compute the gradients of the student given the teacher. * Add back spacy.TransitionBasedParser.v1 references - Accordion in the architecture docs. - Test in test_parse, but disabled until we have a spacy-legacy release. Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com> Co-authored-by: svlandeg <svlandeg@github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: kadarakos <kadar.akos@gmail.com>
2023-01-18 13:27:45 +03:00
if end is not None and end < 0:
end = None
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for word in eg.y[start:end]:
if word.dep != 0:
return True
else:
return False
2016-02-01 05:07:37 +03:00
cdef int set_valid(self, int* output, const StateC* st) nogil:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cdef int[N_MOVES] is_valid
2017-05-30 21:37:24 +03:00
is_valid[SHIFT] = Shift.is_valid(st, 0)
is_valid[REDUCE] = Reduce.is_valid(st, 0)
is_valid[LEFT] = LeftArc.is_valid(st, 0)
is_valid[RIGHT] = RightArc.is_valid(st, 0)
is_valid[BREAK] = Break.is_valid(st, 0)
cdef int i
for i in range(self.n_moves):
if self.c[i].label == SUBTOK_LABEL:
output[i] = self.c[i].is_valid(st, self.c[i].label)
else:
output[i] = is_valid[self.c[i].move]
2020-10-04 12:16:31 +03:00
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def get_cost(self, StateClass stcls, gold, int i):
if not isinstance(gold, ArcEagerGold):
2020-10-04 12:16:31 +03:00
raise TypeError(Errors.E909.format(name="ArcEagerGold"))
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef ArcEagerGold gold_ = gold
gold_state = gold_.c
n_gold = 0
if self.c[i].is_valid(stcls.c, self.c[i].label):
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
cost = self.c[i].get_cost(stcls.c, &gold_state, self.c[i].label)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
else:
cost = 9000
return cost
cdef int set_costs(self, int* is_valid, weight_t* costs,
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
const StateC* state, gold) except -1:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
if not isinstance(gold, ArcEagerGold):
2020-10-04 12:16:31 +03:00
raise TypeError(Errors.E909.format(name="ArcEagerGold"))
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef ArcEagerGold gold_ = gold
gold_state = gold_.c
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
update_gold_state(&gold_state, state)
self.set_valid(is_valid, state)
cdef int n_gold = 0
for i in range(self.n_moves):
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if is_valid[i]:
costs[i] = self.c[i].get_cost(state, &gold_state, self.c[i].label)
if costs[i] <= 0:
n_gold += 1
2015-06-10 07:56:35 +03:00
else:
costs[i] = 9000
if n_gold < 1:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
for i in range(self.n_moves):
print(self.get_class_name(i), is_valid[i], costs[i])
print("Gold sent starts?", is_sent_start(&gold_state, state.B(0)), is_sent_start(&gold_state, state.B(1)))
raise ValueError(Errors.E1031)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
def get_oracle_sequence_from_state(self, StateClass state, ArcEagerGold gold, _debug=None):
cdef int i
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
cdef Pool mem = Pool()
# n_moves should not be zero at this point, but make sure to avoid zero-length mem alloc
assert self.n_moves > 0
costs = <float*>mem.alloc(self.n_moves, sizeof(float))
is_valid = <int*>mem.alloc(self.n_moves, sizeof(int))
history = []
debug_log = []
failed = False
while not state.is_final():
try:
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
self.set_costs(is_valid, costs, state.c, gold)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
except ValueError:
failed = True
break
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
min_cost = min(costs[i] for i in range(self.n_moves))
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
for i in range(self.n_moves):
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
if is_valid[i] and costs[i] <= min_cost:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
action = self.c[i]
history.append(i)
s0 = state.S(0)
b0 = state.B(0)
if _debug:
example = _debug
debug_log.append(" ".join((
self.get_class_name(i),
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
state.print_state()
)))
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
action.do(state.c, action.label)
Merge the parser refactor into `v4` (#10940) * Try to fix doc.copy * Set dev version * Make vocab always own lexemes * Change version * Add SpanGroups.copy method * Fix set_annotations during Parser.update * Fix dict proxy copy * Upd version * Fix copying SpanGroups * Fix set_annotations in parser.update * Fix parser set_annotations during update * Revert "Fix parser set_annotations during update" This reverts commit eb138c89edb306608826dca50619ea8a60de2b14. * Revert "Fix set_annotations in parser.update" This reverts commit c6df0eafd0046179c1c9fb7840074edf04e4721d. * Fix set_annotations during parser update * Inc version * Handle final states in get_oracle_sequence * Inc version * Try to fix parser training * Inc version * Fix * Inc version * Fix parser oracle * Inc version * Inc version * Fix transition has_gold * Inc version * Try to use real histories, not oracle * Inc version * Upd parser * Inc version * WIP on rewrite parser * WIP refactor parser * New progress on parser model refactor * Prepare to remove parser_model.pyx * Convert parser from cdef class * Delete spacy.ml.parser_model * Delete _precomputable_affine module * Wire up tb_framework to new parser model * Wire up parser model * Uncython ner.pyx and dep_parser.pyx * Uncython * Work on parser model * Support unseen_classes in parser model * Support unseen classes in parser * Cleaner handling of unseen classes * Work through tests * Keep working through errors * Keep working through errors * Work on parser. 15 tests failing * Xfail beam stuff. 9 failures * More xfail. 7 failures * Xfail. 6 failures * cleanup * formatting * fixes * pass nO through * Fix empty doc in update * Hackishly fix resizing. 3 failures * Fix redundant test. 2 failures * Add reference version * black formatting * Get tests passing with reference implementation * Fix missing prints * Add missing file * Improve indexing on reference implementation * Get non-reference forward func working * Start rigging beam back up * removing redundant tests, cf #8106 * black formatting * temporarily xfailing issue 4314 * make flake8 happy again * mypy fixes * ensure labels are added upon predict * cleanup remnants from merge conflicts * Improve unseen label masking Two changes to speed up masking by ~10%: - Use a bool array rather than an array of float32. - Let the mask indicate whether a label was seen, rather than unseen. The mask is most frequently used to index scores for seen labels. However, since the mask marked unseen labels, this required computing an intermittent flipped mask. * Write moves costs directly into numpy array (#10163) This avoids elementwise indexing and the allocation of an additional array. Gives a ~15% speed improvement when using batch_by_sequence with size 32. * Temporarily disable ner and rehearse tests Until rehearse is implemented again in the refactored parser. * Fix loss serialization issue (#10600) * Fix loss serialization issue Serialization of a model fails with: TypeError: array(738.3855, dtype=float32) is not JSON serializable Fix this using float conversion. * Disable CI steps that require spacy.TransitionBasedParser.v2 After finishing the refactor, TransitionBasedParser.v2 should be provided for backwards compat. * Add back support for beam parsing to the refactored parser (#10633) * Add back support for beam parsing Beam parsing was already implemented as part of the `BeamBatch` class. This change makes its counterpart `GreedyBatch`. Both classes are hooked up in `TransitionModel`, selecting `GreedyBatch` when the beam size is one, or `BeamBatch` otherwise. * Use kwarg for beam width Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Avoid implicit default for beam_width and beam_density * Parser.{beam,greedy}_parse: ensure labels are added * Remove 'deprecated' comments Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Parser `StateC` optimizations (#10746) * `StateC`: Optimizations Avoid GIL acquisition in `__init__` Increase default buffer capacities on init Reduce C++ exception overhead * Fix typo * Replace `set::count` with `set::find` * Add exception attribute to c'tor * Remove unused import * Use a power-of-two value for initial capacity Use default-insert to init `_heads` and `_unshiftable` * Merge `cdef` variable declarations and assignments * Vectorize `example.get_aligned_parses` (#10789) * `example`: Vectorize `get_aligned_parse` Rename `numpy` import * Convert aligned array to lists before returning * Revert import renaming * Elide slice arguments when selecting the entire range * Tagger/morphologizer alignment performance optimizations (#10798) * `example`: Unwrap `numpy` scalar arrays before passing them to `StringStore.__getitem__` * `AlignmentArray`: Use native list as staging buffer for offset calculation * `example`: Vectorize `get_aligned` * Hoist inner functions out of `get_aligned` * Replace inline `if..else` clause in assignment statement * `AlignmentArray`: Use raw indexing into offset and data `numpy` arrays * `example`: Replace array unique value check with `groupby` * `example`: Correctly exclude tokens with no alignment in `_get_aligned_vectorized` Simplify `_get_aligned_non_vectorized` * `util`: Update `all_equal` docstring * Explicitly use `int32_t*` * Restore C CPU inference in the refactored parser (#10747) * Bring back the C parsing model The C parsing model is used for CPU inference and is still faster for CPU inference than the forward pass of the Thinc model. * Use C sgemm provided by the Ops implementation * Make tb_framework module Cython, merge in C forward implementation * TransitionModel: raise in backprop returned from forward_cpu * Re-enable greedy parse test * Return transition scores when forward_cpu is used * Apply suggestions from code review Import `Model` from `thinc.api` Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Use relative imports in tb_framework * Don't assume a default for beam_width * We don't have a direct dependency on BLIS anymore * Rename forwards to _forward_{fallback,greedy_cpu} * Require thinc >=8.1.0,<8.2.0 * tb_framework: clean up imports * Fix return type of _get_seen_mask * Move up _forward_greedy_cpu * Style fixes. * Lower thinc lowerbound to 8.1.0.dev0 * Formatting fix Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Reimplement parser rehearsal function (#10878) * Reimplement parser rehearsal function Before the parser refactor, rehearsal was driven by a loop in the `rehearse` method itself. For each parsing step, the loops would: 1. Get the predictions of the teacher. 2. Get the predictions and backprop function of the student. 3. Compute the loss and backprop into the student. 4. Move the teacher and student forward with the predictions of the student. In the refactored parser, we cannot perform search stepwise rehearsal anymore, since the model now predicts all parsing steps at once. Therefore, rehearsal is performed in the following steps: 1. Get the predictions of all parsing steps from the student, along with its backprop function. 2. Get the predictions from the teacher, but use the predictions of the student to advance the parser while doing so. 3. Compute the loss and backprop into the student. To support the second step a new method, `advance_with_actions` is added to `GreedyBatch`, which performs the provided parsing steps. * tb_framework: wrap upper_W and upper_b in Linear Thinc's Optimizer cannot handle resizing of existing parameters. Until it does, we work around this by wrapping the weights/biases of the upper layer of the parser model in Linear. When the upper layer is resized, we copy over the existing parameters into a new Linear instance. This does not trigger an error in Optimizer, because it sees the resized layer as a new set of parameters. * Add test for TransitionSystem.apply_actions * Better FIXME marker Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> * Fixes from Madeesh * Apply suggestions from Sofie Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Remove useless assignment Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Rename some identifiers in the parser refactor (#10935) * Rename _parseC to _parse_batch * tb_framework: prefix many auxiliary functions with underscore To clearly state the intent that they are private. * Rename `lower` to `hidden`, `upper` to `output` * Parser slow test fixup We don't have TransitionBasedParser.{v1,v2} until we bring it back as a legacy option. * Remove last vestiges of PrecomputableAffine This does not exist anymore as a separate layer. * ner: re-enable sentence boundary checks * Re-enable test that works now. * test_ner: make loss test more strict again * Remove commented line * Re-enable some more beam parser tests * Remove unused _forward_reference function * Update for CBlas changes in Thinc 8.1.0.dev2 Bump thinc dependency to 8.1.0.dev3. * Remove references to spacy.TransitionBasedParser.{v1,v2} Since they will not be offered starting with spaCy v4. * `tb_framework`: Replace references to `thinc.backends.linalg` with `CBlas` * dont use get_array_module (#11056) (#11293) Co-authored-by: kadarakos <kadar.akos@gmail.com> * Move `thinc.extra.search` to `spacy.pipeline._parser_internals` (#11317) * `search`: Move from `thinc.extra.search` Fix NPE in `Beam.__dealloc__` * `pytest`: Add support for executing Cython tests Move `search` tests from thinc and patch them to run with `pytest` * `mypy` fix * Update comment * `conftest`: Expose `register_cython_tests` * Remove unused import * Move `argmax` impls to new `_parser_utils` Cython module (#11410) * Parser does not have to be a cdef class anymore This also fixes validation of the initialization schema. * Add back spacy.TransitionBasedParser.v2 * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Remove module from setup.py that got added during the merge * Bring back support for `update_with_oracle_cut_size` (#12086) * Bring back support for `update_with_oracle_cut_size` This option was available in the pre-refactor parser, but was never implemented in the refactored parser. This option cuts transition sequences that are longer than `update_with_oracle_cut` size into separate sequences that have at most `update_with_oracle_cut` transitions. The oracle (gold standard) transition sequence is used to determine the cuts and the initial states for the additional sequences. Applying this cut makes the batches more homogeneous in the transition sequence lengths, making forward passes (and as a consequence training) much faster. Training time 1000 steps on de_core_news_lg: - Before this change: 149s - After this change: 68s - Pre-refactor parser: 81s * Fix a rename that was missed in #10878. So that rehearsal tests pass. * Apply suggestions from @shadeMe * Use chained conditional * Test with update_with_oracle_cut_size={0, 1, 5, 100} And fix a git that occurs with a cut size of 1. * Fix up some merge fall out * Update parser distillation for the refactor In the old parser, we'd iterate over the transitions in the distill function and compute the loss/gradients on the go. In the refactored parser, we first let the student model parse the inputs. Then we'll let the teacher compute the transition probabilities of the states in the student's transition sequence. We can then compute the gradients of the student given the teacher. * Add back spacy.TransitionBasedParser.v1 references - Accordion in the architecture docs. - Test in test_parse, but disabled until we have a spacy-legacy release. Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com> Co-authored-by: svlandeg <svlandeg@github.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Madeesh Kannan <shadeMe@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: kadarakos <kadar.akos@gmail.com>
2023-01-18 13:27:45 +03:00
state.c.history.push_back(i)
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
break
else:
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
failed = False
break
2021-01-16 05:44:11 +03:00
if failed and _debug not in (False, None):
example = _debug
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
print("Actions")
for i in range(self.n_moves):
print(self.get_class_name(i))
print("Gold")
for token in example.y:
print(token.i, token.text, token.dep_, token.head.text)
aligned_heads, aligned_labels = example.get_aligned_parse()
print("Aligned heads")
for i, head in enumerate(aligned_heads):
print(example.x[i], example.x[head] if head is not None else "__")
Add beam_parser and beam_ner components for v3 (#6369) * Get basic beam tests working * Get basic beam tests working * Compile _beam_utils * Remove prints * Test beam density * Beam parser seems to train * Draft beam NER * Upd beam * Add hypothesis as dev dependency * Implement missing is-gold-parse method * Implement early update * Fix state hashing * Fix test * Fix test * Default to non-beam in parser constructor * Improve oracle for beam * Start refactoring beam * Update test * Refactor beam * Update nn * Refactor beam and weight by cost * Update ner beam settings * Update test * Add __init__.pxd * Upd test * Fix test * Upd test * Fix test * Remove ring buffer history from StateC * WIP change arc-eager transitions * Add state tests * Support ternary sent start values * Fix arc eager * Fix NER * Pass oracle cut size for beam * Fix ner test * Fix beam * Improve StateC.clone * Improve StateClass.borrow * Work directly with StateC, not StateClass * Remove print statements * Fix state copy * Improve state class * Refactor parser oracles * Fix arc eager oracle * Fix arc eager oracle * Use a vector to implement the stack * Refactor state data structure * Fix alignment of sent start * Add get_aligned_sent_starts method * Add test for ae oracle when bad sentence starts * Fix sentence segment handling * Avoid Reduce that inserts illegal sentence * Update preset SBD test * Fix test * Remove prints * Fix sent starts in Example * Improve python API of StateClass * Tweak comments and debug output of arc eager * Upd test * Fix state test * Fix state test
2020-12-13 04:08:32 +03:00
print("Aligned sent starts")
print(example.get_aligned_sent_starts())
Improve spacy.gold (no GoldParse, no json format!) (#5555) * Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
2020-06-26 20:34:12 +03:00
print("Predicted tokens")
print([(w.i, w.text) for w in example.x])
s0 = state.S(0)
b0 = state.B(0)
debug_log.append(" ".join((
"?",
"S0=", (example.x[s0].text if s0 >= 0 else "-"),
"B0=", (example.x[b0].text if b0 >= 0 else "-"),
"S0 head?", str(state.has_head(state.S(0))),
)))
s0 = state.S(0)
b0 = state.B(0)
print("\n".join(debug_log))
print("Arc is gold B0, S0?", arc_is_gold(&gold.c, b0, s0))
print("Arc is gold S0, B0?", arc_is_gold(&gold.c, s0, b0))
print("is_head_unknown(s0)", is_head_unknown(&gold.c, s0))
print("is_head_unknown(b0)", is_head_unknown(&gold.c, b0))
print("b0", b0, "gold.heads[s0]", gold.c.heads[s0])
print("Stack", [example.x[i] for i in state.stack])
print("Buffer", [example.x[i] for i in state.queue])
raise ValueError(Errors.E024)
return history