BaderLab / saber

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.
https://baderlab.github.io/saber/
MIT License
102 stars 17 forks source link

⬆️ Update spacy requirement from <=2.0.13,>=2.0.11 to >=2.0.11,<2.2.1 #182

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Updates the requirements on spacy to permit the latest version.

Release notes *Sourced from [spacy's releases](https://github.com/explosion/spaCy/releases).* > ## v2.2.0: Norwegian & Lithuanian models, better Dutch NER, smaller install, faster matching & more > > ⚠️ This version of spaCy requires downloading **new models**. You can use the [`spacy validate`](https://spacy.io/api/cli#validate) command to find out which models need updating, and print update instructions. If you've been training **your own models**, you'll need to **retrain them** with the new version. > > ## ✨ New features and improvements > > * **NEW:** Pretrained **core models** for [Norwegian](https://spacy.io/models/no) (MIT) and [Lithuanian](https://spacy.io/models/lt) (CC BY-SA). > * **NEW:** Better pre-trained [Dutch](https://spacy.io/models/nl) NER using custom labelled UD corpus instead of WikiNER. > * **NEW:** Make spaCy roughly **5-10× smaller on disk** (depending on your platform) by compressing and moving lookups to a [separate package](https://github.com/explosion/spacy-lookups-data). > * **NEW:** `EntityLinker` and `KnowledgeBase` API to train and access entity linking models, plus scripts to train your own Wikidata models. > * **NEW:** 10× faster `PhraseMatcher` and improved phrase matching algorithm. > * **NEW:** `DocBin` class to efficiently serialize collections of `Doc` objects. > * **NEW:** Train text classification models on the command line with `spacy train` and get `textcat` results via the `Scorer`. > * **NEW:** [`debug-data`](https://spacy.io/api/cli#debug-data) command to validate your training and development data, get useful stats, and find problems like invalid entity annotations, cyclic dependencies, low data labels and more. > * **NEW:** Efficient `Lookups` class using Bloom filters that allows storing, accessing and serializing large dictionaries via `vocab.lookups`. > * Data augmentation in `spacy train` via the `--orth-variant-level` flag, which defines the percentage of occurrences of some tokens subject to replacement during training. > * Add `nlp.pipe_labels` (labels assigned by pipeline components) and include `"labels"` in `nlp.meta`. > * Support `spacy_displacy_colors` entry point to allow packages to add entity colors to `displacy`. > * Allow `template` config option in `displacy` to customize entity HTML template. > * Improve match pattern validation and handling of unsupported attributes. > * Add lookup lemmatization data for [Croatian](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/hr) and [Serbian](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/sr). > * Update and improve language data for [Chinese](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/zh), [Croatian](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/hr), [Thai](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/th), [Romanian](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/ro), [Hindi](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/hi) and [English](https://github.com/explosion/spaCy/blob/HEAD/spacy/lang/en). > > ## 🔴 Bug fixes > > * Fix issue [#3258](https://github-redirect.dependabot.com/explosion/spaCy/issues/3258): Reduce package size on disk by moving and compressing large dictionaries. > * Fix issue [#3540](https://github-redirect.dependabot.com/explosion/spaCy/issues/3540): Update lemma and vector information after splitting a token. > * Fix issue [#3687](https://github-redirect.dependabot.com/explosion/spaCy/issues/3687): Automatically skip duplicates in `Doc.retokenize`. > * Fix issue [#3830](https://github-redirect.dependabot.com/explosion/spaCy/issues/3830): Retrain German model and fix `subtok` errors. > * Fix issue [#3850](https://github-redirect.dependabot.com/explosion/spaCy/issues/3850): Allow customizing entity HTML template in displaCy. > * Fix issue [#3879](https://github-redirect.dependabot.com/explosion/spaCy/issues/3879), [#3951](https://github-redirect.dependabot.com/explosion/spaCy/issues/3951), [#4154](https://github-redirect.dependabot.com/explosion/spaCy/issues/4154): Fix bug in `Matcher` retry loop that'd cause problems with `?` operator. > * Fix issue [#3917](https://github-redirect.dependabot.com/explosion/spaCy/issues/3917): Raise error for negative token indices in `displacy`. > * Fix issue [#3922](https://github-redirect.dependabot.com/explosion/spaCy/issues/3922): Add `PhraseMatcher.remove` method. > * Fix issue [#3959](https://github-redirect.dependabot.com/explosion/spaCy/issues/3959), [#4133](https://github-redirect.dependabot.com/explosion/spaCy/issues/4133): Make sure both `pos` and `tag` are correctly serialized. > * Fix issue [#3972](https://github-redirect.dependabot.com/explosion/spaCy/issues/3972): Ensure `PhraseMatcher` returns multiple matches for identical rules. > * Fix issue [#4020](https://github-redirect.dependabot.com/explosion/spaCy/issues/4020): Raise error for overlapping entities in `biluo_tags_from_offsets`. > * Fix issue [#4051](https://github-redirect.dependabot.com/explosion/spaCy/issues/4051): Ensure retokenizer sets POS tags correctly on merge. > * Fix issue [#4070](https://github-redirect.dependabot.com/explosion/spaCy/issues/4070): Improve token pattern checking without validation. > * Fix issue [#4096](https://github-redirect.dependabot.com/explosion/spaCy/issues/4096): Add checks for cycles in `debug-data`. > * Fix issue [#4100](https://github-redirect.dependabot.com/explosion/spaCy/issues/4100): Improve docs on phrase pattern attributes. > * Fix issue [#4102](https://github-redirect.dependabot.com/explosion/spaCy/issues/4102): Correct mistakes in English lookup lemmatizer data. > * Fix issue [#4104](https://github-redirect.dependabot.com/explosion/spaCy/issues/4104): Make visualized NER examples in docs more clear. > * Fix issue [#4107](https://github-redirect.dependabot.com/explosion/spaCy/issues/4107): Automatically set span root attributes on merging. > * Fix issue [#4111](https://github-redirect.dependabot.com/explosion/spaCy/issues/4111), [#4170](https://github-redirect.dependabot.com/explosion/spaCy/issues/4170): Improve NER/IOB converters. > * Fix issue [#4120](https://github-redirect.dependabot.com/explosion/spaCy/issues/4120): Correctly handle `?` operator at the end of pattern. > * Fix issue [#4123](https://github-redirect.dependabot.com/explosion/spaCy/issues/4123): Provide more details in cycle error message `E069`. > * Fix issue [#4138](https://github-redirect.dependabot.com/explosion/spaCy/issues/4138): Correctly open `.html` files as UTF-8 in `evaluate` command. > * Fix issue [#4139](https://github-redirect.dependabot.com/explosion/spaCy/issues/4139): Make emoticon data a raw string. > * Fix issue [#4148](https://github-redirect.dependabot.com/explosion/spaCy/issues/4148): Add missing API docs for `force` flag on `set_extension`. > * Fix issue [#4155](https://github-redirect.dependabot.com/explosion/spaCy/issues/4155): Correct language code for Serbian. > * Fix issue [#4165](https://github-redirect.dependabot.com/explosion/spaCy/issues/4165): Add more attributes to matcher validation schema. > ... (truncated)
Commits - [`2eb3101`](https://github.com/explosion/spaCy/commit/2eb31012e7af1ad752cefdfecace13a257e4282c) Set version to v2.2.0 - [`796072e`](https://github.com/explosion/spaCy/commit/796072e56050ff0546e2c7c57f41190480774616) Set version to v2.2.0.dev19 - [`9d3ce7c`](https://github.com/explosion/spaCy/commit/9d3ce7cba237361fd9f442f3b02abfa464eac666) Ensure training doesn't crash with empty batches ([#4360](https://github-redirect.dependabot.com/explosion/spaCy/issues/4360)) - [`52b5912`](https://github.com/explosion/spaCy/commit/52b5912dbf4a17ea2be1b725ff27c410c8b9b94e) Tidy up [ci skip] - [`d822412`](https://github.com/explosion/spaCy/commit/d82241218a5b8240e0072b1c1ad92b61275d7f71) Make the default NER labels less model-specific [ci skip] ([#4361](https://github-redirect.dependabot.com/explosion/spaCy/issues/4361)) - [`dda8611`](https://github.com/explosion/spaCy/commit/dda86118bd04f4b653e6e9e612998273a6011f4d) Update Ukrainian lemmatizer with new lookups ([#4359](https://github-redirect.dependabot.com/explosion/spaCy/issues/4359)) - [`b6670bf`](https://github.com/explosion/spaCy/commit/b6670bf0c25906709b39a553fbd43881c8a0a9e2) Use consistent spelling - [`2086296`](https://github.com/explosion/spaCy/commit/208629615d46be5cf6f5d8462b452c4016f79ecf) Auto-format - [`867e93a`](https://github.com/explosion/spaCy/commit/867e93aae2503abe08c10dd577b7dc5d592823f7) Add Streamlit example [ci skip] - [`38b6e69`](https://github.com/explosion/spaCy/commit/38b6e69389a24412dafc43baa3f072b8d7272d03) Merge branch 'master' of https://github.com/explosion/spaCy - Additional commits viewable in [compare view](https://github.com/explosion/spaCy/compare/v2.0.11...v2.2.0)


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coveralls commented 4 years ago

Pull Request Test Coverage Report for Build 518


Totals Coverage Status
Change from base Build 441: 0.0%
Covered Lines:
Relevant Lines: 0

💛 - Coveralls
dependabot-preview[bot] commented 4 years ago

Superseded by #183.