* Fix `spacy.util.minibatch` when the size iterator is finished (#6745)
* Skip 0-length matches (#6759)
Add hack to prevent matcher from returning 0-length matches.
* support IS_SENT_START in PhraseMatcher (#6771)
* support IS_SENT_START in PhraseMatcher
* add unit test and friendlier error
* use IDS.get instead
* ensure span.text works for an empty span (#6772)
* Remove unicode_literals
Co-authored-by: Santiago Castro <bryant@montevideo.com.uy>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Adding contributor agreement for user werew
* [DependencyMatcher] Comment and clean code
* [DependencyMatcher] Use defaultdicts
* [DependencyMatcher] Simplify _retrieve_tree method
* [DependencyMatcher] Remove prepended underscores
* [DependencyMatcher] Address TODO and move grouping of token's positions out of the loop
* [DependencyMatcher] Remove _nodes attribute
* [DependencyMatcher] Use enumerate in _retrieve_tree method
* [DependencyMatcher] Clean unused vars and use camel_case naming
* [DependencyMatcher] Memoize node+operator map
* Add root property to Token
* [DependencyMatcher] Groups matches by root
* [DependencyMatcher] Remove unused _keys_to_token attribute
* [DependencyMatcher] Use a list to map tokens to matcher's keys
* [DependencyMatcher] Remove recursion
* [DependencyMatcher] Use a generator to retrieve matches
* [DependencyMatcher] Remove unused memory pool
* [DependencyMatcher] Hide private methods and attributes
* [DependencyMatcher] Improvements to the matches validation
* Apply suggestions from code review
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* [DependencyMatcher] Fix keys_to_position_maps
* Remove Token.root property
* [DependencyMatcher] Remove functools' lru_cache
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* raise NotImplementedError when noun_chunks iterator is not implemented
* bring back, fix and document span.noun_chunks
* formatting
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Handle unset token.morph in Morphologizer
Handle unset `token.morph` in `Morphologizer.initialize` and
`Morphologizer.get_loss`. If both `token.morph` and `token.pos` are
unset, treat the annotation as missing rather than empty.
* Add token.has_morph()
* Draft out initial Spans data structure
* Initial span group commit
* Basic span group support on Doc
* Basic test for span group
* Compile span_group.pyx
* Draft addition of SpanGroup to DocBin
* Add deserialization for SpanGroup
* Add tests for serializing SpanGroup
* Fix serialization of SpanGroup
* Add EdgeC and GraphC structs
* Add draft Graph data structure
* Compile graph
* More work on Graph
* Update GraphC
* Upd graph
* Fix walk functions
* Let Graph take nodes and edges on construction
* Fix walking and getting
* Add graph tests
* Fix import
* Add module with the SpanGroups dict thingy
* Update test
* Rename 'span_groups' attribute
* Try to fix c++11 compilation
* Fix test
* Update DocBin
* Try to fix compilation
* Try to fix graph
* Improve SpanGroup docstrings
* Add doc.spans to documentation
* Fix serialization
* Tidy up and add docs
* Update docs [ci skip]
* Add SpanGroup.has_overlap
* WIP updated Graph API
* Start testing new Graph API
* Update Graph tests
* Update Graph
* Add docstring
Co-authored-by: Ines Montani <ines@ines.io>
Instead of unsetting lemmas on retokenized tokens, set the default
lemmas to:
* merge: concatenate any existing lemmas with `SPACY` preserved
* split: use the new `ORTH` values if lemmas were previously set,
otherwise leave unset
* Only set NORM on Token in retokenizer
Instead of setting `NORM` on both the token and lexeme, set `NORM` only
on the token.
The retokenizer tries to set all possible attributes with
`Token/Lexeme.set_struct_attr` so that it doesn't have to enumerate
which attributes are available for each. `NORM` is the only attribute
that's stored on both and for most cases it doesn't make sense to set
the global norms based on a individual retokenization. For lexeme-only
attributes like `IS_STOP` there's no way to avoid the global side
effects, but I think that `NORM` would be better only on the token.
* Fix test
* Handle missing reference values in scorer
Handle missing values in reference doc during scoring where it is
possible to detect an unset state for the attribute. If no reference
docs contain annotation, `None` is returned instead of a score. `spacy
evaluate` displays `-` for missing scores and the missing scores are
saved as `None`/`null` in the metrics.
Attributes without unset states:
* `token.head`: relies on `token.dep` to recognize unset values
* `doc.cats`: unable to handle missing annotation
Additional changes:
* add optional `has_annotation` check to `score_scans` to replace
`doc.sents` hack
* update `score_token_attr_per_feat` to handle missing and empty morph
representations
* fix bug in `Doc.has_annotation` for normalization of `IS_SENT_START`
vs. `SENT_START`
* Fix import
* Update return types
* add informative warning when messing up store_user_data DocBin flags
* add informative warning when messing up store_user_data DocBin flags
* cleanup test
* rename to patterns_path
* Refactor Token morph setting
* Remove `Token.morph_`
* Add `Token.set_morph()`
* `0` resets `token.c.morph` to unset
* Any other values are passed to `Morphology.add`
* Add token.morph setter to set from MorphAnalysis
In order to make it easier to construct `Doc` objects as training data,
modify how missing and blocked entity tokens are set to prioritize
setting `O` and missing entity tokens for training purposes over setting
blocked entity tokens.
* `Doc.ents` setter sets tokens outside entity spans to `O` regardless
of the current state of each token
* For `Doc.ents`, setting a span with a missing label sets the `ent_iob`
to missing instead of blocked
* `Doc.block_ents(spans)` marks spans as hard `O` for use with the
`EntityRecognizer`
* Refactor Docs.is_ flags
* Add derived `Doc.has_annotation` method
* `Doc.has_annotation(attr)` returns `True` for partial annotation
* `Doc.has_annotation(attr, require_complete=True)` returns `True` for
complete annotation
* Add deprecation warnings to `is_tagged`, `is_parsed`, `is_sentenced`
and `is_nered`
* Add `Doc._get_array_attrs()`, which returns a full list of `Doc` attrs
for use with `Doc.to_array`, `Doc.to_bytes` and `Doc.from_docs`. The
list is the `DocBin` attributes list plus `SPACY` and `LENGTH`.
Notes on `Doc.has_annotation`:
* `HEAD` is converted to `DEP` because heads don't have an unset state
* Accept `IS_SENT_START` as a synonym of `SENT_START`
Additional changes:
* Add `NORM`, `ENT_ID` and `SENT_START` to default attributes for
`DocBin`
* In `Doc.from_array()` the presence of `DEP` causes `HEAD` to override
`SENT_START`
* In `Doc.from_array()` using `attrs` other than
`Doc._get_array_attrs()` (i.e., a user's custom list rather than our
default internal list) with both `HEAD` and `SENT_START` shows a warning
that `HEAD` will override `SENT_START`
* `set_children_from_heads` does not require dependency labels to set
sentence boundaries and sets `sent_start` for all non-sentence starts to
`-1`
* Fix call to set_children_form_heads
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Clean up spacy.tokens
* Update `set_children_from_heads`:
* Don't check `dep` when setting lr_* or sentence starts
* Set all non-sentence starts to `False`
* Use `set_children_from_heads` in `Token.head` setter
* Reduce similar/duplicate code (admittedly adds a bit of overhead)
* Update sentence starts consistently
* Remove unused `Doc.set_parse`
* Minor changes:
* Declare cython variables (to avoid cython warnings)
* Clean up imports
* Modify set_children_from_heads to set token range
Modify `set_children_from_heads` so that it adjust tokens within a
specified range rather then the whole document.
Modify the `Token.head` setter to adjust only the tokens affected by the
new head assignment.
Modify `Token.morph` property so that `Token.c.morph` can be reset back
to an internal value of `0`. Allow setting `Token.morph` from a hash as
long as the morph string is already in the `StringStore`, setting it
indirectly through `Token.morph_` so that the value is added to the
morphology. If the hash is not in the `StringStore`, raise an error.
* Add Lemmatizer and simplify related components
* Add `Lemmatizer` pipe with `lookup` and `rule` modes using the
`Lookups` tables.
* Reduce `Tagger` to a simple tagger that sets `Token.tag` (no pos or lemma)
* Reduce `Morphology` to only keep track of morph tags (no tag map, lemmatizer,
or morph rules)
* Remove lemmatizer from `Vocab`
* Adjust many many tests
Differences:
* No default lookup lemmas
* No special treatment of TAG in `from_array` and similar required
* Easier to modify labels in a `Tagger`
* No extra strings added from morphology / tag map
* Fix test
* Initial fix for Lemmatizer config/serialization
* Adjust init test to be more generic
* Adjust init test to force empty Lookups
* Add simple cache to rule-based lemmatizer
* Convert language-specific lemmatizers
Convert language-specific lemmatizers to component lemmatizers. Remove
previous lemmatizer class.
* Fix French and Polish lemmatizers
* Remove outdated UPOS conversions
* Update Russian lemmatizer init in tests
* Add minimal init/run tests for custom lemmatizers
* Add option to overwrite existing lemmas
* Update mode setting, lookup loading, and caching
* Make `mode` an immutable property
* Only enforce strict `load_lookups` for known supported modes
* Move caching into individual `_lemmatize` methods
* Implement strict when lang is not found in lookups
* Fix tables/lookups in make_lemmatizer
* Reallow provided lookups and allow for stricter checks
* Add lookups asset to all Lemmatizer pipe tests
* Rename lookups in lemmatizer init test
* Clean up merge
* Refactor lookup table loading
* Add helper from `load_lemmatizer_lookups` that loads required and
optional lookups tables based on settings provided by a config.
Additional slight refactor of lookups:
* Add `Lookups.set_table` to set a table from a provided `Table`
* Reorder class definitions to be able to specify type as `Table`
* Move registry assets into test methods
* Refactor lookups tables config
Use class methods within `Lemmatizer` to provide the config for
particular modes and to load the lookups from a config.
* Add pipe and score to lemmatizer
* Simplify Tagger.score
* Add missing import
* Clean up imports and auto-format
* Remove unused kwarg
* Tidy up and auto-format
* Update docstrings for Lemmatizer
Update docstrings for Lemmatizer.
Additionally modify `is_base_form` API to take `Token` instead of
individual features.
* Update docstrings
* Remove tag map values from Tagger.add_label
* Update API docs
* Fix relative link in Lemmatizer API docs
* Add AttributeRuler for token attribute exceptions
Add the `AttributeRuler` to handle exceptions for token-level
attributes. The `AttributeRuler` uses `Matcher` patterns to identify
target spans and applies the specified attributes to the token at the
provided index in the matched span. A negative index can be used to
index from the end of the matched span. The retokenizer is used to
"merge" the individual tokens and assign them the provided attributes.
Helper functions can import existing tag maps and morph rules to the
corresponding `Matcher` patterns.
There is an additional minor bug fix for `MORPH` attributes in the
retokenizer to correctly normalize the values and to handle `MORPH`
alongside `_` in an attrs dict.
* Fix default name
* Update name in error message
* Extend AttributeRuler functionality
* Add option to initialize with a dict of AttributeRuler patterns
* Instead of silently discarding overlapping matches (the default
behavior for the retokenizer if only the attrs differ), split the
matches into disjoint sets and retokenize each set separately. This
allows, for instance, one pattern to set the POS and another pattern to
set the lemma. (If two matches modify the same attribute, it looks like
the attrs are applied in the order they were added, but it may not be
deterministic?)
* Improve types
* Sort spans before processing
* Fix index boundaries in Span
* Refactor retokenizer to separate attrs methods
Add top-level `normalize_token_attrs` and `set_token_attrs` methods.
* Update AttributeRuler to use refactored methods
Update `AttributeRuler` to replace use of full retokenizer with only the
relevant methods for normalizing and setting attributes for a single
token.
* Update spacy/pipeline/attributeruler.py
Co-authored-by: Ines Montani <ines@ines.io>
* Make API more similar to EntityRuler
* Add `AttributeRuler.add_patterns` to add patterns from a list of dicts
* Return list of dicts as property `AttributeRuler.patterns`
* Make attrs_unnormed private
* Add test loading patterns from assets
* Revert "Fix index boundaries in Span"
This reverts commit 8f8a5c3386.
* Add Span index boundary checks (#5861)
* Add Span index boundary checks
* Return Span-specific IndexError in all cases
* Simplify and fix if/else
Co-authored-by: Ines Montani <ines@ines.io>
* Allow Doc.char_span to snap to token boundaries
Add a `mode` option to allow `Doc.char_span` to snap to token
boundaries. The `mode` options:
* `strict`: character offsets must match token boundaries (default, same as
before)
* `inside`: all tokens completely within the character span
* `outside`: all tokens at least partially covered by the character span
Add a new helper function `token_by_char` that returns the token
corresponding to a character position in the text. Update
`token_by_start` and `token_by_end` to use `token_by_char` for more
efficient searching.
* Remove unused import
* Rename mode to alignment_mode
Rename `mode` to `alignment_mode` with the options
`strict`/`contract`/`expand`. Any unrecognized modes are silently
converted to `strict`.
* `MorphAnalysis.get` returns only the field values
* Move `_normalize_props` inside `Morphology` as
`Morphology.normalize_attrs` and simplify
* Simplify POS field detection/conversion
* Convert all non-POS features to strings
* `Morphology` returns an empty string for a missing morph to align
with the FEATS string returned for an existing morph
* Remove unused `list_to_feats`
* Add morph to morphology in Doc.from_array
Add morphological analyses to morphology table in `Doc.from_array`.
* Use separate vocab in DocBin roundtrip test
* add keyword separator for update functions and drop unused "state"
* few more Example tests and various small fixes
* consistently return losses after update call
* eliminate unused tensors field across pipe components
* fix name
* fix arg name
* Tell convert CLI to store user data for Doc
* Remove assert
* Add has_unknwon_spaces flag on Doc
* Do not tokenize docs with unknown spaces in Corpus
* Handle conversion of unknown spaces in Example
* Fixes
* Fixes
* Draft has_known_spaces support in DocBin
* Add test for serialize has_unknown_spaces
* Fix DocBin serialization when has_unknown_spaces
* Use serialization in test
* Add static method to Doc to allow merging of multiple docs.
* Add error description for the error that occurs if docs with different
vocabs (from different languages) are merged in Doc.from_docs().
* Add test for Doc.from_docs() implementation.
* Fix using numpy's concatenate in Doc.from_docs.
* Replace typing's type annotations in from_docs.
* Simply remove type annotations in from_docs.
* Add documentation for Doc.from_docs to api.
* Simplify from_docs, its test and the api doc for codebase consistency.
* Fix merging of Doc objects that end with whitespaces (Achieved by simply not setting the SPACY attribute on whitespace tokens). Remove two unnecessary imports of attributes.
* Add merging of user data from Doc objects in from_docs. Add user data test case to corresponding test. Add applicable warning messages.
* Fix incorrect setting of tokens idx by using concatenated spaces (again). Add test case to corresponding test.
* Add MORPH to attrs
* Update warnings calls
* Remove out-dated error from merge
* Rename space_delimiter to ensure_whitespace
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add version number to DocBin
Add a version number to DocBin for future use.
* Add POS to all attributes in DocBin
* Add morph string to strings in DocBin
* Update DocBin API
* Add string for ENT_KB_ID in DocBin
* fixes in ud_train, UX for morphs
* update pyproject with new version of thinc
* fixes in debug_data script
* cleanup of old unused error messages
* remove obsolete TempErrors
* move error messages to errors.py
* add ENT_KB_ID to default DocBin serialization
* few fixes to simple_ner
* fix tags
* 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>
