* Handle docs with no entities
If a whole batch contains no entities it won't make it to the model, but
it's possible for individual Docs to have no entities. Before this
commit, those Docs would cause an error when attempting to concatenate
arrays because the dimensions didn't match.
It turns out the process of preparing the Ragged at the end of the span
maker forward was a little different from list2ragged, which just uses
the flatten function directly. Letting list2ragged do the conversion
avoids the dimension issue.
This did not come up before because in NEL demo projects it's typical
for data with no entities to be discarded before it reaches the NEL
component.
This includes a simple direct test that shows the issue and checks it's
resolved. It doesn't check if there are any downstream changes, so a
more complete test could be added. A full run was tested by adding an
example with no entities to the Emerson sample project.
* Add a blank instance to default training data in tests
Rather than adding a specific test, since not failing on instances with
no entities is basic functionality, it makes sense to add it to the
default set.
* Fix without modifying architecture
If the architecture is modified this would have to be a new version, but
this change isn't big enough to merit that.
* Fix multiple extensions and character offset
* Rename token_start/end to start/end
* Refactor Doc.from_json based on review
* Iterate over user_data items
* Only add non-empty underscore entries
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Change enable/disable behavior so that arguments take precedence over config options. Extend error message on conflict. Add warning message in case of overwriting config option with arguments.
* Fix tests in test_serialize_pipeline.py to reflect changes to handling of enable/disable.
* Fix type issue.
* Move comment.
* Move comment.
* Issue UserWarning instead of printing wasabi message. Adjust test.
* Added pytest.warns(UserWarning) for expected warning to fix tests.
* Update warning message.
* Move type handling out of fetch_pipes_status().
* Add global variable for default value. Use id() to determine whether used values are default value.
* Fix default value for disable.
* Rename DEFAULT_PIPE_STATUS to _DEFAULT_EMPTY_PIPES.
Preserve both `-` and `O` annotation in augmenters rather than relying
on `Example.to_dict`'s default support for one option outside of labeled
entity spans.
This is intended as a temporary workaround for augmenters for v3.4.x.
The behavior of `Example` and related IOB utils could be improved in the
general case for v3.5.
* Remove side effects from Doc.__init__()
* Changes based on review comment
* Readd test
* Change interface of Doc.__init__()
* Simplify test
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update doc.md
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add a dry run flag to download
* Remove --dry-run, add --url option to `spacy info` instead
* Make mypy happy
* Print only the URL, so it's easier to use in scripts
* Don't add the egg hash unless downloading an sdist
* Update spacy/cli/info.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Add two implementations of requirements
* Clean up requirements sample slightly
This should make mypy happy
* Update URL help string
* Remove requirements option
* Add url option to docs
* Add URL to spacy info model output, when available
* Add types-setuptools to testing reqs
* Add types-setuptools to requirements
* Add "compatible", expand docstring
* Update spacy/cli/info.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Run prettier on CLI docs
* Update docs
Add a sidebar about finding download URLs, with some examples of the new
command.
* Add download URLs to table on model page
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Updates from review
* download url -> download link
* Update docs
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* `Matcher`: Better type checking of values in `SetPredicate`
`SetPredicate`: Emit warning and return `False` on unexpected value types
* Rename `value_type_mismatch` variable
* Inline warning
* Remove unexpected type warning from `_SetPredicate`
* Ensure that `str` values are not interpreted as sequences
Check elements of sequence values for convertibility to `str` or `int`
* Add more `INTERSECT` and `IN` test cases
* Test for inputs with multiple characters
* Return `False` early instead of using a boolean flag
* Remove superfluous `int` check, parentheses
* Apply suggestions from code review
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Appy suggestions from code review
* Clarify test comment
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* adding unit test for spacy.load with disable/exclude string arg
* allow pure strings in from_config
* update docs
* upstream type adjustements
* docs update
* make docstring more consistent
* Update spacy/language.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* two more cleanups
* fix type in internal method
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Fix `test_{prefer,require}_gpu`
These tests assumed that GPUs are only supported with CuPy, but since Thinc 8.1
we also support Metal Performance Shaders.
* test_misc: arrange thinc imports to be together
* Add lang folder for la (Latin)
* Add Latin lang classes
* Add minimal tokenizer exceptions
* Add minimal stopwords
* Add minimal lex_attrs
* Update stopwords, tokenizer exceptions
* Add la tests; register la_tokenizer in conftest.py
* Update spacy/lang/la/lex_attrs.py
Remove duplicate form in Latin lex_attrs
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Update natto-py version spec (#11222)
* Update natto-py version spec
* Update setup.cfg
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Add scorer to textcat API docs config settings (#11263)
* Update docs for pipeline initialize() methods (#11221)
* Update documentation for dependency parser
* Update documentation for trainable_lemmatizer
* Update documentation for entity_linker
* Update documentation for ner
* Update documentation for morphologizer
* Update documentation for senter
* Update documentation for spancat
* Update documentation for tagger
* Update documentation for textcat
* Update documentation for tok2vec
* Run prettier on edited files
* Apply similar changes in transformer docs
* Remove need to say annotated example explicitly
I removed the need to say "Must contain at least one annotated Example"
because it's often a given that Examples will contain some gold-standard
annotation.
* Run prettier on transformer docs
* chore: add 'concepCy' to spacy universe (#11255)
* chore: add 'concepCy' to spacy universe
* docs: add 'slogan' to concepCy
* Support full prerelease versions in the compat table (#11228)
* Support full prerelease versions in the compat table
* Fix types
* adding spans to doc_annotation in Example.to_dict (#11261)
* adding spans to doc_annotation in Example.to_dict
* to_dict compatible with from_dict: tuples instead of spans
* use strings for label and kb_id
* Simplify test
* Update data formats docs
Co-authored-by: Stefanie Wolf <stefanie.wolf@vitecsoftware.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Fix regex invalid escape sequences (#11276)
* Add W605 to the errors raised by flake8 in the CI (#11283)
* Clean up automated label-based issue handling (#11284)
* Clean up automated label-based issue handline
1. upgrade tiangolo/issue-manager to latest
2. move needs-more-info to tiangolo
3. change needs-more-info close time to 7 days
4. delete old needs-more-info config
* Use old, longer message
* Fix label name
* Fix Dutch noun chunks to skip overlapping spans (#11275)
* Add test for overlapping noun chunks
* Skip overlapping noun chunks
* Update spacy/tests/lang/nl/test_noun_chunks.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Docs: displaCy documentation - data types, `parse_{deps,ents,spans}`, spans example (#10950)
* add in spans example and parse references
* rm autoformatter
* rm extra ents copy
* TypedDict draft
* type fixes
* restore non-documentation files
* docs update
* fix spans example
* fix hyperlinks
* add parse example
* example fix + argument fix
* fix api arg in docs
* fix bad variable replacement
* fix spacing in style
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* fix spacing on table
* fix spacing on table
* rm temp files
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* include span_ruler for default warning filter (#11333)
* Add uk pipelines to website (#11332)
* Check for . in factory names (#11336)
* Make fixes for PR #11349
* Fix roman numeral coverage in #11349
Co-authored-by: Patrick J. Burns <patricks@diyclassics.org>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Lj Miranda <12949683+ljvmiranda921@users.noreply.github.com>
Co-authored-by: Jules Belveze <32683010+JulesBelveze@users.noreply.github.com>
Co-authored-by: stefawolf <wlf.ste@gmail.com>
Co-authored-by: Stefanie Wolf <stefanie.wolf@vitecsoftware.com>
Co-authored-by: Peter Baumgartner <5107405+pmbaumgartner@users.noreply.github.com>
* Add token and span custom attributes to to_json()
* Change logic for to_json
* Add functionality to from_json
* Small adjustments
* Move token/span attributes to new dict key
* Fix test
* Fix the same test but much better
* Add backwards compatibility tests and adjust logic
* Add test to check if attributes not set in underscore are not saved in the json
* Add tests for json compatibility
* Adjust test names
* Fix tests and clean up code
* Fix assert json tests
* small adjustment
* adjust naming and code readability
* Adjust naming, added more tests and changed logic
* Fix typo
* Adjust errors, naming, and small test optimization
* Fix byte tests
* Fix bytes tests
* Change naming and json structure
* update schema
* Update spacy/schemas.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update spacy/tokens/doc.pyx
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update spacy/tokens/doc.pyx
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update spacy/schemas.py
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Update schema for underscore attributes
* Adjust underscore schema
* adjust schema tests
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* adding spans to doc_annotation in Example.to_dict
* to_dict compatible with from_dict: tuples instead of spans
* use strings for label and kb_id
* Simplify test
* Update data formats docs
Co-authored-by: Stefanie Wolf <stefanie.wolf@vitecsoftware.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* add additional REL_OP
* change to condition and new rel_op symbols
* add operators to docs
* add the anchor while we're in here
* add tests
Co-authored-by: Peter Baumgartner <5107405+pmbaumgartner@users.noreply.github.com>
* Min_max_operators
1. Modified API and Usage for spaCy website to include min_max operator
2. Modified matcher.pyx to include min_max function {n,m} and its variants
3. Modified schemas.py to include min_max validation error
4. Added test cases to test_matcher_api.py, test_matcher_logic.py and test_pattern_validation.py
* attempt to fix mypy/pydantic compat issue
* formatting
* Update spacy/tests/matcher/test_pattern_validation.py
Co-authored-by: Source-Shen <82353723+Source-Shen@users.noreply.github.com>
Co-authored-by: svlandeg <svlandeg@github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Distinguish between vectors that are 0 vs. missing vectors when warning
about missing vectors.
Update `Doc.has_vector` to match `Span.has_vector` and
`Token.has_vector` for cases where the vocab has vectors but none of the
tokens in the container have vectors.
* Handle Russian, Ukrainian and Bulgarian
* Corrections
* Correction
* Correction to comment
* Changes based on review
* Correction
* Reverted irrelevant change in punctuation.py
* Remove unnecessary group
* Reverted accidental change
* 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>
* account for NER labels with a hyphen in the name
* cleanup
* fix docstring
* add return type to helper method
* shorter method and few more occurrences
* user helper method across repo
* fix circular import
* partial revert to avoid circular import
* detect cycle during projectivize
* not complete test to detect cycle in projectivize
* boolean to int type to propagate error
* use unordered_set instead of set
* moved error message to errors
* removed cycle from test case
* use find instead of count
* cycle check: only perform one lookup
* Return bool again from _has_head_as_ancestor
Communicate presence of cycles through an output argument.
* Switch to returning std::pair to encode presence of a cycle
The has_cycle pointer is too easy to misuse. Ideally, we would have a
sum type like Rust's `Result` here, but C++ is not there yet.
* _is_non_proj_arc: clarify what we are returning
* _has_head_as_ancestor: remove count
We are now explicitly checking for cycles, so the algorithm must always
terminate. Either we encounter the head, we find a root, or a cycle.
* _is_nonproj_arc: simplify condition
* Another refactor using C++ exceptions
* Remove unused error code
* Print graph with cycle on exception
* Include .hh files in source package
* Add FIXME comment
* cycle detection test
* find cycle when starting from problematic vertex
Co-authored-by: Daniël de Kok <me@danieldk.eu>
* fix: De/Serialize `SpanGroups` including the SpanGroup keys
This prevents the loss of `SpanGroup`s that have the same .name as other `SpanGroup`s within the same `SpanGroups` object (upon de/serialization of the `SpanGroups`).
Fixes#10685
* Maintain backwards compatibility for serialized `SpanGroups`
(serialized as: a list of `SpanGroup`s, or b'')
* Add tests for `SpanGroups` deserialization backwards-compatibility
* Move a `SpanGroups` de/serialization test (test_issue10685)
to tests/serialize/test_serialize_spangroups.py
* Output a warning if deserializing a `SpanGroups` with duplicate .name-d `SpanGroup`s
* Minor refactor
* `SpanGroups.from_bytes` handles only `list` and `dict` types with
`dict` as the expected default
* For lists, keep first rather than last value encountered
* Update error message
* Rename and update tests
* Update to preserve list serialization of SpanGroups
To avoid breaking compatibility of serialized `Doc` and `DocBin` with
earlier versions of spacy v3, revert back to a list-only serialization,
but update the names just for serialization so that the SpanGroups keys
override the SpanGroup names.
* Preserve object identity and current key overwrite
* Preserve SpanGroup object identity
* Preserve last rather than first span group from SpanGroup list
format without SpanGroups keys
* Update inline comments
* Fix types
* Add type info for SpanGroup.copy
* Deserialize `SpanGroup`s as copies
when a single SpanGroup is the value for more than 1 `SpanGroups` key.
This is because we serialize `SpanGroups` as dicts (to maintain backward-
and forward-compatibility) and we can't assume `SpanGroup`s with the same
bytes/serialization were the same (identical) object, pre-serialization.
* Update spacy/tokens/_dict_proxies.py
* Add more SpanGroups serialization tests
Test that serialized SpanGroups maintain their Span order
* small clarification on older spaCy version
* Update spacy/tests/serialize/test_serialize_span_groups.py
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>
