Bump iqtree3 from 993275d to 7cded0c
#836
Workflow file for this run
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| name: CI | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "35 4 */6 * *" # Every 6 days. | |
| pull_request: | |
| push: | |
| branches-ignore: | |
| - 'dependabot/**' | |
| permissions: | |
| contents: read | |
| jobs: | |
| build-iqtree: | |
| name: Fetch or Build IQ-TREE Static Library on ${{matrix.os}} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - id: build | |
| uses: ./.github/actions/build-iqtree | |
| with: | |
| os: ${{ matrix.os }} | |
| outputs: | |
| iqtree-sha: ${{steps.build.outputs.iqtree-sha}} | |
| tests: | |
| name: Run Tests with Python ${{matrix.python-version}} on ${{matrix.os}} | |
| needs: build-iqtree | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows | |
| python-version: ["3.11", "3.12", "3.13.5"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - uses: ./.github/actions/setup-piqtree | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree-sha }} | |
| - name: Install llvm (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install llvm | |
| - name: Install llvm (Windows) | |
| if: runner.os == 'Windows' | |
| run: | | |
| choco install -y llvm --version=14.0.6 --allow-downgrade | |
| - name: Run Nox Testing | |
| run: | | |
| pip install nox | |
| nox -s test-${{ matrix.python-version }} -- --cov --cov-report=lcov:${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report=term --cov-append --durations=20 | |
| - name: Coveralls Parallel | |
| if: matrix.os != 'macos-13' | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| parallel: true | |
| github-token: ${{secrets.github_token}} | |
| flag-name: run-${{matrix.python-version}}-${{matrix.os}} | |
| file: "${{matrix.os}}-${{matrix.python-version}}.lcov" | |
| upload-coverage: | |
| name: Finish Coveralls | |
| needs: tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| parallel-finished: true | |
| type_check: | |
| name: Type Check | |
| needs: build-iqtree | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.13.5"] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: ./.github/actions/setup-piqtree | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree-sha }} | |
| - name: "Run Type Checking for ${{ matrix.python-version }}" | |
| run: | | |
| pip install nox | |
| nox -s type_check-${{ matrix.python-version }} | |
| lint: | |
| name: Linting | |
| needs: build-iqtree | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.13.5"] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: ./.github/actions/setup-piqtree | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree-sha }} | |
| - name: "Run Linting for ${{ matrix.python-version }}" | |
| run: | | |
| pip install nox | |
| nox -s ruff-${{ matrix.python-version }} | |
| test-docs: | |
| name: Test Code Blocks in Docs | |
| needs: build-iqtree | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.13.5"] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - uses: ./.github/actions/setup-piqtree | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree-sha }} | |
| - name: Test Code Blocks in Docs | |
| run: | | |
| pip install nox | |
| nox -s test_docs-3.13.5 |