Adjust default behavior of MFA2Tree.build - disable UFBoot and scfl #35
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| name: CI/build and test | |
| on: | |
| push: | |
| branches: ["main", "dev"] | |
| paths: ["**.py", "requirements.txt"] | |
| pull_request: | |
| branches: ["main", "dev"] | |
| paths: ["**.py", "requirements.txt"] | |
| workflow_dispatch: | |
| workflow_call: | |
| jobs: | |
| build-muscle: | |
| uses: ./.github/workflows/build_muscle.yml | |
| build-aster: | |
| uses: ./.github/workflows/build_aster.yml | |
| build-fasttree: | |
| uses: ./.github/workflows/build_fasttree.yml | |
| build-raxml: | |
| uses: ./.github/workflows/build_raxml.yml | |
| build-iqtree: | |
| uses: ./.github/workflows/build_iqtree.yml | |
| build-and-test: | |
| name: Build and test | |
| runs-on: ubuntu-latest | |
| env: | |
| OS: Linux | |
| needs: | |
| [build-muscle, build-aster, build-fasttree, build-raxml, build-iqtree] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: ["3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-tags: true | |
| - run: git fetch --tags | |
| - name: Cache Python packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ runner.os }}-${{ matrix.python }}-${{ hashFiles('requirements.txt') }} | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov pytest-dependency pytest-env pytest-order | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with Ruff | |
| uses: astral-sh/ruff-action@v3 | |
| - name: Install package | |
| run: pip install . | |
| - name: Cache muscle | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/.local/bin/muscle | |
| key: ${{ runner.os }}-muscle | |
| - name: Cache ASTER | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/.local/bin/astral | |
| key: ${{ runner.os }}-ASTER | |
| - name: Cache FastTree | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/.local/bin/VeryFastTree | |
| key: ${{ runner.os }}-VeryFastTree | |
| - name: Cache RAxML | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/.local/bin/raxml-ng | |
| key: ${{ runner.os }}-raxml-ng | |
| - name: Cache IQTree | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/.local/bin/iqtree2 | |
| key: ${{ runner.os }}-IQTree | |
| - name: Test with pytest | |
| run: | | |
| package_name=$(grep '^name = ' pyproject.toml | sed 's/name = "\(.*\)"/\1/' | tr -d '[:space:]') | |
| pytest -vv --cov=$package_name --cov-report=xml --runslow | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| flags: ${{ matrix.python }} | |
| env_vars: OS | |
| files: ./coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true |