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jandom
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Feb 6, 2026
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| 2) Sanity check locally (recommended) | ||
| ```bash | ||
| python -m venv .venv | ||
| source .venv/bin/activate | ||
| python -m pip install -U pip build twine | ||
| python -m build | ||
| twine check dist/* |
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| def test_cli_align_fasta_to_stdout() -> None: | ||
| repo_root = Path(__file__).resolve().parents[2] | ||
| input_fasta = repo_root / "tests" / "data" / "tiny.fa" | ||
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| result = subprocess.run( |
| user: __token__ | ||
| password: ${{ secrets.PYPI_API_TOKEN }} | ||
| packages_dir: dist/ No newline at end of file | ||
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} |
| if: env.PYPI_API_TOKEN != '' | ||
| with: | ||
| user: __token__ | ||
| password: ${{ env.PYPI_API_TOKEN }} |
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This should really be a secret, no?
One pattern to take is to have two secrets
- PYPI_API_TOKEN
- TEST_PYPI_API_TOKEN
And use the an input to decide which secret to read
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The PR improves aims to make kalign publishable to PyPI. It adds a publishing workflow and makes the python
kalignCLI work reliably. I have done my own test publish to TestPyPI to make sure it works. You can test it out usingChanges
kalignconsole script implementation to run the Python bindings directly (instead of shelling out to a separately-installedkalignbinary, which could recurse into itself afterpip install). (python-kalign/cli.py:1)kalign.__version__resolve from installed distribution metadata to avoid version drift. (python-kalign/__init__.py)README-python.mdfor PyPI long description.license = "GPL-3.0-or-later", includeCOPYINGvialicense-files, and removed the deprecatedLicense ::classifier to satisfy modern metadata validation. (pyproject.toml)workflow_dispatchinput to optionally publish to TestPyPI usingTEST_PYPI_API_TOKEN.macos-14to avoiddelocatefailures withlibompbuilt for macOS 15.kalign-test). (.github/workflows/wheels.yml:1)tests/python/test_cli.py)README.md:245)Let me know how it looks @TimoLassmann, and if you have any other recommendations! Thanks again for being open for a contribution like this.
I believe on your end once everything behaves as expected, you will have to make a PyPI account and add your token to the github repository secrets so that the
PYPI_API_TOKENvariable will be set in the workflow. I added instructions in the README about how to cut a new release in this workflow.cc: @jnwei, @jandom