* Fix ent_ids and labels properties when id attribute used in patterns
* use set for labels
* sort end_ids for comparison in entity_ruler tests
* fixing entity_ruler ent_ids test
* add to set
* move nlp processing for el pipe to batch training instead of preprocessing
* adding dev eval back in, and limit in articles instead of entities
* use pipe whenever possible
* few more small doc changes
* access dev data through generator
* tqdm description
* small fixes
* update documentation
* Add sent_starts to GoldParse
* Add SentTagger pipeline component
Add `SentTagger` pipeline component as a subclass of `Tagger`.
* Model reduces default parameters from `Tagger` to be small and fast
* Hard-coded set of two labels:
* S (1): token at beginning of sentence
* I (0): all other sentence positions
* Sets `token.sent_start` values
* Add sentence segmentation to Scorer
Report `sent_p/r/f` for sentence boundaries, which may be provided by
various pipeline components.
* Add sentence segmentation to CLI evaluate
* Add senttagger metrics/scoring to train CLI
* Rename SentTagger to SentenceRecognizer
* Add SentenceRecognizer to spacy.pipes imports
* Add SentenceRecognizer serialization test
* Shorten component name to sentrec
* Remove duplicates from train CLI output metrics
* Restructure Sentencizer to follow Pipe API
Restructure Sentencizer to follow Pipe API so that it can be scored with
`nlp.evaluate()`.
* Add Sentencizer pipe() test
* 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
* 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`
* 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
* Update test for ignore_misaligned
* 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
The `Matcher` in `merge_subtokens()` returns all possible subsequences
of `subtok`, so for sequences of two or more subtoks it's necessary to
filter the matches so that the retokenizer is only merging the longest
matches with no overlapping spans.
* Fix get labels for textcat
* Fix char_embed for gpu
* Revert "Fix char_embed for gpu"
This reverts commit 055b9a9e85.
* Fix passing of cats in gold.pyx
* Revert "Match pop with append for training format (#4516)"
This reverts commit 8e7414dace.
* Fix popping gold parses
* Fix handling of cats in gold tuples
* Fix name
* Fix ner_multitask_objective script
* Add test for 4402
* 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)
* Add work in progress
* Update analysis helpers and component decorator
* Fix porting of docstrings for Python 2
* Fix docstring stuff on Python 2
* Support meta factories when loading model
* Put auto pipeline analysis behind flag for now
* Analyse pipes on remove_pipe and replace_pipe
* Move analysis to root for now
Try to find a better place for it, but it needs to go for now to avoid circular imports
* Simplify decorator
Don't return a wrapped class and instead just write to the object
* Update existing components and factories
* Add condition in factory for classes vs. functions
* Add missing from_nlp classmethods
* Add "retokenizes" to printed overview
* Update assigns/requires declarations of builtins
* Only return data if no_print is enabled
* Use multiline table for overview
* Don't support Span
* Rewrite errors/warnings and move them to spacy.errors
* 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
* test and fix for second bug of issue 4042
* fix for first bug in 4042
* crashing test for Issue 4313
* forgot one instance of resize
* remove prints
* undo uncomment
* delete test for 4313 (uses third party lib)
* add fix for Issue 4313
* unit test for 4313
* remove redundant __call__ method in pipes.TextCategorizer
Because the parent __call__ method behaves in the same way.
* fix: Pipe.__call__ arg
* fix: invalid arg in Pipe.__call__
* modified: spacy/tests/regression/test_issue4278.py (#4278)
* deleted: Pipfile
* Add doc.cats to spacy.gold at the paragraph level
Support `doc.cats` as `"cats": [{"label": string, "value": number}]` in
the spacy JSON training format at the paragraph level.
* `spacy.gold.docs_to_json()` writes `docs.cats`
* `GoldCorpus` reads in cats in each `GoldParse`
* Update instances of gold_tuples to handle cats
Update iteration over gold_tuples / gold_parses to handle addition of
cats at the paragraph level.
* Add textcat to train CLI
* Add textcat options to train CLI
* Add textcat labels in `TextCategorizer.begin_training()`
* Add textcat evaluation to `Scorer`:
* For binary exclusive classes with provided label: F1 for label
* For 2+ exclusive classes: F1 macro average
* For multilabel (not exclusive): ROC AUC macro average (currently
relying on sklearn)
* Provide user info on textcat evaluation settings, potential
incompatibilities
* Provide pipeline to Scorer in `Language.evaluate` for textcat config
* Customize train CLI output to include only metrics relevant to current
pipeline
* Add textcat evaluation to evaluate CLI
* Fix handling of unset arguments and config params
Fix handling of unset arguments and model confiug parameters in Scorer
initialization.
* Temporarily add sklearn requirement
* Remove sklearn version number
* Improve Scorer handling of models without textcats
* Fixing Scorer handling of models without textcats
* Update Scorer output for python 2.7
* Modify inf in Scorer for python 2.7
* Auto-format
Also make small adjustments to make auto-formatting with black easier and produce nicer results
* Move error message to Errors
* Update documentation
* Add cats to annotation JSON format [ci skip]
* Fix tpl flag and docs [ci skip]
* Switch to internal roc_auc_score
Switch to internal `roc_auc_score()` adapted from scikit-learn.
* Add AUCROCScore tests and improve errors/warnings
* Add tests for AUCROCScore and roc_auc_score
* Add missing error for only positive/negative values
* Remove unnecessary warnings and errors
* Make reduced roc_auc_score functions private
Because most of the checks and warnings have been stripped for the
internal functions and access is only intended through `ROCAUCScore`,
make the functions for roc_auc_score adapted from scikit-learn private.
* Check that data corresponds with multilabel flag
Check that the training instances correspond with the multilabel flag,
adding the multilabel flag if required.
* Add textcat score to early stopping check
* Add more checks to debug-data for textcat
* Add example training data for textcat
* Add more checks to textcat train CLI
* Check configuration when extending base model
* Fix typos
* Update textcat example data
* Provide licensing details and licenses for data
* Remove two labels with no positive instances from jigsaw-toxic-comment
data.
Co-authored-by: Ines Montani <ines@ines.io>
Most of these characters are for languages / writing systems that aren't
supported by spacy, but I don't think it causes problems to include
them. In the UD evals, Hindi and Urdu improve a lot as expected (from
0-10% to 70-80%) and Persian improves a little (90% to 96%). Tamil
improves in combination with #4288.
The punctuation list is converted to a set internally because of its
increased length.
Sentence final punctuation generated with:
```
unichars -gas '[\p{Sentence_Break=STerm}\p{Sentence_Break=ATerm}]' '\p{Terminal_Punctuation}'
```
See: https://stackoverflow.com/a/9508766/461847Fixes#4269.
* Prevent subtok label if not learning tokens
The parser introduces the subtok label to mark tokens that should be
merged during post-processing. Previously this happened even if we did
not have the --learn-tokens flag set. This patch passes the config
through to the parser, to prevent the problem.
* Make merge_subtokens a parser post-process if learn_subtokens
* Fix train script
* Add test for 3830: subtok problem
* Fix handlign of non-subtok in parser training
* Fix typo in rule-based matching docs
* Improve token pattern checking without validation
Add more detailed token pattern checks without full JSON pattern validation and
provide more detailed error messages.
Addresses #4070 (also related: #4063, #4100).
* Check whether top-level attributes in patterns and attr for PhraseMatcher are
in token pattern schema
* Check whether attribute value types are supported in general (as opposed to
per attribute with full validation)
* Report various internal error types (OverflowError, AttributeError, KeyError)
as ValueError with standard error messages
* Check for tagger/parser in PhraseMatcher pipeline for attributes TAG, POS,
LEMMA, and DEP
* Add error messages with relevant details on how to use validate=True or nlp()
instead of nlp.make_doc()
* Support attr=TEXT for PhraseMatcher
* Add NORM to schema
* Expand tests for pattern validation, Matcher, PhraseMatcher, and EntityRuler
* Remove unnecessary .keys()
* Rephrase error messages
* Add another type check to Matcher
Add another type check to Matcher for more understandable error messages
in some rare cases.
* Support phrase_matcher_attr=TEXT for EntityRuler
* Don't use spacy.errors in examples and bin scripts
* Fix error code
* Auto-format
Also try get Azure pipelines to finally start a build :(
* Update errors.py
Co-authored-by: Ines Montani <ines@ines.io>
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* document token ent_kb_id
* document span kb_id
* update pipeline documentation
* prior and context weights as bool's instead
* entitylinker api documentation
* drop for both models
* finish entitylinker documentation
* small fixes
* documentation for KB
* candidate documentation
* links to api pages in code
* small fix
* frequency examples as counts for consistency
* consistent documentation about tensors returned by predict
* add entity linking to usage 101
* add entity linking infobox and KB section to 101
* entity-linking in linguistic features
* small typo corrections
* training example and docs for entity_linker
* predefined nlp and kb
* revert back to similarity encodings for simplicity (for now)
* set prior probabilities to 0 when excluded
* code clean up
* bugfix: deleting kb ID from tokens when entities were removed
* refactor train el example to use either model or vocab
* pretrain_kb example for example kb generation
* add to training docs for KB + EL example scripts
* small fixes
* error numbering
* ensure the language of vocab and nlp stay consistent across serialization
* equality with =
* avoid conflict in errors file
* add error 151
* final adjustements to the train scripts - consistency
* update of goldparse documentation
* small corrections
* push commit
* turn kb_creator into CLI script (wip)
* proper parameters for training entity vectors
* wikidata pipeline split up into two executable scripts
* remove context_width
* move wikidata scripts in bin directory, remove old dummy script
* refine KB script with logs and preprocessing options
* small edits
* small improvements to logging of EL CLI script
* Improve error message when model.from_bytes() dies
When Thinc's model.from_bytes() is called with a mismatched model, often
we get a particularly ungraceful error,
e.g. "AttributeError: FunctionLayer has no attribute G"
This is because we're trying to load the parameters for something like
a LayerNorm layer, and the model architecture has some other layer there
instead. This is obviously terrible, especially since the error *type*
is wrong.
I've changed it to raise a ValueError. The error message is still
probably a bit terse, but it's hard to be sure exactly what's gone
wrong.
* Update spacy/pipeline/pipes.pyx
* Update spacy/pipeline/pipes.pyx
* Update spacy/pipeline/pipes.pyx
* Update spacy/syntax/nn_parser.pyx
* Update spacy/syntax/nn_parser.pyx
* Update spacy/pipeline/pipes.pyx
Co-Authored-By: Matthew Honnibal <honnibal+gh@gmail.com>
* Update spacy/pipeline/pipes.pyx
Co-Authored-By: Matthew Honnibal <honnibal+gh@gmail.com>
Co-authored-by: Ines Montani <ines@ines.io>
Expected an `entity_ruler.jsonl` file in the top-level model directory, so the path passed to from_disk by default (model path plus componentn name), but with the suffix ".jsonl".
* Perserve flags in EntityRuler
The EntityRuler (explosion/spaCy#3526) does not preserve
overwrite flags (or `ent_id_sep`) when serialized. This
commit adds support for serialization/deserialization preserving
overwrite and ent_id_sep flags.
* add signed contributor agreement
* flake8 cleanup
mostly blank line issues.
* mark test from the issue as needing a model
The test from the issue needs some language model for serialization
but the test wasn't originally marked correctly.
* Adds `phrase_matcher_attr` to allow args to PhraseMatcher
This is an added arg to pass to the `PhraseMatcher`. For example,
this allows creation of a case insensitive phrase matcher when the
`EntityRuler` is created. References explosion/spaCy#3822
* remove unneeded model loading
The model didn't need to be loaded, and I replaced it with
a change that doesn't require it (using existings fixtures)
* updated docstring for new argument
* updated docs to reflect new argument to the EntityRuler constructor
* change tempdir handling to be compatible with python 2.7
* return conflicted code to entityruler
Some stuff got cut out because of merge conflicts, this
returns that code for the phrase_matcher_attr.
* fixed typo in the code added back after conflicts
* flake8 compliance
When I deconflicted the branch there were some flake8 issues
introduced. This resolves the spacing problems.
* test changes: attempts to fix flaky test in python3.5
These tests seem to be alittle flaky in 3.5 so I changed the check to avoid
the comparisons that seem to be fail sometimes.
* Perserve flags in EntityRuler
The EntityRuler (explosion/spaCy#3526) does not preserve
overwrite flags (or `ent_id_sep`) when serialized. This
commit adds support for serialization/deserialization preserving
overwrite and ent_id_sep flags.
* add signed contributor agreement
* flake8 cleanup
mostly blank line issues.
* mark test from the issue as needing a model
The test from the issue needs some language model for serialization
but the test wasn't originally marked correctly.
* remove unneeded model loading
The model didn't need to be loaded, and I replaced it with
a change that doesn't require it (using existings fixtures)
* change tempdir handling to be compatible with python 2.7
* Adds code to handle item saved before this change.
This code chanes how the save files are handled and how the bytes
are stored as well. This code adds check to dispatch correctly
if it encounters bytes or files saved in the old format (and tests
for those cases).
* use util function for tempdir management
Updated after PR comments: this code now uses the make_tempdir function from util
instead of doing it by hand.
* Adding support for entity_id in EntityRuler pipeline component
* Adding Spacy Contributor aggreement
* Updating EntityRuler to use string.format instead of f strings
* Update Entity Ruler to support an 'id' attribute per pattern that explicitly identifies an entity.
* Fixing tests
* Remove custom extension entity_id and use built in ent_id token attribute.
* Changing entity_id to ent_id for consistent naming
* entity_ids => ent_ids
* Removing kb, cleaning up tests, making util functions private, use rsplit instead of split
adrianeboyd