Improve GoldParse NER alignment by including all cases where the start
and end of the NER span can be aligned, regardless of internal
tokenization differences.
To do this, convert BILUO tags to character offsets, check start/end
alignment with `doc.char_span()`, and assign the BILUO tags for the
aligned spans. Alignment for `O/-` tags is handled through the
one-to-one and multi alignments.
* Xfail new tokenization test
* Put new alignment behind feature flag
* Move USE_ALIGN to top of the file [ci skip]
Co-authored-by: Ines Montani <ines@ines.io>
* Support train dict format as JSONL
* Add (overly simple) check for dict vs. tuple to read JSONL lines as
either train dicts or train tuples
* Extend JSON/JSONL roundtrip conversion tests using `docs_to_json()`
and `GoldCorpus.train_tuples`
* Revert docs to default JSON output with convert
* Error for ill-formed input to iob_to_biluo()
Check for empty label in iob_to_biluo(), which can result from
ill-formed input.
* Check for empty NER label in debug-data
* Add doc.cats to spacy.gold at the paragraph level
Support `doc.cats` as `"cats": [{"label": string, "value": number}]` in
the spacy JSON training format at the paragraph level.
* `spacy.gold.docs_to_json()` writes `docs.cats`
* `GoldCorpus` reads in cats in each `GoldParse`
* Update instances of gold_tuples to handle cats
Update iteration over gold_tuples / gold_parses to handle addition of
cats at the paragraph level.
* Add textcat to train CLI
* Add textcat options to train CLI
* Add textcat labels in `TextCategorizer.begin_training()`
* Add textcat evaluation to `Scorer`:
* For binary exclusive classes with provided label: F1 for label
* For 2+ exclusive classes: F1 macro average
* For multilabel (not exclusive): ROC AUC macro average (currently
relying on sklearn)
* Provide user info on textcat evaluation settings, potential
incompatibilities
* Provide pipeline to Scorer in `Language.evaluate` for textcat config
* Customize train CLI output to include only metrics relevant to current
pipeline
* Add textcat evaluation to evaluate CLI
* Fix handling of unset arguments and config params
Fix handling of unset arguments and model confiug parameters in Scorer
initialization.
* Temporarily add sklearn requirement
* Remove sklearn version number
* Improve Scorer handling of models without textcats
* Fixing Scorer handling of models without textcats
* Update Scorer output for python 2.7
* Modify inf in Scorer for python 2.7
* Auto-format
Also make small adjustments to make auto-formatting with black easier and produce nicer results
* Move error message to Errors
* Update documentation
* Add cats to annotation JSON format [ci skip]
* Fix tpl flag and docs [ci skip]
* Switch to internal roc_auc_score
Switch to internal `roc_auc_score()` adapted from scikit-learn.
* Add AUCROCScore tests and improve errors/warnings
* Add tests for AUCROCScore and roc_auc_score
* Add missing error for only positive/negative values
* Remove unnecessary warnings and errors
* Make reduced roc_auc_score functions private
Because most of the checks and warnings have been stripped for the
internal functions and access is only intended through `ROCAUCScore`,
make the functions for roc_auc_score adapted from scikit-learn private.
* Check that data corresponds with multilabel flag
Check that the training instances correspond with the multilabel flag,
adding the multilabel flag if required.
* Add textcat score to early stopping check
* Add more checks to debug-data for textcat
* Add example training data for textcat
* Add more checks to textcat train CLI
* Check configuration when extending base model
* Fix typos
* Update textcat example data
* Provide licensing details and licenses for data
* Remove two labels with no positive instances from jigsaw-toxic-comment
data.
Co-authored-by: Ines Montani <ines@ines.io>
* Check whether two entities overlap
- biluo_gold_biluo_overlap now throw exception when entities passed in have overlaps
- added unit test
* SCA agreement
* 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.
* 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
* 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
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.
## 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.
