* 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>
* remove duplicate line
* add sent start/end token attributes to the docs
* let has_annotation work with IS_SENT_END
* elif instead of if
* add has_annotation test for sent attributes
* fix typo
* remove duplicate is_sent_start entry in docs
* Corrected Span's __richcmp__ implementation to take end, label and kb_id in consideration
* Updated test
* Updated test
* Removed formatting from a test for readability sake
* Use same tuples for all comparisons
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Span/SpanGroup: wrap SpanC in shared_ptr
When a Span that was retrieved from a SpanGroup was modified, these
changes were not reflected in the SpanGroup because the underlying
SpanC struct was copied.
This change applies the solution proposed by @nrodnova, to wrap SpanC in
a shared_ptr. This makes a SpanGroup and Spans derived from it share the
same SpanC. So, changes made through a Span are visible in the SpanGroup
as well.
Fixes#9556
* Test that a SpanGroup is modified through its Spans
* SpanGroup.push_back: remove nogil
Modifying std::vector is not thread-safe.
* C++ >= 11 does not allow const T in vector<T>
* Add Span.span_c as a shorthand for Span.c.get
Since this method is cdef'ed, it is only visible from Cython, so we
avoid using raw pointers in Python
Replace existing uses of span.c.get() to use this new method.
* Fix formatting
* Style fix: pointer types
* SpanGroup.to_bytes: reduce number of shared_ptr::get calls
* Mark SpanGroup modification test with issue
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Added sents property to Span class that returns a generator of sentences the Span belongs to
* Added description to Span.sents property
* Update test_span to clarify the difference between span.sent and span.sents
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Update spacy/tests/doc/test_span.py
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Fix documentation typos in spacy/tokens/span.pyx
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Update Span.sents doc string in spacy/tokens/span.pyx
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Parametrized test_span_spans
* Corrected Span.sents to check for span-level hook first. Also, made Span.sent respect doc-level sents hook if no span-level hook is provided
* Corrected Span ocumentation copy/paste issue
* Put back accidentally deleted lines
* Fixed formatting in span.pyx
* Moved check for SENT_START annotation after user hooks in Span.sents
* add version where the property was introduced
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
* Validate pos values when creating Doc
* Add clear error when setting invalid pos
This also changes the error language slightly.
* Fix variable name
* Update spacy/tokens/doc.pyx
* Test that setting invalid pos raises an error
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Support a cfg field in transition system
* Make NER 'has gold' check use right alignment for span
* Pass 'negative_samples_key' property into NER transition system
* Add field for negative samples to NER transition system
* Check neg_key in NER has_gold
* Support negative examples in NER oracle
* Test for negative examples in NER
* Fix name of config variable in NER
* Remove vestiges of old-style partial annotation
* Remove obsolete tests
* Add comment noting lack of support for negative samples in parser
* Additions to "neg examples" PR (#8201)
* add custom error and test for deprecated format
* add test for unlearning an entity
* add break also for Begin's cost
* add negative_samples_key property on Parser
* rename
* extend docs & fix some older docs issues
* add subclass constructors, clean up tests, fix docs
* add flaky test with ValueError if gold parse was not found
* remove ValueError if n_gold == 0
* fix docstring
* Hack in environment variables to try out training
* Remove hack
* Remove NER hack, and support 'negative O' samples
* Fix O oracle
* Fix transition parser
* Remove 'not O' from oracle
* Fix NER oracle
* check for spans in both gold.ents and gold.spans and raise if so, to prevent memory access violation
* use set instead of list in consistency check
Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Change span lemmas to use original whitespace (fix#8368)
This is a redo of #8371 based off master.
The test for this required some changes to existing tests. I don't think
the changes were significant but I'd like someone to check them.
* Remove mystery docstring
This sentence was uncompleted for years, and now we will never know how
it ends.
* Fill in deps if not provided with heads
Before this change, if heads were passed without deps they would be
silently ignored, which could be confusing. See #8334.
* Use "dep" instead of a blank string
This is the customary placeholder dep. It might be better to show an
error here instead though.
* Throw error on heads without deps
* Add a test
* Fix tests
* Formatting
* Fix all tests
* Fix a test I missed
* Revise error message
* Clean up whitespace
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Fix range in Span.get_lca_matrix
Fix the adjusted token index / lca matrix index ranges for
`_get_lca_matrix` for spans.
* The range for `k` should correspond to the adjusted indices in
`lca_matrix` with the `start` indexed at `0`
* Update test for v3.x
* Handle partial entities in Span.as_doc
In `Span.as_doc` replace partial entities at the beginning or end of the
span with missing entity annotation.
Fixes a bug where invalid entity annotation (no initial `B`) was
returned for an initial partial entity.
* Check for empty span in ents conversion
Note: `Span.as_doc()` will still fail on an empty span due to failures
in `Span.vector`.
* Adjust custom extension data when copying user data in `Span.as_doc()`
* Restrict `Doc.from_docs()` to adjusting offsets for custom extension
data
* Update test to use extension
* (Duplicate bug fix for character offset from #7497)
Merge data from `doc.spans` in `Doc.from_docs()`.
* Fix internal character offset set when merging empty docs (only
affects tokens and spans in `user_data` if an empty doc is in the list
of docs)
In the retokenizer, only reset sent starts (with
`set_children_from_head`) if the doc is parsed. If there is no parse,
merged tokens have the unset `token.is_sent_start == None` by default after
retokenization.
* raise NotImplementedError when noun_chunks iterator is not implemented
* bring back, fix and document span.noun_chunks
* formatting
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Draft out initial Spans data structure
* Initial span group commit
* Basic span group support on Doc
* Basic test for span group
* Compile span_group.pyx
* Draft addition of SpanGroup to DocBin
* Add deserialization for SpanGroup
* Add tests for serializing SpanGroup
* Fix serialization of SpanGroup
* Add EdgeC and GraphC structs
* Add draft Graph data structure
* Compile graph
* More work on Graph
* Update GraphC
* Upd graph
* Fix walk functions
* Let Graph take nodes and edges on construction
* Fix walking and getting
* Add graph tests
* Fix import
* Add module with the SpanGroups dict thingy
* Update test
* Rename 'span_groups' attribute
* Try to fix c++11 compilation
* Fix test
* Update DocBin
* Try to fix compilation
* Try to fix graph
* Improve SpanGroup docstrings
* Add doc.spans to documentation
* Fix serialization
* Tidy up and add docs
* Update docs [ci skip]
* Add SpanGroup.has_overlap
* WIP updated Graph API
* Start testing new Graph API
* Update Graph tests
* Update Graph
* Add docstring
Co-authored-by: Ines Montani <ines@ines.io>
Instead of unsetting lemmas on retokenized tokens, set the default
lemmas to:
* merge: concatenate any existing lemmas with `SPACY` preserved
* split: use the new `ORTH` values if lemmas were previously set,
otherwise leave unset
