Commit Graph

387 Commits

Author SHA1 Message Date
Adriane Boyd
260cb9c6fe
Raise error for non-default vectors with PretrainVectors (#12366) 2023-03-06 18:06:31 +01:00
Sofie Van Landeghem
74cae47bf6
rely on is_empty property instead of __len__ (#12347) 2023-03-01 12:06:07 +01:00
Adriane Boyd
8f058e39bd
Fix error message for displacy auto_select_port (#12343) 2023-02-28 16:36:03 +01:00
Paul O'Leary McCann
8e558095a1
Clean up displacy port-related error messages, docs (#12089)
* Clean up displacy port-related error messages, docs

There were some issues in the error messages and docs in #11948.

1. the error messages didn't specify the port argument to displacy.serve correctly
2. the docs didn't mark the auto select argument as new

This addresses those issues.

* Update website/docs/api/top-level.md

Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>

* Apply prettier

Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
2023-01-12 14:54:09 +09:00
Zhangrp
eb8bb35c13
improve ux for displacy when the serve port is in use (#11948)
* check port in use and add itself

* check port in use and add itself

* Auto switch to nearest available port.

* Use bind to check port instead of connect_ex.

* Reformat.

* Add auto_select_port argument.

* update docs for displacy.serve

* Update spacy/errors.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update website/docs/api/top-level.md

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update spacy/errors.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Add test using multiprocessing

* fix argument name

* Increase sleep times

Want to rule this out as a cause of test failure

* Don't terminate a process that isn't alive

* Refactor port finding logic

This moves all the port logic into its own util function, which can be
tested without having to background a server directly.

* Use with for the server

This ensures the server is closed correctly.

* Pass in the host when checking port availability

* Shorten argument name

* Update error codes following merge

* Add types for arguments, specify docstrings.

* Add typing for arguments with default value.

* Update docstring to match spaCy format.

* Update docstring to match spaCy format.

* Fix docs

Arg name changed from `auto_select_port` to just `auto_select`.

* Revert "Fix docs"

This reverts commit 356966fe84.

Co-authored-by: zhiiw <1302593554@qq.com>
Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
Co-authored-by: Raphael Mitsch <r.mitsch@outlook.com>
2023-01-10 15:52:57 +09:00
Madeesh Kannan
aa2b471a6e
New console logger with expanded progress tracking (#11972)
* Add `ConsoleLogger.v3`

This addition expands the progress bar feature to count up the training/distillation steps to either the next evaluation pass or the maximum number of steps.

* Rename progress bar types

* Add defaults to docs
Minor fixes

* Move comment

* Minor punctuation fixes

* Explicitly check for `None` when validating progress bar type

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
2022-12-23 15:21:44 +01:00
Paul O'Leary McCann
5c3a60e8f4
Add in errors used in the beam code that were removed at some point (#11935)
I don't think there's any way to use the beam code at the moment, but as
long as it's around the errors it refers to should also be present.
2022-12-07 15:52:35 +01:00
Paul O'Leary McCann
f54bfb56c9
Don't throw an error if using displacy on an unset span key (#11845)
* Don't throw an error if using displacy on an unset span key

* List available keys in W117
2022-11-28 10:01:09 +01:00
Raphael Mitsch
c0fd8a2e71
find-threshold: CLI command for multi-label classifier threshold tuning (#11280)
* Add foundation for find-threshold CLI functionality.

* Finish first draft for find-threshold.

* Add tests.

* Revert adjusted import statements.

* Fix mypy errors.

* Fix imports.

* Harmonize arguments with spacy evaluate command.

* Generalize component and threshold handling. Harmonize arguments with 'spacy evaluate' CLI.

* Fix Spancat test.

* Add beta parameter to Scorer and PRFScore.

* Make beta a component scorer setting.

* Remove beta.

* Update nlp.config (workaround).

* Reload pipeline on threshold change. Adjust tests. Remove confection reference.

* Remove assumption of component being a Pipe object or having a .cfg attribute.

* Adjust test output and reference values.

* Remove beta references. Delete universe.json.

* Reverting unnecessary changes. Removing unused default values. Renaming variables in find-cli tests.

* Update spacy/cli/find_threshold.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Remove adding labels in tests.

* Remove unused error

* Undo changes to PRFScorer

* Change default value for n_trials. Log table iteratively.

* Add warnings for pointless applications of find_threshold().

* Fix imports.

* Adjust type check of TextCategorizer to exclude subclasses.

* Change check of if there's only one unique value in scores.

* Update spacy/cli/find_threshold.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Incorporate feedback.

* Fix test issue. Update docstring.

* Update docs & docstring.

* Update spacy/tests/test_cli.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Add examples to docs. Rename _nlp to nlp in tests.

* Update spacy/cli/find_threshold.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Update spacy/cli/find_threshold.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-11-25 11:44:55 +01:00
Paul O'Leary McCann
75bb7ad541
Check textcat values for validity (#11763)
* Check textcat values for validity

* Fix error numbers

* Clean up vals reference

* Check category value validity through training

The _validate_categories is called in update, which for multilabel is
inherited from the single label component.

* Formatting
2022-11-17 10:25:01 +01:00
Raphael Mitsch
20bbbe3e44
Revert disable/disabled merging behavior (#11745)
* Merge disable with disabled. Adjust warnings, errors and tests.

* Replace any() with set operation.

* Update spacy/tests/pipeline/test_pipe_methods.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update docs.

* Remve reference to config entry nlp.enabled from docs.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-11-08 14:58:10 +01:00
Adriane Boyd
e91b47a226
Check for unsafe paths in tarfile.extractall (CVE-2007-4559) (#11746)
* Adding tarfile member sanitization to extractall()

* Format

* Simplify and add error message

* Fix import

* Add comment about CVE

Co-authored-by: TrellixVulnTeam <charles.mcfarland@trellix.com>
2022-11-07 10:43:34 +01:00
svlandeg
9c8cdb403e Merge branch 'master_copy' into develop_copy 2022-09-30 15:40:26 +02:00
Raphael Mitsch
aea16719be
Simplify and clarify enable/disable behavior of spacy.load() (#11459)
* 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.
2022-09-27 14:22:36 +02:00
Sofie Van Landeghem
0509f90874
add dot (#11500) 2022-09-15 17:29:42 +02:00
Sofie Van Landeghem
cc10a27c59
Prevent tok2vec to broadcast to listeners when predicting (#11385)
* replicate bug with tok2vec in annotating components

* add overfitting test with a frozen tok2vec

* remove broadcast from predict and check doc.tensor instead

* remove broadcast

* proper error

* slight rephrase of documentation
2022-09-12 15:36:48 +02:00
Raphael Mitsch
1f23c615d7
Refactor KB for easier customization (#11268)
* Add implementation of batching + backwards compatibility fixes. Tests indicate issue with batch disambiguation for custom singular entity lookups.

* Fix tests. Add distinction w.r.t. batch size.

* Remove redundant and add new comments.

* Adjust comments. Fix variable naming in EL prediction.

* Fix mypy errors.

* Remove KB entity type config option. Change return types of candidate retrieval functions to Iterable from Iterator. Fix various other issues.

* Update spacy/pipeline/entity_linker.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update spacy/pipeline/entity_linker.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update spacy/kb_base.pyx

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update spacy/kb_base.pyx

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Update spacy/pipeline/entity_linker.py

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Add error messages to NotImplementedErrors. Remove redundant comment.

* Fix imports.

* Remove redundant comments.

* Rename KnowledgeBase to InMemoryLookupKB and BaseKnowledgeBase to KnowledgeBase.

* Fix tests.

* Update spacy/errors.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Move KB into subdirectory.

* Adjust imports after KB move to dedicated subdirectory.

* Fix config imports.

* Move Candidate + retrieval functions to separate module. Fix other, small issues.

* Fix docstrings and error message w.r.t. class names. Fix typing for candidate retrieval functions.

* Update spacy/kb/kb_in_memory.pyx

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Update spacy/ml/models/entity_linker.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Fix typing.

* Change typing of mentions to be Span instead of Union[Span, str].

* Update docs.

* Update EntityLinker and _architecture docs.

* Update website/docs/api/entitylinker.md

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>

* Adjust message for E1046.

* Re-add section for Candidate in kb.md, add reference to dedicated page.

* Update docs and docstrings.

* Re-add section + reference for KnowledgeBase.get_alias_candidates() in docs.

* Update spacy/kb/candidate.pyx

* Update spacy/kb/kb_in_memory.pyx

* Update spacy/pipeline/legacy/entity_linker.py

* Remove canididate.md. Remove mistakenly added config snippet in entity_linker.py.

Co-authored-by: Paul O'Leary McCann <polm@dampfkraft.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-08 10:38:07 +02:00
Adriane Boyd
78f5503a29
Check for any non-Doc returned value for components (#11424) 2022-09-01 19:37:23 +02:00
Edward
5afa98aabf
Support custom attributes for tokens and spans in json conversion (#11125)
* 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>
2022-08-23 10:05:02 +02:00
Paul O'Leary McCann
0f07defe2c
Remove reference to voting on issue (#11335)
Not clear which issue this refers to, we don't suggest this for any
other issues, and we don't use votes in general.
2022-08-22 11:29:05 +02:00
Adriane Boyd
3e4cf1bbe1
Check for . in factory names (#11336) 2022-08-19 09:52:12 +02:00
Sofie Van Landeghem
cab263791f
include span_ruler for default warning filter (#11333) 2022-08-17 19:55:54 +02:00
Raphael Mitsch
e9eb59699f
NEL confidence threshold (#11016)
* Add base for NEL abstention threshold mechanism.

* Add abstention threshold to entity linker. Add test.

* Fix entity linking tests.

* Changed abstention default threshold from 0 to None.

* Fix default values for abstention thresholds.

* Fix mypy errors.

* Replace assertion with raise of proper error code.

* Simplify threshold check. Remove thresholding from EntityLinker_v1.

* Rename test.

* Update spacy/pipeline/entity_linker.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Update spacy/pipeline/entity_linker.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Make E1043 configurable.

* Update docs.

* Rephrase description in docs. Adjusting error code message.

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-07-04 17:05:21 +02:00
Madeesh Kannan
eaf66e7431
Add NVTX ranges to TrainablePipe components (#10965)
* `TrainablePipe`: Add NVTX range decorator

* Annotate `TrainablePipe` subclasses with NVTX ranges

* Export function signature to allow introspection of args in tests

* Revert "Annotate `TrainablePipe` subclasses with NVTX ranges"

This reverts commit d8684f7372.

* Revert "Export function signature to allow introspection of args in tests"

This reverts commit f4405ca3ad.

* Revert "`TrainablePipe`: Add NVTX range decorator"

This reverts commit 26536eb6b8.

* Add `spacy.pipes_with_nvtx_range` pipeline callback

* Show warnings for all missing user-defined pipe functions that need to be annotated
Fix imports, typos

* Rename `DEFAULT_ANNOTATABLE_PIPE_METHODS` to `DEFAULT_NVTX_ANNOTATABLE_PIPE_METHODS`
Reorder import

* Walk model nodes directly whilst applying NVTX ranges
Ignore pipe method wrapper when applying range
2022-06-30 11:28:12 +02:00
Raphael Mitsch
4c058eb40a
enable argument for spacy.load() (#10784)
* 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>
2022-06-17 20:24:13 +01:00
Madeesh Kannan
41389ffe1e
Avoid pickling Doc inputs passed to Language.pipe() (#10864)
* `Language.pipe()`: Serialize `Doc` objects to bytes when using multiprocessing to avoid pickling overhead

* `Doc.to_dict()`: Serialize `_context` attribute (keeping in line with `(un)pickle_doc()`

* Correct type annotations

* Fix typo

* `Doc`: Do not serialize `_context`

* `Language.pipe`: Send context objects to child processes, Simplify `as_tuples` handling

* Fix type annotation

* `Language.pipe`: Simplify `as_tuple` multiprocessor handling

* Cleanup code, fix typos

* MyPy fixes

* Move doc preparation function into `_multiprocessing_pipe`
Whitespace changes

* Remove superfluous comma

* Rename `prepare_doc` to `prepare_input`

* Update spacy/errors.py

* Undo renaming for error

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-06-02 20:06:49 +02:00
single-fingal
6c6b8da7cc
Fix: De/Serialize SpanGroups including the SpanGroup keys (#10707)
* 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>
2022-06-02 15:56:27 +02:00
Raphael Mitsch
8387ce4c01
Add Doc.from_json() (#10688)
* Implement Doc.from_json: rough draft.

* Implement Doc.from_json: first draft with tests.

* Implement Doc.from_json: added documentation on website for Doc.to_json(), Doc.from_json().

* Implement Doc.from_json: formatting changes.

* Implement Doc.to_json(): reverting unrelated formatting changes.

* Implement Doc.to_json(): fixing entity and span conversion. Moving fixture and doc <-> json conversion tests into single file.

* Implement Doc.from_json(): replaced entity/span converters with doc.char_span() calls.

* Implement Doc.from_json(): handling sentence boundaries in spans.

* Implementing Doc.from_json(): added parser-free sentence boundaries transfer.

* Implementing Doc.from_json(): added parser-free sentence boundaries transfer.

* Implementing Doc.from_json(): incorporated various PR feedback.

* Renaming fixture for document without dependencies.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implementing Doc.from_json(): using two sent_starts instead of one.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implementing Doc.from_json(): doc_without_dependency_parser() -> doc_without_deps.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implementing Doc.from_json(): incorporating various PR feedback. Rebased on latest master.

* Implementing Doc.from_json(): refactored Doc.from_json() to work with annotation IDs instead of their string representations.

* Implement Doc.from_json(): reverting unwanted formatting/rebasing changes.

* Implement Doc.from_json(): added check for char_span() calculation for entities.

* Update spacy/tokens/doc.pyx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): minor refactoring, additional check for token attribute consistency with corresponding test.

* Implement Doc.from_json(): removed redundancy in annotation type key naming.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): Simplifying setting annotation values.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement doc.from_json(): renaming annot_types to token_attrs.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): adjustments for renaming of annot_types to token_attrs.

* Implement Doc.from_json(): removing default categories.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): simplifying lexeme initialization.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): simplifying lexeme initialization.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): refactoring to only have keys for present annotations.

* Implement Doc.from_json(): fix check for tokens' HEAD attributes.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): refactoring Doc.from_json().

* Implement Doc.from_json(): fixing span_group retrieval.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): fixing span retrieval.

* Implement Doc.from_json(): added schema for Doc JSON format. Minor refactoring in Doc.from_json().

* Implement Doc.from_json(): added comment regarding Token and Span extension support.

* Implement Doc.from_json(): renaming inconsistent_props to partial_attrs..

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): adjusting error message.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): extending E1038 message.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): added params to E1038 raises.

* Implement Doc.from_json(): combined attribute collection with partial attributes check.

* Implement Doc.from_json(): added optional schema validation.

* Implement Doc.from_json(): fixed optional fields in schema, tests.

* Implement Doc.from_json(): removed redundant None check for DEP.

* Implement Doc.from_json(): added passing of schema validatoin message to E1037..

* Implement Doc.from_json(): removing redundant error E1040.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): changing message for E1037.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): adjusted website docs and docstring of Doc.from_json().

* Update spacy/tests/doc/test_json_doc_conversion.py

* Implement Doc.from_json(): docstring update.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): docstring update.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): website docs update.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): docstring formatting.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): docstring formatting.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): fixing Doc reference in website docs.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): reformatted website/docs/api/doc.md.

* Implement Doc.from_json(): bumped IDs of new errors to avoid merge conflicts.

* Implement Doc.from_json(): fixing bug in tests.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Implement Doc.from_json(): fix setting of sentence starts for docs without DEP.

* Implement Doc.from_json(): add check for valid char spans when manually setting sentence boundaries. Refactor sentence boundary setting slightly. Move error message for lack of support for partial token annotations to errors.py.

* Implement Doc.from_json(): simplify token sentence start manipulation.

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Combine related error messages

* Update spacy/tests/doc/test_json_doc_conversion.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-06-02 14:03:47 +02:00
Adriane Boyd
a322d6d5f2
Add SpanRuler component (#9880)
* 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>
2022-06-02 13:12:53 +02:00
kadarakos
f6a4b80c0b
Better errors for has_annotation and Matcher (#10830)
* Show input argument instead of None

* catch invalid attr early

* moved error message from code to errors.py

* Update spacy/errors.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/errors.py

* update E153 and E154

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-05-25 11:12:29 +02:00
Richard Hudson
32954c3bcb
Fix issues for Mypy 0.950 and Pydantic 1.9.0 (#10786)
* Make changes to typing

* Correction

* Format with black

* Corrections based on review

* Bumped Thinc dependency version

* Bumped blis requirement

* Correction for older Python versions

* Update spacy/ml/models/textcat.py

Co-authored-by: Daniël de Kok <me@github.danieldk.eu>

* Corrections based on review feedback

* Readd deleted docstring line

Co-authored-by: Daniël de Kok <me@github.danieldk.eu>
2022-05-25 09:33:54 +02:00
Raphael Mitsch
6f9e2ca81f
Ignore overrides for pipe names in config argument (#10779)
* 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>
2022-05-12 11:46:08 +02:00
Raphael Mitsch
f5390e278a
Refactor error messages to remove hardcoded strings (#10729)
* Use custom error msg instead of hardcoded string: replaced remaining hardcoded error message strings.

* Use custom error msg instead of hardcoded string: fixing faulty Errors import.
2022-05-02 13:38:46 +02:00
Richard Hudson
75fbbcdc18
Display warning when spacy.explain() finds no term (#10645)
* Display warning when spacy.explain() finds no term

* Updated warning message text
2022-04-12 10:48:28 +02:00
Adriane Boyd
ca54de27bb
Support more internal methods for SpanGroup (#10476)
* Added new convenience cython functions to SpanGroup to avoid unnecessary allocation/deallocation of objects

* Replaced sorting in has_overlap with C++ for efficiency. Also, added a test for has_overlap

* Added a method to efficiently merge SpanGroups

* Added __delitem__, __add__ and __iadd__. Also, allowed to pass span lists to merge function. Replaced extend() body with call to merge

* Renamed merge to concat and added missing things to documentation

* Added operator+ and operator += in the documentation

* Added a test for Doc deallocation

* Update spacy/tokens/span_group.pyx

* Updated SpanGroup tests to use new span list comparison function rather than assert_span_list_equal, eliminating the need to have a separate assert_not_equal fnction

* Fixed typos in SpanGroup documentation

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Minor changes requested by Sofie: rearranged import statements. Added new=3.2.1 tag to SpanGroup.__setitem__ documentation

* SpanGroup: moved repetitive list index check/adjustment in a separate function

* Turn off formatting that hurts readability spacy/tests/doc/test_span_group.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Remove formatting that hurts readability spacy/tests/doc/test_span_group.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Turn off formatting that hurts readability in spacy/tests/doc/test_span_group.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Support more internal methods for SpanGroup

Add support for:

* `__setitem__`
* `__delitem__`
* `__iadd__`: for `SpanGroup` or `Iterable[Span]`
* `__add__`: for `SpanGroup` only

Adapted from #9698 with the scope limited to the magic methods.

* Use v3.3 as new version in docs

* Add new tag to SpanGroup.copy in API docs

* Remove duplicate import

* Apply suggestions from code review

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Remaining suggestions and formatting

Co-authored-by: nrodnova <nrodnova@hotmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Natalia Rodnova <4512370+nrodnova@users.noreply.github.com>
2022-04-01 09:56:26 +02:00
Daniël de Kok
c90dd6f265
Alignment: use a simplified ragged type for performance (#10319)
* Alignment: use a simplified ragged type for performance

This introduces the AlignmentArray type, which is a simplified version
of Ragged that performs better on the simple(r) indexing performed for
alignment.

* AlignmentArray: raise an error when using unsupported index

* AlignmentArray: move error messages to Errors

* AlignmentArray: remove simlified ... with simplifications

* AlignmentArray: fix typo that broke a[n:n] indexing
2022-04-01 09:02:06 +02:00
Adriane Boyd
f98b41c390
Add vector deduplication (#10551)
* Add vector deduplication

* Add `Vocab.deduplicate_vectors()`
* Always run deduplication in `spacy init vectors`
* Clean up a few vector-related error messages and docs examples

* Always unique with numpy

* Fix types
2022-03-30 08:54:23 +02:00
Adriane Boyd
85778dfcf4
Add edit tree lemmatizer (#10231)
* 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>
2022-03-28 11:13:50 +02:00
Lj Miranda
a79cd3542b
Add displacy support for overlapping Spans (#10332)
* Fix docstring for EntityRenderer

* Add warning in displacy if doc.spans are empty

* Implement parse_spans converter

One notable change here is that the default spans_key is sc, and
it's set by the user through the options.

* Implement SpanRenderer

Here, I implemented a SpanRenderer that looks similar to the
EntityRenderer except for some templates.  The spans_key, by default, is
set to sc, but can be configured in the options (see parse_spans). The
way I rendered these spans is per-token, i.e., I first check if each
token (1) belongs to a given span type and (2) a starting token of a
given span type. Once I have this information, I render them into the
markup.

* Fix mypy issues on typing

* Add tests for displacy spans support

* Update colors from RGB to hex

Co-authored-by: Ines Montani <ines@ines.io>

* Remove unnecessary CSS properties

* Add documentation for website

* Remove unnecesasry scripts

* Update wording on the documentation

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Put typing dependency on top of file

* Put back z-index so that spans overlap properly

* Make warning more explicit for spans_key

Co-authored-by: Ines Montani <ines@ines.io>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-03-16 18:14:34 +01:00
Sofie Van Landeghem
3f68bbcfec
Clean up loggers docs (#10351)
* update docs to point to spacy-loggers docs

* remove unused error code
2022-02-25 16:29:12 +01:00
Edward
7961a0a959
Fix typo in errors (#10256) 2022-02-10 13:45:46 +01:00
Duygu Altinok
47a2916801
Intify IOB (#9738)
* added iob to int

* added tests

* added iob strings

* added error

* blacked attrs

* Update spacy/tests/lang/test_attrs.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/attrs.pyx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* added iob strings as global

* minor refinement with iob

* removed iob strings from token

* changed to uppercase

* cleaned and went back to master version

* imported iob from attrs

* Update and format errors

* Support and test both str and int ENT_IOB key

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2022-01-20 13:19:38 +01:00
Sofie Van Landeghem
56dcb39fb7
Fix references to config file in the docs & UX (#9961)
* doc fixes around config file

* fix typo

* clarify default
2022-01-04 14:31:26 +01:00
Duygu Altinok
b56b9e7f31
Entity ruler remove pattern (#9685)
* 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>
2021-12-06 15:32:49 +01:00
Duygu Altinok
a7d7e80adb
EntityRuler improve disk load error message (#9658)
* added error string

* added serialization test

* added more to if statements

* wrote file to tempdir

* added tempdir

* changed parameter a bit

* Update spacy/tests/pipeline/test_entity_ruler.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2021-11-23 16:26:05 +01:00
Adriane Boyd
9ac6d4991e
Add doc_cleaner component (#9659)
* Add doc_cleaner component

* Fix types

* Fix loop

* Rephrase method description
2021-11-23 15:33:33 +01:00
Adriane Boyd
07dea324f6 Merge remote-tracking branch 'upstream/develop' into chore/switch-to-master-v3.2.0 2021-11-03 15:32:18 +01:00
Bram Vanroy
cab9209c3d
use metaclass to decorate errors (#9593) 2021-11-03 15:29:32 +01:00
Adriane Boyd
2d430958e1 Merge remote-tracking branch 'upstream/master' into chore/update-develop-from-master-v3.2-3 2021-10-29 12:18:15 +02:00
Paul O'Leary McCann
006df1ae1f
Clarify error when words are of wrong type (#9541)
* Clarify error when words are of wrong type

See #9437

* Update docs

* Use try/except

* Apply suggestions from code review

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2021-10-29 12:08:40 +02:00