Snakemake compatibility #49
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| name: Snakemake compatibility | |
| # Re-runs the test suite against the latest snakemake release that | |
| # satisfies our version constraint. The detect job asks `uv` itself | |
| # what would be resolved if `uv.lock` were upgraded for snakemake; the | |
| # resolved version is used as the actions/cache key, so the matrix | |
| # only runs when the upgrade would land on a snakemake version we have | |
| # not tested before. | |
| # | |
| # Trigger paths: | |
| # - schedule: backstop daily poll | |
| # - workflow_dispatch: manual run | |
| # - repository_dispatch (snakemake-release): external bot can ping us | |
| # directly so we don't have to wait for the next cron tick | |
| on: | |
| schedule: | |
| - cron: "17 6 * * *" | |
| workflow_dispatch: | |
| repository_dispatch: | |
| types: [snakemake-release] | |
| env: | |
| UV_VERSION: "0.11.6" | |
| UV_PYTHON_PREFERENCE: "managed" | |
| permissions: | |
| contents: read | |
| jobs: | |
| detect: | |
| name: Resolve latest snakemake | |
| runs-on: ubuntu-latest | |
| outputs: | |
| version: ${{ steps.resolve.outputs.version }} | |
| changed: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| version: ${{ env.UV_VERSION }} | |
| enable-cache: true | |
| - name: Resolve latest snakemake under current constraint | |
| id: resolve | |
| run: | | |
| uv lock --upgrade-package snakemake | |
| version=$(python3 -c 'import tomllib; d=tomllib.load(open("uv.lock","rb")); print(next(p["version"] for p in d["package"] if p["name"]=="snakemake"))') | |
| echo "version=$version" >> "$GITHUB_OUTPUT" | |
| echo "Resolved snakemake==$version" | |
| - name: Check whether this resolved version has already been tested | |
| uses: actions/cache@v4 | |
| id: cache | |
| with: | |
| path: .snakemake-compat-marker | |
| key: snakemake-compat-${{ steps.resolve.outputs.version }} | |
| - name: Record marker for new version | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: echo "${{ steps.resolve.outputs.version }}" > .snakemake-compat-marker | |
| compat: | |
| name: Test against snakemake ${{ needs.detect.outputs.version }} (Python ${{ matrix.python-version }}) | |
| needs: detect | |
| if: | | |
| needs.detect.outputs.changed == 'true' | |
| || github.event_name == 'workflow_dispatch' | |
| || github.event_name == 'repository_dispatch' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.14"] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| version: ${{ env.UV_VERSION }} | |
| enable-cache: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Upgrade snakemake in uv.lock | |
| run: uv lock --upgrade-package snakemake | |
| - name: Install project dependencies | |
| run: uv sync --all-groups | |
| - name: Run tests | |
| run: uv run tox -e py${{ matrix.python-version }} |