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jeromekelleherjeromekelleher
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Align CI with bio2zarr/vcztools patterns
Update ci.yml to mirror bio2zarr conventions: weekly cron run, action SHA version comments, fetch-depth: 0 in test job checkout, --locked and --no-default-groups flags throughout, biofuse --help smoke test, and Coveralls coverage upload. Rewrite the packaging job to install the built wheel into a fresh venv and exercise the CLI; drop the unnecessary libfuse3-dev/pkg-config install (biofuse is pure-Python). Add .github/dependabot.yml for monthly github-actions updates, and a new cd.yml that builds sdist+wheel and publishes to PyPI on release and TestPyPI on tag pushes via trusted publishing.
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: github-actions
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directory: /
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schedule:
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interval: monthly
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open-pull-requests-limit: 5
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commit-message:
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prefix: ci

‎.github/workflows/cd.yml‎

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name: CD
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on:
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merge_group:
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push:
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branches:
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- main
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tags:
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- '*'
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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packaging:
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if: github.repository_owner == 'sgkit-dev'
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name: Packaging
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
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with:
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python-version: "3.12"
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enable-cache: false
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- name: Build artefacts
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run: uv build
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- name: Store the distribution packages
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uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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if: github.repository_owner == 'sgkit-dev' && github.event_name == 'release'
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needs:
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- packaging
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/biofuse
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
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with:
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name: python-package-distributions
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path: dist/
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- uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # release/v1
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publish-to-testpypi:
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if: github.repository_owner == 'sgkit-dev' && github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
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needs:
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- packaging
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runs-on: ubuntu-latest
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environment:
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name: testpypi
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url: https://test.pypi.org/p/biofuse
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
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with:
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name: python-package-distributions
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path: dist/
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- uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # release/v1
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with:
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repository-url: https://test.pypi.org/legacy/

‎.github/workflows/ci.yml‎

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push:
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branches:
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- main
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schedule:
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# At 04:44 on Monday, see https://crontab.guru/
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- cron: "44 4 * * 1"
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permissions:
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contents: read
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name: Lint
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
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with:
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persist-credentials: false
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
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with:
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python-version: "3.11"
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matrix:
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python-version: ["3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Install system packages
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plink1.9 plink2
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- name: Install uv
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: uv sync --group test
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run: uv sync --locked --group test --no-default-groups
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- name: Test console script entry point
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run: |
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uv run biofuse --help
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- name: Run tests with coverage
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run: uv run pytest --cov=biofuse --cov-report=term-missing
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- name: Upload coverage to Coveralls
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uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b # v2.3.6
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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# The first coveralls upload will succeed and others seem to fail now.
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# This is a quick workaround for doing a proper "parallel" setup:
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# https://github.com/coverallsapp/github-action
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fail-on-error: false
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packaging:
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name: Packaging
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runs-on: ubuntu-latest
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
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- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
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with:
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fetch-depth: 0
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persist-credentials: false
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- name: Install system packages
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run: sudo apt-get update && sudo apt-get install -y libfuse3-dev pkg-config
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- name: Install uv
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@d0cc045d04ccac9d8b7881df0226f9e82c39688e # v6.8.0
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with:
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python-version: "3.12"
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- name: Install packaging deps
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run: uv sync --group packaging --no-default-groups
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run: uv sync --locked --group packaging --no-default-groups
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- name: Validate pyproject
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run: uv run validate-pyproject pyproject.toml -v
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run: uv run --locked --group packaging --no-default-groups validate-pyproject pyproject.toml -v
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- name: Build artefacts
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run: uv build
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- name: Twine check
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run: uv run twine check --strict dist/*
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run: uv run --locked --group packaging --no-default-groups twine check --strict dist/*
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- name: Install into venv
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run: |
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uv venv cli-test
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uv pip install --python=cli-test dist/*.whl
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- name: Check biofuse CLI
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run: |
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./cli-test/bin/biofuse --help

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