pyobo 0.12.10__py3-none-any.whl → 0.12.12__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pyobo/__init__.py +6 -0
- pyobo/api/__init__.py +11 -1
- pyobo/api/alts.py +18 -4
- pyobo/api/embedding.py +108 -9
- pyobo/api/names.py +28 -6
- pyobo/api/xrefs.py +21 -1
- pyobo/cli/cli.py +9 -3
- pyobo/cli/database.py +63 -22
- pyobo/cli/lookup.py +39 -24
- pyobo/cli/utils.py +6 -2
- pyobo/constants.py +66 -7
- pyobo/getters.py +8 -3
- pyobo/ner/api.py +17 -10
- pyobo/ner/scispacy_utils.py +2 -0
- pyobo/plugins.py +3 -1
- pyobo/sources/__init__.py +2 -0
- pyobo/sources/antibodyregistry.py +3 -3
- pyobo/sources/bigg/bigg_compartment.py +1 -1
- pyobo/sources/complexportal.py +3 -3
- pyobo/sources/conso.py +3 -3
- pyobo/sources/famplex.py +3 -3
- pyobo/sources/goldbook.py +86 -0
- pyobo/sources/hgnc/hgnc.py +157 -96
- pyobo/sources/hgnc/hgncgenefamily.py +14 -13
- pyobo/sources/msigdb.py +3 -3
- pyobo/sources/omim_ps.py +8 -2
- pyobo/sources/reactome.py +3 -3
- pyobo/sources/rgd.py +7 -11
- pyobo/sources/slm.py +3 -3
- pyobo/sources/uniprot/uniprot.py +3 -3
- pyobo/sources/wikipathways.py +7 -2
- pyobo/struct/__init__.py +2 -2
- pyobo/struct/functional/macros.py +1 -1
- pyobo/struct/functional/obo_to_functional.py +7 -3
- pyobo/struct/obo/reader.py +4 -4
- pyobo/struct/struct.py +48 -18
- pyobo/struct/struct_utils.py +19 -5
- pyobo/struct/typedef.py +19 -3
- pyobo/struct/vocabulary.py +6 -3
- pyobo/utils/path.py +5 -4
- pyobo/version.py +1 -1
- {pyobo-0.12.10.dist-info → pyobo-0.12.12.dist-info}/METADATA +45 -23
- {pyobo-0.12.10.dist-info → pyobo-0.12.12.dist-info}/RECORD +46 -45
- {pyobo-0.12.10.dist-info → pyobo-0.12.12.dist-info}/WHEEL +1 -1
- {pyobo-0.12.10.dist-info → pyobo-0.12.12.dist-info}/entry_points.txt +0 -0
- {pyobo-0.12.10.dist-info → pyobo-0.12.12.dist-info}/licenses/LICENSE +0 -0
pyobo/utils/path.py
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dtype=str,
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verify: bool = True,
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backend: Literal["requests", "urllib"] | None = None,
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**kwargs,
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**kwargs: Any,
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"""Download a file and open as a dataframe."""
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_path = ensure_path(
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version: VersionHint = None,
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name: str | None = None,
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force: bool = False,
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dtype=str,
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"""Download a file and open as JSON."""
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_path = ensure_path(
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prefix,
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prefixes = "prefixes.json"
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metadata = "metadata.json"
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embeddings = "embeddings.tsv.gz"
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ontology: str,
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pyobo/version.py
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Metadata-Version: 2.4
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Name: pyobo
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Version: 0.12.
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Version: 0.12.12
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Summary: A python package for handling and generating OBO
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Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
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Author: Charles Tapley Hoyt
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Requires-Dist: obographs>=0.0.8
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Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
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Requires-Dist: ssslm[gilda] ; extra == 'gilda'
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Provides-Extra: drugcentral
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Description-Content-Type: text/markdown
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```
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### Updating Package Boilerplate
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### 🥼 Testing
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with `tox -e docs-test`) but also that
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</details>
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## 🧑💻 For Maintainers
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<summary>See maintainer instructions</summary>
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to each release of your package. Do the following for each repository:
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</details>
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pyobo/__init__.py,sha256=
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pyobo/__init__.py,sha256=WQCfhng88j77GTYJKw5YmTv6p0U7sRA5RVMMts1DWSc,4063
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pyobo/__main__.py,sha256=cOYQ2OELxF-9T6nuZ9xnLSu9bLHk6einrsSoz7EcD9M,83
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pyobo/api/__init__.py,sha256=
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pyobo/api/alts.py,sha256=v177QYdo5LVmlau0CF6FiN3vGYisuWBHFJnzZVpWv68,3477
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pyobo/api/combine.py,sha256=7T8Qj8W1wWQ1KgKJsO1kFRHZxkQcrfKM1hBrhqHsEkU,1106
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pyobo/api/embedding.py,sha256=
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pyobo/api/embedding.py,sha256=lLJDj_QsL7eqjHq_qaoJ4Dzhi3ucWtMoMfduDsUp1PU,8291
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pyobo/api/species.py,sha256=YxzJeClfuKI-pjYLpu5797jdDeyTkXpjQDgdmc9MKwo,2376
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pyobo/utils/__init__.py,sha256=CANSY8vGq_6v8rWhWRIdnk-Wo5LA2R9Wjg1nqbWqLOw,17
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pyobo-0.12.12.dist-info/RECORD,,
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File without changes
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