added: csubst_cli.sh, modified: csubst_smoke.sh and csubst-smoke.yml #8
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| name: csubst smoke | |
| on: | |
| push: | |
| branches: [ "**" ] | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: smoke-csubst-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| smoke: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python: ['3.10'] # ← 3.10 に統一 | |
| install: [source] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: csubst-smoke | |
| # まずは軽い環境（Python+pip）だけ作る | |
| create-args: >- | |
| python=${{ matrix.python }} | |
| pip | |
| condarc: | | |
| channels: | |
| - bioconda | |
| - conda-forge | |
| channel_priority: strict | |
| cache-environment: true | |
| cache-downloads: true | |
| # 共通の実行時依存は conda でピン留め（NumPy 1.26 / Cython 0.29） | |
| - name: Install runtime deps (common) | |
| shell: bash -l {0} | |
| run: | | |
| micromamba install -y numpy=1.26.* cython=0.29.* iqtree | |
| # ---- source ビルド ---- | |
| - name: Install csubst (from source) | |
| if: matrix.install == 'source' | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| # 環境内の numpy/cython を使わせる | |
| pip install --no-build-isolation . | |
| # ---- bioconda ---- | |
| - name: Install csubst (from Bioconda) | |
| if: matrix.install == 'bioconda' | |
| shell: bash -l {0} | |
| run: | | |
| micromamba install -y csubst | |
| - name: Run smoke test | |
| shell: bash -l {0} | |
| run: | | |
| bash ci/csubst_smoke.sh | |
| - name: Upload smoke logs (always) | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: smoke-logs-${{ matrix.os }}-${{ matrix.install }} | |
| path: $RUNNER_TEMP/csubst_smoke/_artifacts | |
| if-no-files-found: ignore | |
| retention-days: 7 |