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
* 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
These experiments were completed a few weeks ago, but I didn't make the PR, pending model release.
Token vector width: 128->96
Hidden width: 128->64
Embed size: 5000->2000
Dropout: 0.2->0.1
Updated optimizer defaults (unclear how important?)
This should improve speed, model size and load time, while keeping
similar or slightly better accuracy.
The tl;dr is we prefer to prevent over-fitting by reducing model size,
rather than using more dropout.
Our epic matrix multiplication odyssey is drawing to a close...
I've now finally got the Blis linear algebra routines in a self-contained Python package, with wheels for Windows, Linux and OSX. The only missing platform at the moment is Windows Python 2.7. The result is at https://github.com/explosion/cython-blis
Thinc v7.0.0 will make the change to Blis. I've put a Thinc v7.0.0.dev0 up on PyPi so that we can test these changes with the CI, and even get them out to spacy-nightly, before Thinc v7.0.0 is released. This PR also updates the other dependencies to be in line with the current versions master is using. I've also resolved the msgpack deprecation problems, and gotten spaCy and Thinc up to date with the latest Cython.
The point of switching to Blis is to have control of how our matrix multiplications are executed across platforms. When we were using numpy for this, a different library would be used on pip and conda, OSX would use Accelerate, etc. This would open up different bugs and performance problems, especially when multi-threading was introduced.
With the change to Blis, we now strictly single-thread the matrix multiplications. This will make it much easier to use multiprocessing to parallelise the runtime, since we won't have nested parallelism problems to deal with.
* Use blis
* Use -2 arg to Cython
* Update dependencies
* Fix requirements
* Update setup dependencies
* Fix requirement typo
* Fix msgpack errors
* Remove Python27 test from Appveyor, until Blis works there
* Auto-format setup.py
* Fix murmurhash version
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.
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.
The parser.begin_training() method was rewritten in v2.1. The rewrite
introduced a regression, where if you added labels prior to
begin_training(), these labels were discarded. This patch fixes that.
* Work on refactoring greedy parser
* Compile updated parser
* Fix refactored parser
* Update test
* Fix refactored parser
* Fix refactored parser
* Readd beam search after refactor
* Fix beam search after refactor
* Fix parser
* Fix beam parsing
* Support oracle segmentation in ud-train CLI command
* Avoid relying on final gold check in beam search
* Add a keyword argument sink to GoldParse
* Bug fixes to beam search after refactor
* Avoid importing fused token symbol in ud-run-test, untl that's added
* Avoid importing fused token symbol in ud-run-test, untl that's added
* Don't modify Token in global scope
* Fix error in beam gradient calculation
* Default to beam_update_prob 1
* Set a more aggressive threshold on the max violn update
* Disable some tests to figure out why CI fails
* Disable some tests to figure out why CI fails
* Add some diagnostics to travis.yml to try to figure out why build fails
* Tell Thinc to link against system blas on Travis
* Point thinc to libblas on Travis
* Try running sudo=true for travis
* Unhack travis.sh
* Restore beam_density argument for parser beam
* Require thinc 6.11.1.dev16
* Revert hacks to tests
* Revert hacks to travis.yml
* Update thinc requirement
* Fix parser model loading
* Fix size limits in training data
* Add missing name attribute for parser
* Fix appveyor for Windows
* 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 addresses #1660, which was caused by keying all pre-trained
vectors with the same ID when telling Thinc how to refer to them. This
meant that if multiple models were loaded that had pre-trained vectors,
errors or incorrect behaviour resulted.
The vectors class now includes a .name attribute, which defaults to:
{nlp.meta['lang']_nlp.meta['name']}.vectors
The vectors name is set in the cfg of the pipeline components under the
key pretrained_vectors. This replaces the previous cfg key
pretrained_dims.
In order to make existing models compatible with this change, we check
for the pretrained_dims key when loading models in from_disk and
from_bytes, and add the cfg key pretrained_vectors if we find it.
This patch does a few smallish things that tighten up the training workflow a little, and allow memory use during training to be reduced by letting the GoldCorpus stream data properly.
Previously, the parser and entity recognizer read and saved labels as lists, with extra labels noted separately. Lists were used becaue ordering is very important, to ensure that the label-to-class mapping is stable.
We now manage labels as nested dictionaries, first keyed by the action, and then keyed by the label. Values are frequencies. The trick is, how do we save new labels? We need to make sure we iterate over these in the same order they're added. Otherwise, we'll get different class IDs, and the model's predictions won't make sense.
To allow stable sorting, we map the new labels to negative values. If we have two new labels, they'll be noted as having "frequency" -1 and -2. The next new label will then have "frequency" -3. When we sort by (frequency, label), we then get a stable sort.
Storing frequencies then allows us to make the next nice improvement. Previously we had to iterate over the whole training set, to pre-process it for the deprojectivisation. This led to storing the whole training set in memory. This was most of the required memory during training.
To prevent this, we now store the frequencies as we stream in the data, and deprojectivize as we go. Once we've built the frequencies, we can then apply a frequency cut-off when we decide how many classes to make.
Finally, to allow proper data streaming, we also have to have some way of shuffling the iterator. This is awkward if the training files have multiple documents in them. To solve this, the GoldCorpus class now writes the training data to disk in msgpack files, one per document. We can then shuffle the data by shuffling the paths.
This is a squash merge, as I made a lot of very small commits. Individual commit messages below.
* Simplify label management for TransitionSystem and its subclasses
* Fix serialization for new label handling format in parser
* Simplify and improve GoldCorpus class. Reduce memory use, write to temp dir
* Set actions in transition system
* Require thinc 6.11.1.dev4
* Fix error in parser init
* Add unicode declaration
* Fix unicode declaration
* Update textcat test
* Try to get model training on less memory
* Print json loc for now
* Try rapidjson to reduce memory use
* Remove rapidjson requirement
* Try rapidjson for reduced mem usage
* Handle None heads when projectivising
* Stream json docs
* Fix train script
* Handle projectivity in GoldParse
* Fix projectivity handling
* Add minibatch_by_words util from ud_train
* Minibatch by number of words in spacy.cli.train
* Move minibatch_by_words util to spacy.util
* Fix label handling
* More hacking at label management in parser
* Fix encoding in msgpack serialization in GoldParse
* Adjust batch sizes in parser training
* Fix minibatch_by_words
* Add merge_subtokens function to pipeline.pyx
* Register merge_subtokens factory
* Restore use of msgpack tmp directory
* Use minibatch-by-words in train
* Handle retokenization in scorer
* Change back-off approach for missing labels. Use 'dep' label
* Update NER for new label management
* Set NER tags for over-segmented words
* Fix label alignment in gold
* Fix label back-off for infrequent labels
* Fix int type in labels dict key
* Fix int type in labels dict key
* Update feature definition for 8 feature set
* Update ud-train script for new label stuff
* Fix json streamer
* Print the line number if conll eval fails
* Update children and sentence boundaries after deprojectivisation
* Export set_children_from_heads from doc.pxd
* Render parses during UD training
* Remove print statement
* Require thinc 6.11.1.dev6. Try adding wheel as install_requires
* Set different dev version, to flush pip cache
* Update thinc version
* Update GoldCorpus docs
* Remove print statements
* Fix formatting and links [ci skip]
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.
