This PR adds a test for an untested case of `Span.get_lca_matrix`, and fixes a bug for that scenario, which I introduced in [this PR](https://github.com/explosion/spaCy/pull/3089) (sorry!).
## Description
The previous implementation of get_lca_matrix was failing for the case `doc[j:k].get_lca_matrix()` where `j > 0`. A test has been added for this case and the bug has been fixed.
### Types of change
Bug fix
## Checklist
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
The doc.retokenize() context manager wasn't resizing doc.tensor, leading to a mismatch between the number of tokens in the doc and the number of rows in the tensor. We fix this by deleting rows from the tensor. Merged spans are represented by the vector of their last token.
* Add test for resizing doc.tensor when merging
* Add test for resizing doc.tensor when merging. Closes#1963
* Update get_lca_matrix test for develop
* Fix retokenize if tensor unset
* Test on #2396: bug in Doc.get_lca_matrix()
* reimplementation of Doc.get_lca_matrix(), (closes#2396)
* reimplement Span.get_lca_matrix(), and call it from Doc.get_lca_matrix()
* tests Span.get_lca_matrix() as well as Doc.get_lca_matrix()
* implement _get_lca_matrix as a helper function in doc.pyx; call it from Doc.get_lca_matrix and Span.get_lca_matrix
* use memory view instead of np.ndarray in _get_lca_matrix (faster)
* fix bug when calling Span.get_lca_matrix; return lca matrix as np.array instead of memoryview
* cleaner conditional, add comment
* Test on #2396: bug in Doc.get_lca_matrix()
* reimplementation of Doc.get_lca_matrix(), (closes#2396)
* reimplement Span.get_lca_matrix(), and call it from Doc.get_lca_matrix()
* tests Span.get_lca_matrix() as well as Doc.get_lca_matrix()
* implement _get_lca_matrix as a helper function in doc.pyx; call it from Doc.get_lca_matrix and Span.get_lca_matrix
* use memory view instead of np.ndarray in _get_lca_matrix (faster)
* fix bug when calling Span.get_lca_matrix; return lca matrix as np.array instead of memoryview
* cleaner conditional, add comment
* Add failing test for matcher bug #3009
* Deduplicate matches from Matcher
* Update matcher ? quantifier test
* Fix bug with ? quantifier in Matcher
The ? quantifier indicates a token may occur zero or one times. If the
token pattern fit, the matcher would fail to consider valid matches
where the token pattern did not fit. Consider a simple regex like:
.?b
If we have the string 'b', the .? part will fit --- but then the 'b' in
the pattern will not fit, leaving us with no match. The same bug left us
with too few matches in some cases. For instance, consider:
.?.?
If we have a string of length two, like 'ab', we actually have three
possible matches here: [a, b, ab]. We were only recovering 'ab'. This
should now be fixed. Note that the fix also uncovered another bug, where
we weren't deduplicating the matches. There are actually two ways we
might match 'a' and two ways we might match 'b': as the second token of the pattern,
or as the first token of the pattern. This ambiguity is spurious, so we
need to deduplicate.
Closes#2464 and #3009
* Fix Python2
* issue #3012: add test
* add contributor aggreement
* Make test work without models and fix typos
ten.pos_ instead of ten.orth_ and comparison against "10" instead of integer 10
See #3028. The solution in this patch is pretty debateable.
What we do is give the TokenC struct a .norm field, by repurposing the previously idle .sense attribute. It's nice to repurpose a previous field because it means the TokenC doesn't change size, so even if someone's using the internals very deeply, nothing will break.
The weird thing here is that the TokenC and the LexemeC both have an attribute named NORM. This arguably assists in backwards compatibility. On the other hand, maybe it's really bad! We're changing the semantics of the attribute subtly, so maybe it's better if someone calling lex.norm gets a breakage, and instead is told to write lex.default_norm?
Overall I believe this patch makes the NORM feature work the way we sort of expected it to work. Certainly it's much more like how the docs describe it, and more in line with how we've been directing people to use the norm attribute. We'll also be able to use token.norm to do stuff like spelling correction, which is pretty cool.
<!--- Provide a general summary of your changes in the title. -->
## Description
- [x] Use [`black`](https://github.com/ambv/black) to auto-format all `.py` files.
- [x] Update flake8 config to exclude very large files (lemmatization tables etc.)
- [x] Update code to be compatible with flake8 rules
- [x] Fix various small bugs, inconsistencies and messy stuff in the language data
- [x] Update docs to explain new code style (`black`, `flake8`, when to use `# fmt: off` and `# fmt: on` and what `# noqa` means)
Once #2932 is merged, which auto-formats and tidies up the CLI, we'll be able to run `flake8 spacy` actually get meaningful results.
At the moment, the code style and linting isn't applied automatically, but I'm hoping that the new [GitHub Actions](https://github.com/features/actions) will let us auto-format pull requests and post comments with relevant linting information.
### Types of change
enhancement, code style
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Create aryaprabhudesai.md (#2681)
* Update _install.jade (#2688)
Typo fix: "models" -> "model"
* Add FAC to spacy.explain (resolves#2706)
* Remove docstrings for deprecated arguments (see #2703)
* When calling getoption() in conftest.py, pass a default option (#2709)
* When calling getoption() in conftest.py, pass a default option
This is necessary to allow testing an installed spacy by running:
pytest --pyargs spacy
* Add contributor agreement
* update bengali token rules for hyphen and digits (#2731)
* Less norm computations in token similarity (#2730)
* Less norm computations in token similarity
* Contributor agreement
* Remove ')' for clarity (#2737)
Sorry, don't mean to be nitpicky, I just noticed this when going through the CLI and thought it was a quick fix. That said, if this was intention than please let me know.
* added contributor agreement for mbkupfer (#2738)
* Basic support for Telugu language (#2751)
* Lex _attrs for polish language (#2750)
* Signed spaCy contributor agreement
* Added polish version of english lex_attrs
* Introduces a bulk merge function, in order to solve issue #653 (#2696)
* Fix comment
* Introduce bulk merge to increase performance on many span merges
* Sign contributor agreement
* Implement pull request suggestions
* Describe converters more explicitly (see #2643)
* Add multi-threading note to Language.pipe (resolves#2582) [ci skip]
* Fix formatting
* Fix dependency scheme docs (closes#2705) [ci skip]
* Don't set stop word in example (closes#2657) [ci skip]
* Add words to portuguese language _num_words (#2759)
* Add words to portuguese language _num_words
* Add words to portuguese language _num_words
* Update Indonesian model (#2752)
* adding e-KTP in tokenizer exceptions list
* add exception token
* removing lines with containing space as it won't matter since we use .split() method in the end, added new tokens in exception
* add tokenizer exceptions list
* combining base_norms with norm_exceptions
* adding norm_exception
* fix double key in lemmatizer
* remove unused import on punctuation.py
* reformat stop_words to reduce number of lines, improve readibility
* updating tokenizer exception
* implement is_currency for lang/id
* adding orth_first_upper in tokenizer_exceptions
* update the norm_exception list
* remove bunch of abbreviations
* adding contributors file
* Fixed spaCy+Keras example (#2763)
* bug fixes in keras example
* created contributor agreement
* Adding French hyphenated first name (#2786)
* Fix typo (closes#2784)
* Fix typo (#2795) [ci skip]
Fixed typo on line 6 "regcognizer --> recognizer"
* Adding basic support for Sinhala language. (#2788)
* adding Sinhala language package, stop words, examples and lex_attrs.
* Adding contributor agreement
* Updating contributor agreement
* Also include lowercase norm exceptions
* Fix error (#2802)
* Fix error
ValueError: cannot resize an array that references or is referenced
by another array in this way. Use the resize function
* added spaCy Contributor Agreement
* Add charlax's contributor agreement (#2805)
* agreement of contributor, may I introduce a tiny pl languge contribution (#2799)
* Contributors agreement
* Contributors agreement
* Contributors agreement
* Add jupyter=True to displacy.render in documentation (#2806)
* Revert "Also include lowercase norm exceptions"
This reverts commit 70f4e8adf3.
* Remove deprecated encoding argument to msgpack
* Set up dependency tree pattern matching skeleton (#2732)
* Fix bug when too many entity types. Fixes#2800
* Fix Python 2 test failure
* Require older msgpack-numpy
* Restore encoding arg on msgpack-numpy
* Try to fix version pin for msgpack-numpy
* Update Portuguese Language (#2790)
* Add words to portuguese language _num_words
* Add words to portuguese language _num_words
* Portuguese - Add/remove stopwords, fix tokenizer, add currency symbols
* Extended punctuation and norm_exceptions in the Portuguese language
* Correct error in spacy universe docs concerning spacy-lookup (#2814)
* Update Keras Example for (Parikh et al, 2016) implementation (#2803)
* bug fixes in keras example
* created contributor agreement
* baseline for Parikh model
* initial version of parikh 2016 implemented
* tested asymmetric models
* fixed grevious error in normalization
* use standard SNLI test file
* begin to rework parikh example
* initial version of running example
* start to document the new version
* start to document the new version
* Update Decompositional Attention.ipynb
* fixed calls to similarity
* updated the README
* import sys package duh
* simplified indexing on mapping word to IDs
* stupid python indent error
* added code from https://github.com/tensorflow/tensorflow/issues/3388 for tf bug workaround
* Fix typo (closes#2815) [ci skip]
* Update regex version dependency
* Set version to 2.0.13.dev3
* Skip seemingly problematic test
* Remove problematic test
* Try previous version of regex
* Revert "Remove problematic test"
This reverts commit bdebbef455.
* Unskip test
* Try older version of regex
* 💫 Update training examples and use minibatching (#2830)
<!--- Provide a general summary of your changes in the title. -->
## Description
Update the training examples in `/examples/training` to show usage of spaCy's `minibatch` and `compounding` helpers ([see here](https://spacy.io/usage/training#tips-batch-size) for details). The lack of batching in the examples has caused some confusion in the past, especially for beginners who would copy-paste the examples, update them with large training sets and experienced slow and unsatisfying results.
### Types of change
enhancements
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Visual C++ link updated (#2842) (closes#2841) [ci skip]
* New landing page
* Add contribution agreement
* Correcting lang/ru/examples.py (#2845)
* Correct some grammatical inaccuracies in lang\ru\examples.py; filled Contributor Agreement
* Correct some grammatical inaccuracies in lang\ru\examples.py
* Move contributor agreement to separate file
* Set version to 2.0.13.dev4
* Add Persian(Farsi) language support (#2797)
* Also include lowercase norm exceptions
* Remove in favour of https://github.com/explosion/spaCy/graphs/contributors
* Rule-based French Lemmatizer (#2818)
<!--- Provide a general summary of your changes in the title. -->
## Description
<!--- Use this section to describe your changes. If your changes required
testing, include information about the testing environment and the tests you
ran. If your test fixes a bug reported in an issue, don't forget to include the
issue number. If your PR is still a work in progress, that's totally fine – just
include a note to let us know. -->
Add a rule-based French Lemmatizer following the english one and the excellent PR for [greek language optimizations](https://github.com/explosion/spaCy/pull/2558) to adapt the Lemmatizer class.
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
- Lemma dictionary used can be found [here](http://infolingu.univ-mlv.fr/DonneesLinguistiques/Dictionnaires/telechargement.html), I used the XML version.
- Add several files containing exhaustive list of words for each part of speech
- Add some lemma rules
- Add POS that are not checked in the standard Lemmatizer, i.e PRON, DET, ADV and AUX
- Modify the Lemmatizer class to check in lookup table as a last resort if POS not mentionned
- Modify the lemmatize function to check in lookup table as a last resort
- Init files are updated so the model can support all the functionalities mentioned above
- Add words to tokenizer_exceptions_list.py in respect to regex used in tokenizer_exceptions.py
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [X] I have submitted the spaCy Contributor Agreement.
- [X] I ran the tests, and all new and existing tests passed.
- [X] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Set version to 2.0.13
* Fix formatting and consistency
* Update docs for new version [ci skip]
* Increment version [ci skip]
* Add info on wheels [ci skip]
* Adding "This is a sentence" example to Sinhala (#2846)
* Add wheels badge
* Update badge [ci skip]
* Update README.rst [ci skip]
* Update murmurhash pin
* Increment version to 2.0.14.dev0
* Update GPU docs for v2.0.14
* Add wheel to setup_requires
* Import prefer_gpu and require_gpu functions from Thinc
* Add tests for prefer_gpu() and require_gpu()
* Update requirements and setup.py
* Workaround bug in thinc require_gpu
* Set version to v2.0.14
* Update push-tag script
* Unhack prefer_gpu
* Require thinc 6.10.6
* Update prefer_gpu and require_gpu docs [ci skip]
* Fix specifiers for GPU
* Set version to 2.0.14.dev1
* Set version to 2.0.14
* Update Thinc version pin
* Increment version
* Fix msgpack-numpy version pin
* Increment version
* Update version to 2.0.16
* Update version [ci skip]
* Redundant ')' in the Stop words' example (#2856)
<!--- Provide a general summary of your changes in the title. -->
## Description
<!--- Use this section to describe your changes. If your changes required
testing, include information about the testing environment and the tests you
ran. If your test fixes a bug reported in an issue, don't forget to include the
issue number. If your PR is still a work in progress, that's totally fine – just
include a note to let us know. -->
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [ ] I have submitted the spaCy Contributor Agreement.
- [ ] I ran the tests, and all new and existing tests passed.
- [ ] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Documentation improvement regarding joblib and SO (#2867)
Some documentation improvements
## Description
1. Fixed the dead URL to joblib
2. Fixed Stack Overflow brand name (with space)
### Types of change
Documentation
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
* raise error when setting overlapping entities as doc.ents (#2880)
* Fix out-of-bounds access in NER training
The helper method state.B(1) gets the index of the first token of the
buffer, or -1 if no such token exists. Normally this is safe because we
pass this to functions like state.safe_get(), which returns an empty
token. Here we used it directly as an array index, which is not okay!
This error may have been the cause of out-of-bounds access errors during
training. Similar errors may still be around, so much be hunted down.
Hunting this one down took a long time...I printed out values across
training runs and diffed, looking for points of divergence between
runs, when no randomness should be allowed.
* Change PyThaiNLP Url (#2876)
* Fix missing comma
* Add example showing a fix-up rule for space entities
* Set version to 2.0.17.dev0
* Update regex version
* Revert "Update regex version"
This reverts commit 62358dd867.
* Try setting older regex version, to align with conda
* Set version to 2.0.17
* Add spacy-js to universe [ci-skip]
* Add spacy-raspberry to universe (closes#2889)
* Add script to validate universe json [ci skip]
* Removed space in docs + added contributor indo (#2909)
* - removed unneeded space in documentation
* - added contributor info
* Allow input text of length up to max_length, inclusive (#2922)
* Include universe spec for spacy-wordnet component (#2919)
* feat: include universe spec for spacy-wordnet component
* chore: include spaCy contributor agreement
* Minor formatting changes [ci skip]
* Fix image [ci skip]
Twitter URL doesn't work on live site
* Check if the word is in one of the regular lists specific to each POS (#2886)
* 💫 Create random IDs for SVGs to prevent ID clashes (#2927)
Resolves#2924.
## Description
Fixes problem where multiple visualizations in Jupyter notebooks would have clashing arc IDs, resulting in weirdly positioned arc labels. Generating a random ID prefix so even identical parses won't receive the same IDs for consistency (even if effect of ID clash isn't noticable here.)
### Types of change
bug fix
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Fix typo [ci skip]
* fixes symbolic link on py3 and windows (#2949)
* fixes symbolic link on py3 and windows
during setup of spacy using command
python -m spacy link en_core_web_sm en
closes#2948
* Update spacy/compat.py
Co-Authored-By: cicorias <cicorias@users.noreply.github.com>
* Fix formatting
* Update universe [ci skip]
* Catalan Language Support (#2940)
* Catalan language Support
* Ddding Catalan to documentation
* Sort languages alphabetically [ci skip]
* Update tests for pytest 4.x (#2965)
<!--- Provide a general summary of your changes in the title. -->
## Description
- [x] Replace marks in params for pytest 4.0 compat ([see here](https://docs.pytest.org/en/latest/deprecations.html#marks-in-pytest-mark-parametrize))
- [x] Un-xfail passing tests (some fixes in a recent update resolved a bunch of issues, but tests were apparently never updated here)
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
* Fix regex pin to harmonize with conda (#2964)
* Update README.rst
* Fix bug where Vocab.prune_vector did not use 'batch_size' (#2977)
Fixes#2976
* Fix typo
* Fix typo
* Remove duplicate file
* Require thinc 7.0.0.dev2
Fixes bug in gpu_ops that would use cupy instead of numpy on CPU
* Add missing import
* Fix error IDs
* Fix tests
* Auto-format tests with black
* Add flake8 config
* Tidy up and remove unused imports
* Fix redefinitions of test functions
* Replace orths_and_spaces with words and spaces
* Fix compatibility with pytest 4.0
* xfail test for now
Test was previously overwritten by following test due to naming conflict, so failure wasn't reported
* Unfail passing test
* Only use fixture via arguments
Fixes pytest 4.0 compatibility
<!--- Provide a general summary of your changes in the title. -->
## Description
- [x] Replace marks in params for pytest 4.0 compat ([see here](https://docs.pytest.org/en/latest/deprecations.html#marks-in-pytest-mark-parametrize))
- [x] Un-xfail passing tests (some fixes in a recent update resolved a bunch of issues, but tests were apparently never updated here)
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
The set_children_from_heads function assumed parse trees were
projective. However, non-projective parses may be passed in during
deserialization, or after deprojectivising. This caused incorrect
sentence boundaries to be set for non-projective parses. Close#2772.
## Description
Related issues: #2379 (should be fixed by separating model tests)
* **total execution time down from > 300 seconds to under 60 seconds** 🎉
* removed all model-specific tests that could only really be run manually anyway – those will now live in a separate test suite in the [`spacy-models`](https://github.com/explosion/spacy-models) repository and are already integrated into our new model training infrastructure
* changed all relative imports to absolute imports to prepare for moving the test suite from `/spacy/tests` to `/tests` (it'll now always test against the installed version)
* merged old regression tests into collections, e.g. `test_issue1001-1500.py` (about 90% of the regression tests are very short anyways)
* tidied up and rewrote existing tests wherever possible
### Todo
- [ ] move tests to `/tests` and adjust CI commands accordingly
- [x] move model test suite from internal repo to `spacy-models`
- [x] ~~investigate why `pipeline/test_textcat.py` is flakey~~
- [x] review old regression tests (leftover files) and see if they can be merged, simplified or deleted
- [ ] update documentation on how to run tests
### Types of change
enhancement, tests
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [ ] My changes don't require a change to the documentation, or if they do, I've added all required information.
* issue_2385 add tests for iob_to_biluo converter function
* issue_2385 fix and modify iob_to_biluo function to accept either iob or biluo tags in cli.converter
* issue_2385 add test to fix b char bug
* add contributor agreement
* fill contributor agreement
## Description
Fix for issue #2361 :
replace &, <, >, " with &amp; , &lt; , &gt; , &quot; in before rendering svg
## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [ ] I ran the tests, and all new and existing tests passed.
(As discussed in the comments to #2361)
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
Patterns that end in variable-length operators e.g. * and ? now end on
the correct token. Previously, they were off by 1: the next token was
pulled into the match, even if that's where the pattern failed.
If a Doc object had been previously parsed, it was possible for
invalid parses to be added. There were two problems:
1) The parse was only being partially erased
2) The RightArc action was able to create a 1-cycle.
This patch fixes both errors, and avoids resetting the parse if one is
present. In theory this might allow a better parse to be predicted by
running the parser twice.
Closes#1253.
* Obsolete .parser, .entity etc names in favour of .pipeline
* Components no longer create models on initialization
* Models created by loading method (from_disk(), from_bytes() etc), or
.begin_training()
* Add .predict(), .set_annotations() methods in components
* Pass state through pipeline, to allow components to share information
more flexibly.
Fixes check that an adjective is a base form (as opposed to a
comparative or superlative), so that it's not lemmatized.
e.g. inner -!> inn. Closes#912.
