ci(commands): skip site without PyMOL; skip simulate without pyvolve;… #21
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| name: csubst ci | |
| on: | |
| push: | |
| branches: [ "**" ] | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: csubst-ci-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| smoke: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python: ['3.9', '3.10', '3.11', '3.12'] | |
| install: [source] # bioconda は後で復活可 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: csubst-smoke | |
| create-args: >- | |
| python=${{ matrix.python }} | |
| iqtree numpy scipy cython biopython requests pip | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: strict | |
| cache-environment: true | |
| cache-downloads: true | |
| # ← 追加：post の ENOENT / “not find … in .bash_profile” 回避 | |
| - name: Workaround micromamba post-step quirks | |
| if: always() | |
| run: | | |
| # post が探す一時ファイルを用意 | |
| mkdir -p "$RUNNER_TEMP/setup-micromamba" | |
| : > "$RUNNER_TEMP/setup-micromamba/micromamba-shell" | |
| # post が .bash_profile から消そうとする行をダミーで用意 | |
| touch "$HOME/.bash_profile" | |
| grep -q 'micromamba activate csubst-smoke' "$HOME/.bash_profile" \ | |
| || echo 'micromamba activate csubst-smoke' >> "$HOME/.bash_profile" | |
| # ← 追加: pyvolve は pip から入れる | |
| - name: Install pyvolve (pip) | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --no-input pyvolve==1.1.0 | |
| - name: Install runtime deps | |
| shell: bash -l {0} | |
| run: | | |
| micromamba install -y \ | |
| numpy=1.26.* cython=0.29.* iqtree \ | |
| conda-forge::biopython conda-forge::requests \ | |
| - name: Install csubst (from source) | |
| if: matrix.install == 'source' | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --no-build-isolation . | |
| # --- Smoke --- | |
| - name: Run smoke test | |
| shell: bash -l {0} | |
| run: bash ci/csubst_smoke.sh | |
| # --- CLI tests --- | |
| - name: Run CLI tests | |
| shell: bash -l {0} | |
| run: bash ci/csubst_cli.sh | |
| - name: Upload artifacts (always) | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: smoke-and-cli-${{ matrix.os }}-${{ matrix.install }} | |
| path: | | |
| $RUNNER_TEMP/csubst_smoke/_artifacts* | |
| if-no-files-found: ignore | |
| retention-days: 7 | |
| - name: Run command tests | |
| shell: bash -l {0} | |
| env: | |
| MPLBACKEND: Agg | |
| run: bash ci/csubst_commands.sh | |
| - name: Validate outputs (schema-lite) | |
| shell: bash -l {0} | |
| run: python ci/check_csubst_outputs.py |