├── .git-blame-ignore-revs ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── create_release.yaml │ ├── test_coverage.yml │ └── test_python_versions.yaml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.rst ├── CONTRIBUTING ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── RELEASE_CHECKLIST.md ├── docs ├── Makefile ├── annotations.rst ├── conf.py ├── data.rst ├── hpoterm.rst ├── index.rst ├── matrix.rst ├── ontology.rst ├── parser.rst ├── requirements.txt ├── set.rst ├── similarity.rst ├── stats.rst └── tutorial │ ├── basics.rst │ ├── data.rst │ ├── enrichment.rst │ ├── examples.rst │ ├── installation.rst │ ├── ontology.rst │ ├── sets.rst │ └── terms.rst ├── pyhpo ├── __init__.py ├── annotations.py ├── config.py ├── data │ ├── genes_to_phenotype.txt │ ├── hp.obo │ ├── phenotype.hpoa │ └── phenotype_to_genes.txt ├── matrix.py ├── ontology.py ├── parser │ ├── __init__.py │ ├── diseases.py │ ├── generics.py │ ├── genes.py │ └── obo.py ├── py.typed ├── set.py ├── similarity │ ├── __init__.py │ ├── base.py │ └── defaults.py ├── stats.py ├── term.py └── update_data.py ├── pyproject.toml ├── requirements.txt ├── requirements_dev.txt ├── setup.py └── tests ├── benchmarking.py ├── mockontology.py ├── py.typed ├── test_annotations.py ├── test_decipher_annotation.py ├── test_information_content.py ├── test_integration.py ├── test_matrix.py ├── test_obo_parser.py ├── test_omim_annotation.py ├── test_orpha_annotation.py ├── test_set.py ├── test_similarity_base.py ├── test_similarity_default_methods.py ├── test_stats.py ├── test_term.py └── test_term_ontology.py /.git-blame-ignore-revs: -------------------------------------------------------------------------------- 1 | # Black linting 2 | f1d2bb9a5163967260ba6d7b79c36b72a1ee7b0f 3 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: 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