fix: csubst-ci.yml and csubst_commands.sh #23
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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: ${{ matrix.os }} | ||
| timeout-minutes: 30 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest] | ||
| python: ['3.9', '3.10', '3.11', '3.12'] | ||
| install: [source] | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| - name: Set up micromamba | ||
| uses: mamba-org/setup-micromamba@v1 | ||
| with: | ||
| environment-name: csubst-smoke | ||
| create-args: >- | ||
| python=${{ matrix.python }} | ||
| iqtree numpy scipy cython biopython requests pip | ||
| condarc: | | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| channel_priority: strict | ||
| cache-environment: true | ||
| cache-downloads: true | ||
| # post の ENOENT 回避 | ||
| - name: Workaround micromamba post-step quirks | ||
| if: always() | ||
| run: | | ||
| mkdir -p "$RUNNER_TEMP/setup-micromamba" | ||
| : > "$RUNNER_TEMP/setup-micromamba/micromamba-shell" | ||
| touch "$HOME/.bash_profile" | ||
| grep -q 'micromamba activate csubst-smoke' "$HOME/.bash_profile" \ | ||
| || echo 'micromamba activate csubst-smoke' >> "$HOME/.bash_profile" | ||
| # pyvolve を pip から | ||
| - name: Install pyvolve (pip) | ||
| shell: bash -l {0} | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install --no-input pyvolve==1.1.0 | ||
| - name: Install runtime deps | ||
| shell: bash -l {0} | ||
| run: | | ||
| micromamba install -y \ | ||
| numpy=1.26.* cython=0.29.* iqtree \ | ||
| conda-forge::biopython conda-forge::requests | ||
| - name: Install csubst (from source) | ||
| if: matrix.install == 'source' | ||
| shell: bash -l {0} | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install --no-build-isolation . | ||
| # --- Smoke --- | ||
| - name: Run smoke test | ||
| shell: bash -l {0} | ||
| run: bash ci/csubst_smoke.sh | ||
| # --- CLI tests --- | ||
| - name: Run CLI tests | ||
| shell: bash -l {0} | ||
| run: bash ci/csubst_cli.sh | ||
| - name: Upload artifacts (always) | ||
| if: always() | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: smoke-and-cli-${{ matrix.os }}-${{ matrix.install }} | ||
| path: | | ||
| $RUNNER_TEMP/csubst_smoke/_artifacts* | ||
| if-no-files-found: ignore | ||
| retention-days: 7 | ||
| # PyMOL の有無を検出（heredoc の閉じは行頭に PY） | ||
| - name: Check PyMOL | ||
| id: pymol | ||
| shell: bash -l {0} | ||
| run: | | ||
| HAVE=$(python - <<'PY' | ||
| try: | ||
| import pymol # noqa: F401 | ||
| print("true") | ||
| except Exception: | ||
| print("false") | ||
| PY | ||
| ) | ||
| echo "have=$HAVE" >> "$GITHUB_OUTPUT" | ||
| - name: Run command tests | ||
| shell: bash -l {0} | ||
| env: | ||
| MPLBACKEND: Agg | ||
| HAVE_PYMOL: ${{ steps.pymol.outputs.have }} | ||
| run: bash ci/csubst_commands.sh | ||
| - name: Validate outputs (schema-lite) | ||
| shell: bash -l {0} | ||
| run: python ci/check_csubst_outputs.py | ||
