* 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>
* verbose and tag_map options
* adding init_tok2vec option and only changing the tok2vec that is specified
* adding omit_extra_lookups and verifying textcat config
* wip
* pretrain bugfix
* add replace and resume options
* train_textcat fix
* raw text functionality
* improve UX when KeyError or when input data can't be parsed
* avoid unnecessary access to goldparse in TextCat pipe
* save performance information in nlp.meta
* add noise_level to config
* move nn_parser's defaults to config file
* multitask in config - doesn't work yet
* scorer offering both F and AUC options, need to be specified in config
* add textcat verification code from old train script
* small fixes to config files
* clean up
* set default config for ner/parser to allow create_pipe to work as before
* two more test fixes
* small fixes
* cleanup
* fix NER pickling + additional unit test
* create_pipe as before
* Fix most_similar for vectors with unused rows
Address issues related to the unused rows in the vector table and
`most_similar`:
* Update `most_similar()` to search only through rows that are in use
according to `key2row`.
* Raise an error when `most_similar(n=n)` is larger than the number of
vectors in the table.
* Set and restore `_unset` correctly when vectors are added or
deserialized so that new vectors are added in the correct row.
* Set data and keys to the same length in `Vocab.prune_vectors()` to
avoid spurious entries in `key2row`.
* Fix regression test using `most_similar`
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* make disable_pipes deprecated in favour of the new toggle_pipes
* rewrite disable_pipes statements
* update documentation
* remove bin/wiki_entity_linking folder
* one more fix
* remove deprecated link to documentation
* few more doc fixes
* add note about name change to the docs
* restore original disable_pipes
* small fixes
* fix typo
* fix error number to W096
* rename to select_pipes
* also make changes to the documentation
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Draft layer for BILUO actions
* Fixes to biluo layer
* WIP on BILUO layer
* Add tests for BILUO layer
* Format
* Fix transitions
* Update test
* Link in the simple_ner
* Update BILUO tagger
* Update __init__
* Import simple_ner
* Update test
* Import
* Add files
* Add config
* Fix label passing for BILUO and tagger
* Fix label handling for simple_ner component
* Update simple NER test
* Update config
* Hack train script
* Update BILUO layer
* Fix SimpleNER component
* Update train_from_config
* Add biluo_to_iob helper
* Add IOB layer
* Add IOBTagger model
* Update biluo layer
* Update SimpleNER tagger
* Update BILUO
* Read random seed in train-from-config
* Update use of normal_init
* Fix normalization of gradient in SimpleNER
* Update IOBTagger
* Remove print
* Tweak masking in BILUO
* Add dropout in SimpleNER
* Update thinc
* Tidy up simple_ner
* Fix biluo model
* Unhack train-from-config
* Update setup.cfg and requirements
* Add tb_framework.py for parser model
* Try to avoid memory leak in BILUO
* Move ParserModel into spacy.ml, avoid need for subclass.
* Use updated parser model
* Remove incorrect call to model.initializre in PrecomputableAffine
* Update parser model
* Avoid divide by zero in tagger
* Add extra dropout layer in tagger
* Refine minibatch_by_words function to avoid oom
* Fix parser model after refactor
* Try to avoid div-by-zero in SimpleNER
* Fix infinite loop in minibatch_by_words
* Use SequenceCategoricalCrossentropy in Tagger
* Fix parser model when hidden layer
* Remove extra dropout from tagger
* Add extra nan check in tagger
* Fix thinc version
* Update tests and imports
* Fix test
* Update test
* Update tests
* Fix tests
* Fix test
Co-authored-by: Ines Montani <ines@ines.io>
* simplify creation of KB by skipping dim reduction
* small fixes to train EL example script
* add KB creation and NEL training example scripts to example section
* update descriptions of example scripts in the documentation
* moving wiki_entity_linking folder from bin to projects
* remove test for wiki NEL functionality that is being moved
* Check whether doc is instantiated
When creating docs to pair with gold parses, modify test to check
whether a doc is unset rather than whether it contains tokens.
* Restore test of evaluate on an empty doc
* Set a minimal gold.orig for the scorer
Without a minimal gold.orig the scorer can't evaluate empty docs. This
is the v3 equivalent of #4925.
* merge_entities sets the vector in the vocab for the merged token
* add unit test
* import unicode_literals
* move code to _merge function
* only set vector if vocab has non-zero vectors
* fix grad_clip naming
* cleaning up pretrained_vectors out of cfg
* further refactoring Model init's
* move Model building out of pipes
* further refactor to require a model config when creating a pipe
* small fixes
* making cfg in nn_parser more consistent
* fixing nr_class for parser
* fixing nn_parser's nO
* fix printing of loss
* architectures in own file per type, consistent naming
* convenience methods default_tagger_config and default_tok2vec_config
* let create_pipe access default config if available for that component
* default_parser_config
* move defaults to separate folder
* allow reading nlp from package or dir with argument 'name'
* architecture spacy.VocabVectors.v1 to read static vectors from file
* cleanup
* default configs for nel, textcat, morphologizer, tensorizer
* fix imports
* fixing unit tests
* fixes and clean up
* fixing defaults, nO, fix unit tests
* restore parser IO
* fix IO
* 'fix' serialization test
* add *.cfg to manifest
* fix example configs with additional arguments
* replace Morpohologizer with Tagger
* add IO bit when testing overfitting of tagger (currently failing)
* fix IO - don't initialize when reading from disk
* expand overfitting tests to also check IO goes OK
* remove dropout from HashEmbed to fix Tagger performance
* add defaults for sentrec
* update thinc
* always pass a Model instance to a Pipe
* fix piped_added statement
* remove obsolete W029
* remove obsolete errors
* restore byte checking tests (work again)
* clean up test
* further test cleanup
* convert from config to Model in create_pipe
* bring back error when component is not initialized
* cleanup
* remove calls for nlp2.begin_training
* use thinc.api in imports
* allow setting charembed's nM and nC
* fix for hardcoded nM/nC + unit test
* formatting fixes
* trigger build
* Add load_from_config function
* Add train_from_config script
* Merge configs and expose via spacy.config
* Fix script
* Suggest create_evaluation_callback
* Hard-code for NER
* Fix errors
* Register command
* Add TODO
* Update train-from-config todos
* Fix imports
* Allow delayed setting of parser model nr_class
* Get train-from-config working
* Tidy up and fix scores and printing
* Hide traceback if cancelled
* Fix weighted score formatting
* Fix score formatting
* Make output_path optional
* Add Tok2Vec component
* Tidy up and add tok2vec_tensors
* Add option to copy docs in nlp.update
* Copy docs in nlp.update
* Adjust nlp.update() for set_annotations
* Don't shuffle pipes in nlp.update, decruft
* Support set_annotations arg in component update
* Support set_annotations in parser update
* Add get_gradients method
* Add get_gradients to parser
* Update errors.py
* Fix problems caused by merge
* Add _link_components method in nlp
* Add concept of 'listeners' and ControlledModel
* Support optional attributes arg in ControlledModel
* Try having tok2vec component in pipeline
* Fix tok2vec component
* Fix config
* Fix tok2vec
* Update for Example
* Update for Example
* Update config
* Add eg2doc util
* Update and add schemas/types
* Update schemas
* Fix nlp.update
* Fix tagger
* Remove hacks from train-from-config
* Remove hard-coded config str
* Calculate loss in tok2vec component
* Tidy up and use function signatures instead of models
* Support union types for registry models
* Minor cleaning in Language.update
* Make ControlledModel specifically Tok2VecListener
* Fix train_from_config
* Fix tok2vec
* Tidy up
* Add function for bilstm tok2vec
* Fix type
* Fix syntax
* Fix pytorch optimizer
* Add example configs
* Update for thinc describe changes
* Update for Thinc changes
* Update for dropout/sgd changes
* Update for dropout/sgd changes
* Unhack gradient update
* Work on refactoring _ml
* Remove _ml.py module
* WIP upgrade cli scripts for thinc
* Move some _ml stuff to util
* Import link_vectors from util
* Update train_from_config
* Import from util
* Import from util
* Temporarily add ml.component_models module
* Move ml methods
* Move typedefs
* Update load vectors
* Update gitignore
* Move imports
* Add PrecomputableAffine
* Fix imports
* Fix imports
* Fix imports
* Fix missing imports
* Update CLI scripts
* Update spacy.language
* Add stubs for building the models
* Update model definition
* Update create_default_optimizer
* Fix import
* Fix comment
* Update imports in tests
* Update imports in spacy.cli
* Fix import
* fix obsolete thinc imports
* update srsly pin
* from thinc to ml_datasets for example data such as imdb
* update ml_datasets pin
* using STATE.vectors
* small fix
* fix Sentencizer.pipe
* black formatting
* rename Affine to Linear as in thinc
* set validate explicitely to True
* rename with_square_sequences to with_list2padded
* rename with_flatten to with_list2array
* chaining layernorm
* small fixes
* revert Optimizer import
* build_nel_encoder with new thinc style
* fixes using model's get and set methods
* Tok2Vec in component models, various fixes
* fix up legacy tok2vec code
* add model initialize calls
* add in build_tagger_model
* small fixes
* setting model dims
* fixes for ParserModel
* various small fixes
* initialize thinc Models
* fixes
* consistent naming of window_size
* fixes, removing set_dropout
* work around Iterable issue
* remove legacy tok2vec
* util fix
* fix forward function of tok2vec listener
* more fixes
* trying to fix PrecomputableAffine (not succesful yet)
* alloc instead of allocate
* add morphologizer
* rename residual
* rename fixes
* Fix predict function
* Update parser and parser model
* fixing few more tests
* Fix precomputable affine
* Update component model
* Update parser model
* Move backprop padding to own function, for test
* Update test
* Fix p. affine
* Update NEL
* build_bow_text_classifier and extract_ngrams
* Fix parser init
* Fix test add label
* add build_simple_cnn_text_classifier
* Fix parser init
* Set gpu off by default in example
* Fix tok2vec listener
* Fix parser model
* Small fixes
* small fix for PyTorchLSTM parameters
* revert my_compounding hack (iterable fixed now)
* fix biLSTM
* Fix uniqued
* PyTorchRNNWrapper fix
* small fixes
* use helper function to calculate cosine loss
* small fixes for build_simple_cnn_text_classifier
* putting dropout default at 0.0 to ensure the layer gets built
* using thinc util's set_dropout_rate
* moving layer normalization inside of maxout definition to optimize dropout
* temp debugging in NEL
* fixed NEL model by using init defaults !
* fixing after set_dropout_rate refactor
* proper fix
* fix test_update_doc after refactoring optimizers in thinc
* Add CharacterEmbed layer
* Construct tagger Model
* Add missing import
* Remove unused stuff
* Work on textcat
* fix test (again :)) after optimizer refactor
* fixes to allow reading Tagger from_disk without overwriting dimensions
* don't build the tok2vec prematuraly
* fix CharachterEmbed init
* CharacterEmbed fixes
* Fix CharacterEmbed architecture
* fix imports
* renames from latest thinc update
* one more rename
* add initialize calls where appropriate
* fix parser initialization
* Update Thinc version
* Fix errors, auto-format and tidy up imports
* Fix validation
* fix if bias is cupy array
* revert for now
* ensure it's a numpy array before running bp in ParserStepModel
* no reason to call require_gpu twice
* use CupyOps.to_numpy instead of cupy directly
* fix initialize of ParserModel
* remove unnecessary import
* fixes for CosineDistance
* fix device renaming
* use refactored loss functions (Thinc PR 251)
* overfitting test for tagger
* experimental settings for the tagger: avoid zero-init and subword normalization
* clean up tagger overfitting test
* use previous default value for nP
* remove toy config
* bringing layernorm back (had a bug - fixed in thinc)
* revert setting nP explicitly
* remove setting default in constructor
* restore values as they used to be
* add overfitting test for NER
* add overfitting test for dep parser
* add overfitting test for textcat
* fixing init for linear (previously affine)
* larger eps window for textcat
* ensure doc is not None
* Require newer thinc
* Make float check vaguer
* Slop the textcat overfit test more
* Fix textcat test
* Fix exclusive classes for textcat
* fix after renaming of alloc methods
* fixing renames and mandatory arguments (staticvectors WIP)
* upgrade to thinc==8.0.0.dev3
* refer to vocab.vectors directly instead of its name
* rename alpha to learn_rate
* adding hashembed and staticvectors dropout
* upgrade to thinc 8.0.0.dev4
* add name back to avoid warning W020
* thinc dev4
* update srsly
* using thinc 8.0.0a0 !
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
Co-authored-by: Ines Montani <ines@ines.io>
* Restructure tag maps for MorphAnalysis changes
Prepare tag maps for upcoming MorphAnalysis changes that allow
arbritrary features.
* Use default tag map rather than duplicating for ca / uk / vi
* Import tag map into defaults for ga
* Modify tag maps so all morphological fields and features are strings
* Move features from `"Other"` to the top level
* Rewrite tuples as strings separated by `","`
* Rewrite morph symbols for fr lemmatizer as strings
* Export MorphAnalysis under spacy.tokens
* Modify morphology to support arbitrary features
Modify `Morphology` and `MorphAnalysis` so that arbitrary features are
supported.
* Modify `MorphAnalysisC` so that it can support arbitrary features and
multiple values per field. `MorphAnalysisC` is redesigned to contain:
* key: hash of UD FEATS string of morphological features
* array of `MorphFeatureC` structs that each contain a hash of `Field`
and `Field=Value` for a given morphological feature, which makes it
possible to:
* find features by field
* represent multiple values for a given field
* `get_field()` is renamed to `get_by_field()` and is no longer `nogil`.
Instead a new helper function `get_n_by_field()` is `nogil` and returns
`n` features by field.
* `MorphAnalysis.get()` returns all possible values for a field as a
list of individual features such as `["Tense=Pres", "Tense=Past"]`.
* `MorphAnalysis`'s `str()` and `repr()` are the UD FEATS string.
* `Morphology.feats_to_dict()` converts a UD FEATS string to a dict
where:
* Each field has one entry in the dict
* Multiple values remain separated by a separator in the value string
* `Token.morph_` returns the UD FEATS string and you can set
`Token.morph_` with a UD FEATS string or with a tag map dict.
* Modify get_by_field to use np.ndarray
Modify `get_by_field()` to use np.ndarray. Remove `max_results` from
`get_n_by_field()` and always iterate over all the fields.
* Rewrite without MorphFeatureC
* Add shortcut for existing feats strings as keys
Add shortcut for existing feats strings as keys in `Morphology.add()`.
* Check for '_' as empty analysis when adding morphs
* Extend helper converters in Morphology
Add and extend helper converters that convert and normalize between:
* UD FEATS strings (`"Case=dat,gen|Number=sing"`)
* per-field dict of feats (`{"Case": "dat,gen", "Number": "sing"}`)
* list of individual features (`["Case=dat", "Case=gen",
"Number=sing"]`)
All converters sort fields and values where applicable.
* expand serialization test for custom token attribute
* add failing test for issue 4849
* define ENT_ID as attr and use in doc serialization
* fix few typos
* 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
* Generalize handling of tokenizer special cases
Handle tokenizer special cases more generally by using the Matcher
internally to match special cases after the affix/token_match
tokenization is complete.
Instead of only matching special cases while processing balanced or
nearly balanced prefixes and suffixes, this recognizes special cases in
a wider range of contexts:
* Allows arbitrary numbers of prefixes/affixes around special cases
* Allows special cases separated by infixes
Existing tests/settings that couldn't be preserved as before:
* The emoticon '")' is no longer a supported special case
* The emoticon ':)' in "example:)" is a false positive again
When merged with #4258 (or the relevant cache bugfix), the affix and
token_match properties should be modified to flush and reload all
special cases to use the updated internal tokenization with the Matcher.
* Remove accidentally added test case
* Really remove accidentally added test
* Reload special cases when necessary
Reload special cases when affixes or token_match are modified. Skip
reloading during initialization.
* Update error code number
* Fix offset and whitespace in Matcher special cases
* Fix offset bugs when merging and splitting tokens
* Set final whitespace on final token in inserted special case
* Improve cache flushing in tokenizer
* Separate cache and specials memory (temporarily)
* Flush cache when adding special cases
* Repeated `self._cache = PreshMap()` and `self._specials = PreshMap()`
are necessary due to this bug:
https://github.com/explosion/preshed/issues/21
* Remove reinitialized PreshMaps on cache flush
* Update UD bin scripts
* Update imports for `bin/`
* Add all currently supported languages
* Update subtok merger for new Matcher validation
* Modify blinded check to look at tokens instead of lemmas (for corpora
with tokens but not lemmas like Telugu)
* Use special Matcher only for cases with affixes
* Reinsert specials cache checks during normal tokenization for special
cases as much as possible
* Additionally include specials cache checks while splitting on infixes
* Since the special Matcher needs consistent affix-only tokenization
for the special cases themselves, introduce the argument
`with_special_cases` in order to do tokenization with or without
specials cache checks
* After normal tokenization, postprocess with special cases Matcher for
special cases containing affixes
* Replace PhraseMatcher with Aho-Corasick
Replace PhraseMatcher with the Aho-Corasick algorithm over numpy arrays
of the hash values for the relevant attribute. The implementation is
based on FlashText.
The speed should be similar to the previous PhraseMatcher. It is now
possible to easily remove match IDs and matches don't go missing with
large keyword lists / vocabularies.
Fixes#4308.
* Restore support for pickling
* Fix internal keyword add/remove for numpy arrays
* Add test for #4248, clean up test
* Improve efficiency of special cases handling
* Use PhraseMatcher instead of Matcher
* Improve efficiency of merging/splitting special cases in document
* Process merge/splits in one pass without repeated token shifting
* Merge in place if no splits
* Update error message number
* Remove UD script modifications
Only used for timing/testing, should be a separate PR
* Remove final traces of UD script modifications
* Update UD bin scripts
* Update imports for `bin/`
* Add all currently supported languages
* Update subtok merger for new Matcher validation
* Modify blinded check to look at tokens instead of lemmas (for corpora
with tokens but not lemmas like Telugu)
* Add missing loop for match ID set in search loop
* Remove cruft in matching loop for partial matches
There was a bit of unnecessary code left over from FlashText in the
matching loop to handle partial token matches, which we don't have with
PhraseMatcher.
* Replace dict trie with MapStruct trie
* Fix how match ID hash is stored/added
* Update fix for match ID vocab
* Switch from map_get_unless_missing to map_get
* Switch from numpy array to Token.get_struct_attr
Access token attributes directly in Doc instead of making a copy of the
relevant values in a numpy array.
Add unsatisfactory warning for hash collision with reserved terminal
hash key. (Ideally it would change the reserved terminal hash and redo
the whole trie, but for now, I'm hoping there won't be collisions.)
* Restructure imports to export find_matches
* Implement full remove()
Remove unnecessary trie paths and free unused maps.
Parallel to Matcher, raise KeyError when attempting to remove a match ID
that has not been added.
* Switch to PhraseMatcher.find_matches
* Switch to local cdef functions for span filtering
* Switch special case reload threshold to variable
Refer to variable instead of hard-coded threshold
* Move more of special case retokenize to cdef nogil
Move as much of the special case retokenization to nogil as possible.
* Rewrap sort as stdsort for OS X
* Rewrap stdsort with specific types
* Switch to qsort
* Fix merge
* Improve cmp functions
* Fix realloc
* Fix realloc again
* Initialize span struct while retokenizing
* Temporarily skip retokenizing
* Revert "Move more of special case retokenize to cdef nogil"
This reverts commit 0b7e52c797.
* Revert "Switch to qsort"
This reverts commit a98d71a942.
* Fix specials check while caching
* Modify URL test with emoticons
The multiple suffix tests result in the emoticon `:>`, which is now
retokenized into one token as a special case after the suffixes are
split off.
* Refactor _apply_special_cases()
* Use cdef ints for span info used in multiple spots
* Modify _filter_special_spans() to prefer earlier
Parallel to #4414, modify _filter_special_spans() so that the earlier
span is preferred for overlapping spans of the same length.
* Replace MatchStruct with Entity
Replace MatchStruct with Entity since the existing Entity struct is
nearly identical.
* Replace Entity with more general SpanC
* Replace MatchStruct with SpanC
* Add error in debug-data if no dev docs are available (see #4575)
* Update azure-pipelines.yml
* Revert "Update azure-pipelines.yml"
This reverts commit ed1060cf59.
* Use latest wasabi
* Reorganise install_requires
* add dframcy to universe.json (#4580)
* Update universe.json [ci skip]
* Fix multiprocessing for as_tuples=True (#4582)
* Fix conllu script (#4579)
* force extensions to avoid clash between example scripts
* fix arg order and default file encoding
* add example config for conllu script
* newline
* move extension definitions to main function
* few more encodings fixes
* Add load_from_docbin example [ci skip]
TODO: upload the file somewhere
* Update README.md
* Add warnings about 3.8 (resolves#4593) [ci skip]
* Fixed typo: Added space between "recognize" and "various" (#4600)
* Fix DocBin.merge() example (#4599)
* Replace function registries with catalogue (#4584)
* Replace functions registries with catalogue
* Update __init__.py
* Fix test
* Revert unrelated flag [ci skip]
* Bugfix/dep matcher issue 4590 (#4601)
* add contributor agreement for prilopes
* add test for issue #4590
* fix on_match params for DependencyMacther (#4590)
* Minor updates to language example sentences (#4608)
* Add punctuation to Spanish example sentences
* Combine multilanguage examples for lang xx
* Add punctuation to nb examples
* Always realloc to a larger size
Avoid potential (unlikely) edge case and cymem error seen in #4604.
* Add error in debug-data if no dev docs are available (see #4575)
* Update debug-data for GoldCorpus / Example
* Ignore None label in misaligned NER data
* OrigAnnot class instead of gold.orig_annot list of zipped tuples
* from_orig to replace from_annot_tuples
* rename to RawAnnot
* some unit tests for GoldParse creation and internal format
* removing orig_annot and switching to lists instead of tuple
* rewriting tuples to use RawAnnot (+ debug statements, WIP)
* fix pop() changing the data
* small fixes
* pop-append fixes
* return RawAnnot for existing GoldParse to have uniform interface
* clean up imports
* fix merge_sents
* add unit test for 4402 with new structure (not working yet)
* introduce DocAnnot
* typo fixes
* add unit test for merge_sents
* rename from_orig to from_raw
* fixing unit tests
* fix nn parser
* read_annots to produce text, doc_annot pairs
* _make_golds fix
* rename golds_to_gold_annots
* small fixes
* fix encoding
* have golds_to_gold_annots use DocAnnot
* missed a spot
* merge_sents as function in DocAnnot
* allow specifying only part of the token-level annotations
* refactor with Example class + underlying dicts
* pipeline components to work with Example objects (wip)
* input checking
* fix yielding
* fix calls to update
* small fixes
* fix scorer unit test with new format
* fix kwargs order
* fixes for ud and conllu scripts
* fix reading data for conllu script
* add in proper errors (not fixed numbering yet to avoid merge conflicts)
* fixing few more small bugs
* fix EL script
* trying to fix script - not succesful yet
* match pop() with extend() to avoid changing the data
* few more pop-extend fixes
* reinsert deleted print statement
* fix print statement
* add last tested version
* append instead of extend
* add in few comments
* quick fix for 4402 + unit test
* fixing number of docs (not counting cats)
* more fixes
* fix len
* print tmp file instead of using data from examples dir
* print tmp file instead of using data from examples dir (2)
* Implement new API for {Phrase}Matcher.add (backwards-compatible)
* Update docs
* Also update DependencyMatcher.add
* Update internals
* Rewrite tests to use new API
* Add basic check for common mistake
Raise error with suggestion if user likely passed in a pattern instead of a list of patterns
* Fix typo [ci skip]
* fix overflow error on windows
* more documentation & logging fixes
* md fix
* 3 different limit parameters to play with execution time
* bug fixes directory locations
* small fixes
* exclude dev test articles from prior probabilities stats
* small fixes
* filtering wikidata entities, removing numeric and meta items
* adding aliases from wikidata also to the KB
* fix adding WD aliases
* adding also new aliases to previously added entities
* fixing comma's
* small doc fixes
* adding subclassof filtering
* append alias functionality in KB
* prevent appending the same entity-alias pair
* fix for appending WD aliases
* remove date filter
* remove unnecessary import
* small corrections and reformatting
* remove WD aliases for now (too slow)
* removing numeric entities from training and evaluation
* small fixes
* shortcut during prediction if there is only one candidate
* add counts and fscore logging, remove FP NER from evaluation
* fix entity_linker.predict to take docs instead of single sentences
* remove enumeration sentences from the WP dataset
* entity_linker.update to process full doc instead of single sentence
* spelling corrections and dump locations in readme
* NLP IO fix
* reading KB is unnecessary at the end of the pipeline
* small logging fix
* remove empty files
* Move test
* Allow default in Lookups.get_table
* Start with blank tables in Lookups.from_bytes
* Refactor lemmatizer to hold instance of Lookups
* Get lookups table within the lemmatization methods to make sure it references the correct table (even if the table was replaced or modified, e.g. when loading a model from disk)
* Deprecate other arguments on Lemmatizer.__init__ and expect Lookups for consistency
* Remove old and unsupported Lemmatizer.load classmethod
* Refactor language-specific lemmatizers to inherit as much as possible from base class and override only what they need
* Update tests and docs
* Fix more tests
* Fix lemmatizer
* Upgrade pytest to try and fix weird CI errors
* Try pytest 4.6.5
* Add default to util.get_entry_point
* Tidy up entry points
* Read lookups from entry points
* Remove lookup tables and related tests
* Add lookups install option
* Remove lemmatizer tests
* Remove logic to process language data files
* Update setup.cfg
