* Update gold corpus code to properly ingest a directory of jsonlines files
In response to: https://github.com/explosion/spaCy/issues/3975
* Update spacy/gold.pyx
Co-Authored-By: Ines Montani <ines@ines.io>
<!--- Provide a general summary of your changes in the title. -->
## Description
* tidy up and adjust Cython code to code style
* improve docstrings and make calling `help()` nicer
* add URLs to new docs pages to docstrings wherever possible, mostly to user-facing objects
* fix various typos and inconsistencies in docs
### Types of change
enhancement, docs
## 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.
* Improve handling of missing NER tags
GoldParse can accept missing NER tags, if entities is provided
in BILUO format (rather than as spans). Missing tags can be provided
as None values.
Fix bug that occurred when first tag was a None value. Closes#2603.
* Document specification of missing NER tags.
Fix a bug in the JSON streaming code that GoldCorpus uses. Escaped
slashes were being handled incorrectly. This bug caused low scores for
French in the early v2.1.0 alphas, because most of the data was not
being read in.
Fittingly, the document that triggered the bug was a Wikipedia article about
Perl. Parsing perl remains difficult!
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
Our JSON training format is annoying to work with, and we've wanted to
retire it for some time. In the meantime, we can at least add some
missing functions to make it easier to live with.
This patch adds a function that generates the JSON format from a list
of Doc objects, one per paragraph. This should be a convenient way to handle
a lot of data conversions: whatever format you have the source
information in, you can use it to setup a Doc object. This approach
should offer better future-proofing as well. Hopefully, we can steadily
rewrite code that is sensitive to the current data-format, so that it
instead goes through this function. Then when we change the data format,
we won't have such a problem.
* 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
* 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
The TextCategorizer class is supposed to support multi-label
text classification, and allow training data to contain missing
values.
For this to work, the gradient of the loss should be 0 when labels
are missing. Instead, there was no way to actually denote "missing"
in the GoldParse class, and so the TextCategorizer class treated
the label set within gold.cats as complete.
To fix this, we change GoldParse.cats to be a dict instead of a list.
The GoldParse.cats dict should map to floats, with 1. denoting
'present' and 0. denoting 'absent'. Gradients are zeroed for categories
absent from the gold.cats dict. A nice bonus is that you can also set
values between 0 and 1 for partial membership. You can also set numeric
values, if you're using a text classification model that uses an
appropriate loss function.
Unfortunately this is a breaking change; although the functionality
was only recently introduced and hasn't been properly documented
yet. I've updated the example script accordingly.
