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.
If doc.from_array() was called with say, only entity information, this
would cause doc.is_tagged to be set to False, even if tags were set.
This caused tags to be dropped from serialisation. The same was true for
doc.is_parsed.
Closes#3012.
* 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
Remove hacks and wrappers, keep code in sync across our libraries and move spaCy a few steps closer to only depending on packages with binary wheels 🎉
See here: https://github.com/explosion/srsly
Serialization is hard, especially across Python versions and multiple platforms. After dealing with many subtle bugs over the years (encodings, locales, large files) our libraries like spaCy and Prodigy have steadily grown a number of utility functions to wrap the multiple serialization formats we need to support (especially json, msgpack and pickle). These wrapping functions ended up duplicated across our codebases, so we wanted to put them in one place.
At the same time, we noticed that having a lot of small dependencies was making maintainence harder, and making installation slower. To solve this, we've made srsly standalone, by including the component packages directly within it. This way we can provide all the serialization utilities we need in a single binary wheel.
srsly currently includes forks of the following packages:
ujson
msgpack
msgpack-numpy
cloudpickle
* WIP: replace json/ujson with srsly
* Replace ujson in examples
Use regular json instead of srsly to make code easier to read and follow
* Update requirements
* Fix imports
* Fix typos
* Replace msgpack with srsly
* Fix warning
* Support nowrap setting in util.prints
* Tidy up and fix whitespace
* Simplify script and use read_jsonl helper
* Add JSON schemas (see #2928)
* Deprecate Doc.print_tree
Will be replaced with Doc.to_json, which will produce a unified format
* Add Doc.to_json() method (see #2928)
Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space.
* Remove outdated test
* Add write_json and write_jsonl helpers
* WIP: Update spacy train
* Tidy up spacy train
* WIP: Use wasabi for formatting
* Add GoldParse helpers for JSON format
* WIP: add debug-data command
* Fix typo
* Add missing import
* Update wasabi pin
* Add missing import
* 💫 Refactor CLI (#2943)
To be merged into #2932.
## Description
- [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi)
- [x] use [`black`](https://github.com/ambv/black) for auto-formatting
- [x] add `flake8` config
- [x] move all messy UD-related scripts to `cli.ud`
- [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO)
### Types of change
enhancement
## 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.
* Update wasabi pin
* Delete old test
* Update errors
* Fix typo
* Tidy up and format remaining code
* Fix formatting
* Improve formatting of messages
* Auto-format remaining code
* Add tok2vec stuff to spacy.train
* Fix typo
* Update wasabi pin
* Fix path checks for when train() is called as function
* Reformat and tidy up pretrain script
* Update argument annotations
* Raise error if model language doesn't match lang
* Document new train command
* 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
* 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
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.
* Add logic to filter out warning IDs via environment variable
Usage: SPACY_WARNING_EXCLUDE=W001,W007
* Add warnings for empty vectors
* Add warning if no word vectors are used in .similarity methods
For example, if only tensors are available in small models – should hopefully clear up some confusion around this
* Capture warnings in tests
* Rename SPACY_WARNING_EXCLUDE to SPACY_WARNING_IGNORE
* Add spacy.errors module
* Update deprecation and user warnings
* Replace errors and asserts with new error message system
* Remove redundant asserts
* Fix whitespace
* Add messages for print/util.prints statements
* Fix typo
* Fix typos
* Move CLI messages to spacy.cli._messages
* Add decorator to display error code with message
An implementation like this is nice because it only modifies the string when it's retrieved from the containing class – so we don't have to worry about manipulating tracebacks etc.
* Remove unused link in spacy.about
* Update errors for invalid pipeline components
* Improve error for unknown factories
* Add displaCy warnings
* Update formatting consistency
* Move error message to spacy.errors
* Update errors and check if doc returned by component is None
This patch takes a step towards #1487 by introducing the
doc.retokenize() context manager, to handle merging spans, and soon
splitting tokens.
The idea is to do merging and splitting like this:
with doc.retokenize() as retokenizer:
for start, end, label in matches:
retokenizer.merge(doc[start : end], attrs={'ent_type': label})
The retokenizer accumulates the merge requests, and applies them
together at the end of the block. This will allow retokenization to be
more efficient, and much less error prone.
A retokenizer.split() function will then be added, to handle splitting a
single token into multiple tokens. These methods take `Span` and `Token`
objects; if the user wants to go directly from offsets, they can append
to the .merges and .splits lists on the retokenizer.
The doc.merge() method's behaviour remains unchanged, so this patch
should be 100% backwards incompatible (modulo bugs). Internally,
doc.merge() fixes up the arguments (to handle the various deprecated styles),
opens the retokenizer, and makes the single merge.
We can later start making deprecation warnings on direct calls to doc.merge(),
to migrate people to use of the retokenize context manager.
