* 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
* small fix in example imports
* throw error when train_corpus or dev_corpus is not a string
* small fix in custom logger example
* limit macro_auc to labels with 2 annotations
* fix typo
* also create parents of output_dir if need be
* update documentation of textcat scores
* refactor TextCatEnsemble
* fix tests for new AUC definition
* bump to 3.0.0a42
* update docs
* rename to spacy.TextCatEnsemble.v2
* spacy.TextCatEnsemble.v1 in legacy
* cleanup
* small fix
* update to 3.0.0rc2
* fix import that got lost in merge
* cursed IDE
* fix two typos
* rename Pipe to TrainablePipe
* split functionality between Pipe and TrainablePipe
* remove unnecessary methods from certain components
* cleanup
* hasattr(component, "pipe") should be sufficient again
* remove serialization and vocab/cfg from Pipe
* unify _ensure_examples and validate_examples
* small fixes
* hasattr checks for self.cfg and self.vocab
* make is_resizable and is_trainable properties
* serialize strings.json instead of vocab
* fix KB IO + tests
* fix typos
* more typos
* _added_strings as a set
* few more tests specifically for _added_strings field
* bump to 3.0.0a36
* 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
* Fix skipped documents in entity scorer
* Add back the skipping of unannotated entities
* Update spacy/scorer.py
* Use more specific NER scorer
* Fix import
* Fix get_ner_prf
* Add scorer
* Fix scorer
Co-authored-by: Ines Montani <ines@ines.io>
* Add option to disable Matcher errors
* Add option to disable Matcher errors when a doc doesn't contain a
particular type of annotation
Minor additional change:
* Update `AttributeRuler.load_from_morph_rules` to allow direct `MORPH`
values
* Rename suppress_errors to allow_missing
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Refactor annotation checks in Matcher and PhraseMatcher
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* NEL: read sentences and ents from reference
* fiddling with sent_start annotations
* add KB serialization test
* KB write additional file with strings.json
* score_links function to calculate NEL P/R/F
* formatting
* documentation
* 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.
* ensure Language passes on valid examples for initialization
* fix tagger model initialization
* check for valid get_examples across components
* assume labels were added before begin_training
* fix senter initialization
* fix morphologizer initialization
* use methods to check arguments
* test textcat init, requires thinc>=8.0.0a31
* fix tok2vec init
* fix entity linker init
* use islice
* fix simple NER
* cleanup debug model
* fix assert statements
* fix tests
* throw error when adding a label if the output layer can't be resized anymore
* fix test
* add failing test for simple_ner
* UX improvements
* morphologizer UX
* assume begin_training gets a representative set and processes the labels
* remove assumptions for output of untrained NER model
* restore test for original purpose
Follow-ups to the parser efficiency fix.
* Avoid introducing new counter for number of pushes
* Base cut on number of transitions, keeping it more even
* Reintroduce the randomization we had in v2.
The parser training makes use of a trick for long documents, where we
use the oracle to cut up the document into sections, so that we can have
batch items in the middle of a document. For instance, if we have one
document of 600 words, we might make 6 states, starting at words 0, 100,
200, 300, 400 and 500.
The problem is for v3, I screwed this up and didn't stop parsing! So
instead of a batch of [100, 100, 100, 100, 100, 100], we'd have a batch
of [600, 500, 400, 300, 200, 100]. Oops.
The implementation here could probably be improved, it's annoying to
have this extra variable in the state. But this'll do.
This makes the v3 parser training 5-10 times faster, depending on document
lengths. This problem wasn't in v2.
* Prevent Tagger model init with 0 labels
Raise an error before trying to initialize a tagger model with 0 labels.
* Add dummy tagger label for test
* Remove tagless tagger model initializiation
* Fix error number after merge
* Add dummy tagger label to test
* Fix formatting
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* rename to spacy-transformers.TransformerListener
* add some more tok2vec tests
* use select_pipes
* fix docs - annotation setter was not changed in the end
Sort the returned matches by rule order (the `match_id`) so that the
rules are applied in the order they were added. This is necessary, for
instance, if the `AttributeRuler` is used for the tag map and later
rules require POS tags.
Serialize `AttributeRuler.patterns` instead of the individual lists to
simplify the serialized and so that patterns are reloaded exactly as
they were originally provided (preserving `_attrs_unnormed`).
* Add AttributeRuler.score
Add scoring for TAG / POS / MORPH / LEMMA if these are present in the
assigned token attributes.
Add default score weights (that don't really make a lot of sense) so
that the scores are in the default config in some form.
* Update docs
* candidate generator as separate part of EL config
* update comment
* ent instead of str as input for candidate generation
* Span instead of str: correct type indication
* fix types
* unit test to create new candidate generator
* fix replace_pipe argument passing
* move error message, general cleanup
* add vocab back to KB constructor
* provide KB as callable from Vocab arg
* rename to kb_loader, fix KB serialization as part of the EL pipe
* fix typo
* reformatting
* cleanup
* fix comment
* fix wrongly duplicated code from merge conflict
* rename dump to to_disk
* from_disk instead of load_bulk
* update test after recent removal of set_morphology in tagger
* remove old doc
* 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
* consistently use upper-case IDS in token_annotation format and for get_aligned
* remove ID from to_dict (not used in from_dict either)
* fix test
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* 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>
* moving syntax folder to _parser_internals
* moving nn_parser and transition_system
* move nn_parser and transition_system out of internals folder
* moving nn_parser code into transition_system file
* rename transition_system to transition_parser
* moving parser_model and _state to ml
* move _state back to internals
* The Parser now inherits from Pipe!
* small code fixes
* removing unnecessary imports
* remove link_vectors_to_models
* transition_system to internals folder
* little bit more cleanup
* newlines
* add "greedy" option for match pattern
* distinction between greedy FIRST or LONGEST
* check for proper values, throw custom warning otherwise
* unxfail one more test
* add comment in docstring
* add test that LONGEST also prefers first match if equal length
* use c arrays for more efficient processing
* rename 'greediness' to 'greedy'
Add and update `score` methods, provided `scores`, and default weights
`default_score_weights` for pipeline components.
* `scores` provides all top-level keys returned by `score` (merely informative, similar to `assigns`).
* `default_score_weights` provides the default weights for a default config.
* The keys from `default_score_weights` determine which values will be
shown in the `spacy train` output, so keys with weight `0.0` will be
displayed but not counted toward the overall score.
