build: configure setuptools via pyproject.toml #292
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feat: add oncokb as a source (#170)
- Updated dependencies (civicpy, normalizers, ga4gh)
- `Harvester` base class
- Remove instance var `assertions`
- Create timestamped harvester json if no filename given (now includes empty string)
- `CIViCHarvester`
- Major cleanup. We will only exclude civic fields that start with `_` or `partial`
- We now harvest civic molecular profiles
- We no longer get `civic_actionability_score` and `variant_groups`
- `OncoKBHarvester`
- Use enum values for api endpoints
- `metakb.main`
- Use Path for `/api/v2/search/{id}` rather than Query
- `metakb.normalizers`
- Rename instance var `variation_normalizer` --> `variation_query_handler`
- Allow for query handler instances to be passed as parameters
- `CIViCTransform` : Updates from civicpy 3.0
- Include molecular profile ID to variant ID mapping
- Assertion's now have `assertion_type`
- `drugs` --> `therapies`
- `OncoKBTransform`
- `uuid` for drug returned `None`, so switched to using `ncitCode` for the therapy descriptor mappings
- `setup.cfg`
- license-file --> license_file in setup.cfg
- Tests
- In test_database.py::test_variation_rules, I removed a check since we now support copy number variation from {GENE} Amplification queries
- Updated tests to reflect source changes
- `metakb.cli`
- Added `--update_from_remote` for civicpy cache
- Remove from version.py - Remove from ServiceMeta class
- Update permissions for cool-seq-tool - Update python version to 3.11 - Fix unzipping seqrepo
- Handling null civic therapy ncit_id's - Only look at accepted assertions for civic
* Followed https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/ * Did not include [Signing the distribution packages](https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/#signing-the-distribution-packages) * In `publish-to-pypi`, removed `if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes` since we only make a release when a GH release is created.
jsstevenson
changed the title
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(need to figure out proper PR here, may need to rebase, etc) |
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Per https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html. We've done this for most of our other projects now -- it enables some consolidation of tool configurations, which is nice.