Docs in Examples are allowed to have arbitrarily different whitespace.
Handling that properly would be nice but isn't required, but for now
check for it and blow up.
This test only fails due to the explicity assert False at the moment,
but the debug output shows that the learned spans are all off by one due
to misalignment. So the code still needs fixing.
* Move coref scoring code to scorer.py
Includes some renames to make names less generic.
* Refactor coval code to remove ternary expressions
* Black formatting
* Add header
* Make scorers into registered scorers
* Small test fixes
* Skip coref tests when torch not present
Coref can't be loaded without Torch, so nothing works.
* Fix remaining type issues
Some of this just involves ignoring types in thorny areas. Two main
issues:
1. Some things have weird types due to indirection/ argskwargs
2. xp2torch return type seems to have changed at some point
* Update spacy/scorer.py
Co-authored-by: kadarakos <kadar.akos@gmail.com>
* Small changes from review
* Be specific about the ValueError
* Type fix
Co-authored-by: kadarakos <kadar.akos@gmail.com>
* Enable flag on spacy.load: foundation for include, enable arguments.
* Enable flag on spacy.load: fixed tests.
* Enable flag on spacy.load: switched from pretrained model to empty model with added pipes for tests.
* Enable flag on spacy.load: switched to more consistent error on misspecification of component activity. Test refactoring. Added to default config.
* Enable flag on spacy.load: added support for fields not in pipeline.
* Enable flag on spacy.load: removed serialization fields from supported fields.
* Enable flag on spacy.load: removed 'enable' from config again.
* Enable flag on spacy.load: relaxed checks in _resolve_component_activation_status() to allow non-standard pipes.
* Enable flag on spacy.load: fixed relaxed checks for _resolve_component_activation_status() to allow non-standard pipes. Extended tests.
* Enable flag on spacy.load: comments w.r.t. resolution workarounds.
* Enable flag on spacy.load: remove include fields. Update website docs.
* Enable flag on spacy.load: updates w.r.t. changes in master.
* Implement Doc.from_json(): update docstrings.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Implement Doc.from_json(): remove newline.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Implement Doc.from_json(): change error message for E1038.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Enable flag on spacy.load: wrapped docstring for _resolve_component_status() at 80 chars.
* Enable flag on spacy.load: changed exmples for enable flag.
* Remove newline.
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix docstring for Language._resolve_component_status().
* Rename E1038 to E1042.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add SpanRuler component
Add a `SpanRuler` component similar to `EntityRuler` that saves a list
of matched spans to `Doc.spans[spans_key]`. The matches from the token
and phrase matchers are deduplicated and sorted before assignment but
are not otherwise filtered.
* Update spacy/pipeline/span_ruler.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix cast
* Add self.key property
* Use number of patterns as length
* Remove patterns kwarg from init
* Update spacy/tests/pipeline/test_span_ruler.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add options for spans filter and setting to ents
* Add `spans_filter` option as a registered function'
* Make `spans_key` optional and if `None`, set to `doc.ents` instead of
`doc.spans[spans_key]`.
* Update and generalize tests
* Add test for setting doc.ents, fix key property type
* Fix typing
* Allow independent doc.spans and doc.ents
* If `spans_key` is set, set `doc.spans` with `spans_filter`.
* If `annotate_ents` is set, set `doc.ents` with `ents_fitler`.
* Use `util.filter_spans` by default as `ents_filter`.
* Use a custom warning if the filter does not work for `doc.ents`.
* Enable use of SpanC.id in Span
* Support id in SpanRuler as Span.id
* Update types
* `id` can only be provided as string (already by `PatternType`
definition)
* Update all uses of Span.id/ent_id in Doc
* Rename Span id kwarg to span_id
* Update types and docs
* Add ents filter to mimic EntityRuler overwrite_ents
* Refactor `ents_filter` to take `entities, spans` args for more
filtering options
* Give registered filters more descriptive names
* Allow registered `filter_spans` filter
(`spacy.first_longest_spans_filter.v1`) to take any number of
`Iterable[Span]` objects as args so it can be used for spans filter
or ents filter
* Implement future entity ruler as span ruler
Implement a compatible `entity_ruler` as `future_entity_ruler` using
`SpanRuler` as the underlying component:
* Add `sort_key` and `sort_reverse` to allow the sorting behavior to be
customized. (Necessary for the same sorting/filtering as in
`EntityRuler`.)
* Implement `overwrite_overlapping_ents_filter` and
`preserve_existing_ents_filter` to support
`EntityRuler.overwrite_ents` settings.
* Add `remove_by_id` to support `EntityRuler.remove` functionality.
* Refactor `entity_ruler` tests to parametrize all tests to test both
`entity_ruler` and `future_entity_ruler`
* Implement `SpanRuler.token_patterns` and `SpanRuler.phrase_patterns`
properties.
Additional changes:
* Move all config settings to top-level attributes to avoid duplicating
settings in the config vs. `span_ruler/cfg`. (Also avoids a lot of
casting.)
* Format
* Fix filter make method name
* Refactor to use same error for removing by label or ID
* Also provide existing spans to spans filter
* Support ids property
* Remove token_patterns and phrase_patterns
* Update docstrings
* Add span ruler docs
* Fix types
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Move sorting into filters
* Check for all tokens in seen tokens in entity ruler filters
* Remove registered sort key
* Set Token.ent_id in a backwards-compatible way in Doc.set_ents
* Remove sort options from API docs
* Update docstrings
* Rename entity ruler filters
* Fix and parameterize scoring
* Add id to Span API docs
* Fix typo in API docs
* Include explicit labeled=True for scorer
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add failing test
* Partial fix for issue
This kind of works. The issue with token length mismatches is gone. The
problem is that when you get empty lists of encodings to compare, it
fails because the sizes are not the same, even though they're both zero:
(0, 3) vs (0,). Not sure why that happens...
* Short circuit on empties
* Remove spurious check
The check here isn't needed now the the short circuit is fixed.
* Update spacy/tests/pipeline/test_entity_linker.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Use "eg", not "example"
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Pipe name override in config: added check with warning, added removal of name override from config, extended tests.
* Pipoe name override in config: added pytest UserWarning.
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* add v1 and v2 tests for tok2vec architectures
* textcat architectures are not "layers"
* test older textcat architectures
* test older parser architecture
* Add edit tree lemmatizer
Co-authored-by: Daniël de Kok <me@danieldk.eu>
* Hide edit tree lemmatizer labels
* Use relative imports
* Switch to single quotes in error message
* Type annotation fixes
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Reformat edit_tree_lemmatizer with black
* EditTreeLemmatizer.predict: take Iterable
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Validate edit trees during deserialization
This change also changes the serialized representation. Rather than
mirroring the deep C structure, we use a simple flat union of the match
and substitution node types.
* Move edit_trees to _edit_tree_internals
* Fix invalid edit tree format error message
* edit_tree_lemmatizer: remove outdated TODO comment
* Rename factory name to trainable_lemmatizer
* Ignore type instead of casting truths to List[Union[Ints1d, Floats2d, List[int], List[str]]] for thinc v8.0.14
* Switch to Tagger.v2
* Add documentation for EditTreeLemmatizer
* docs: Fix 3.2 -> 3.3 somewhere
* trainable_lemmatizer documentation fixes
* docs: EditTreeLemmatizer is in edit_tree_lemmatizer.py
Co-authored-by: Daniël de Kok <me@danieldk.eu>
Co-authored-by: Daniël de Kok <me@github.danieldk.eu>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Tagger: use unnormalized probabilities for inference
Using unnormalized softmax avoids use of the relatively expensive exp function,
which can significantly speed up non-transformer models (e.g. I got a speedup
of 27% on a German tagging + parsing pipeline).
* Add spacy.Tagger.v2 with configurable normalization
Normalization of probabilities is disabled by default to improve
performance.
* Update documentation, models, and tests to spacy.Tagger.v2
* Move Tagger.v1 to spacy-legacy
* docs/architectures: run prettier
* Unnormalized softmax is now a Softmax_v2 option
* Require thinc 8.0.14 and spacy-legacy 3.0.9
* Add save_candidates attribute
* Change spancat api
* Add unit test
* reimplement method to produce a list of doc
* Add method to docs
* Add new version tag
* Add intended use to docstring
* prettier formatting
* Fix get_matching_ents
Not sure what happened here - the code prior to this commit simply does
not work. It's already covered by entity linker tests, which were
succeeding in the NEL PR, but couldn't possibly succeed on master.
* Fix test
Test was indented inside another test and so doesn't seem to have been
running properly.
* Partial fix of entity linker batching
* Add import
* Better name
* Add `use_gold_ents` option, docs
* Change to v2, create stub v1, update docs etc.
* Fix error type
Honestly no idea what the right type to use here is.
ConfigValidationError seems wrong. Maybe a NotImplementedError?
* Make mypy happy
* Add hacky fix for init issue
* Add legacy pipeline entity linker
* Fix references to class name
* Add __init__.py for legacy
* Attempted fix for loss issue
* Remove placeholder V1
* formatting
* slightly more interesting train data
* Handle batches with no usable examples
This adds a test for batches that have docs but not entities, and a
check in the component that detects such cases and skips the update step
as thought the batch were empty.
* Remove todo about data verification
Check for empty data was moved further up so this should be OK now - the
case in question shouldn't be possible.
* Fix gradient calculation
The model doesn't know which entities are not in the kb, so it generates
embeddings for the context of all of them.
However, the loss does know which entities aren't in the kb, and it
ignores them, as there's no sensible gradient.
This has the issue that the gradient will not be calculated for some of
the input embeddings, which causes a dimension mismatch in backprop.
That should have caused a clear error, but with numpyops it was causing
nans to happen, which is another problem that should be addressed
separately.
This commit changes the loss to give a zero gradient for entities not in
the kb.
* add failing test for v1 EL legacy architecture
* Add nasty but simple working check for legacy arch
* Clarify why init hack works the way it does
* Clarify use_gold_ents use case
* Fix use gold ents related handling
* Add tests for no gold ents and fix other tests
* Use aligned ents function (not working)
This doesn't actually work because the "aligned" ents are gold-only. But
if I have a different function that returns the intersection, *then*
this will work as desired.
* Use proper matching ent check
This changes the process when gold ents are not used so that the
intersection of ents in the pred and gold is used.
* Move get_matching_ents to Example
* Use model attribute to check for legacy arch
* Rename flag
* bump spacy-legacy to lower 3.0.9
Co-authored-by: svlandeg <svlandeg@github.com>
* Fix Scorer.score_cats for missing labels
* Add test case for Scorer.score_cats missing labels
* semantic nitpick
* black formatting
* adjust test to give different results depending on multi_label setting
* fix loss function according to whether or not missing values are supported
* add note to docs
* small fixes
* make mypy happy
* Update spacy/pipeline/textcat.py
Co-authored-by: Florian Cäsar <florian.caesar@pm.me>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: svlandeg <svlandeg@github.com>
* added ruler coe
* added error for none existing pattern
* changed error to warning
* changed error to warning
* added basic tests
* fixed place
* added test files
* went back to error
* went back to pattern error
* minor change to docs
* changed style
* changed doc
* changed error slightly
* added remove to phrasem api
* error key already existed
* phrase matcher match code to api
* blacked tests
* moved comments before expr
* corrected error no
* Update website/docs/api/entityruler.md
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Update website/docs/api/entityruler.md
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Migrate regressions 1-1000
* Move serialize test to correct file
* Remove tests that won't work in v3
* Migrate regressions 1000-1500
Removed regression test 1250 because v3 doesn't support the old LEX
scheme anymore.
* Add missing imports in serializer tests
* Migrate tests 1500-2000
* Migrate regressions from 2000-2500
* Migrate regressions from 2501-3000
* Migrate regressions from 3000-3501
* Migrate regressions from 3501-4000
* Migrate regressions from 4001-4500
* Migrate regressions from 4501-5000
* Migrate regressions from 5001-5501
* Migrate regressions from 5501 to 7000
* Migrate regressions from 7001 to 8000
* Migrate remaining regression tests
* Fixing missing imports
* Update docs with new system [ci skip]
* Update CONTRIBUTING.md
- Fix formatting
- Update wording
* Remove lemmatizer tests in el lang
* Move a few tests into the general tokenizer
* Separate Doc and DocBin tests
