feat(pdm): Add get_nearest_taxa. #20
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| name: Version, build, publish | |
| on: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| semantic_release_next_version: | |
| name: Next version | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| cache: npm | |
| node-version: lts/Iron | |
| - run: npm install | |
| - run: npx semantic-release --dry-run | |
| id: semantic_release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: semantic-release | |
| path: | | |
| Cargo.toml | |
| pyproject.toml | |
| CITATION.cff | |
| retention-days: 1 | |
| outputs: | |
| version: ${{ steps.semantic_release.outputs.version }} | |
| test_rust: | |
| name: Test Rust | |
| needs: semantic_release_next_version | |
| if: needs.semantic_release_next_version.outputs.version != '' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rust-lang/setup-rust-toolchain@v1 | |
| with: | |
| toolchain: stable | |
| - run: | |
| cargo test --release --all-features | |
| build_linux: | |
| needs: test_rust | |
| runs-on: ${{ matrix.platform.runner }} | |
| strategy: | |
| matrix: | |
| platform: | |
| - runner: ubuntu-latest | |
| target: x86_64 | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build wheel | |
| uses: PyO3/maturin-action@v1 | |
| with: | |
| target: ${{ matrix.platform.target }} | |
| args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} | |
| sccache: 'true' | |
| manylinux: auto | |
| - name: Test wheel | |
| run: | | |
| echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree | |
| python -m pip install dendropy | |
| python -m pip install dist/*.whl --force-reinstall | |
| python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-linux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} | |
| path: dist | |
| retention-days: 1 | |
| musllinux: | |
| needs: test_rust | |
| runs-on: ${{ matrix.platform.runner }} | |
| strategy: | |
| matrix: | |
| platform: | |
| - runner: ubuntu-latest | |
| target: x86_64 | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build wheel | |
| uses: PyO3/maturin-action@v1 | |
| with: | |
| target: ${{ matrix.platform.target }} | |
| args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} | |
| sccache: 'true' | |
| manylinux: musllinux_1_2 | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-musllinux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} | |
| path: dist | |
| retention-days: 1 | |
| windows: | |
| needs: test_rust | |
| runs-on: ${{ matrix.platform.runner }} | |
| strategy: | |
| matrix: | |
| platform: | |
| - runner: windows-latest | |
| target: x64 | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build wheel | |
| uses: PyO3/maturin-action@v1 | |
| with: | |
| target: ${{ matrix.platform.target }} | |
| args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} | |
| sccache: 'true' | |
| - name: Test wheel | |
| run: | | |
| echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree | |
| python -m pip install dendropy | |
| python -m pip install (get-item .\dist\*.whl) --force-reinstall | |
| python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-windows-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} | |
| path: dist | |
| retention-days: 1 | |
| osx: | |
| needs: test_rust | |
| runs-on: ${{ matrix.platform.runner }} | |
| strategy: | |
| matrix: | |
| platform: | |
| - runner: macos-12 | |
| target: x86_64 | |
| - runner: macos-14 | |
| target: aarch64 | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build wheel | |
| uses: PyO3/maturin-action@v1 | |
| with: | |
| target: ${{ matrix.platform.target }} | |
| args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} | |
| sccache: 'true' | |
| - name: Test wheel | |
| run: | | |
| echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree | |
| python -m pip install dendropy | |
| python -m pip install dist/*.whl --force-reinstall | |
| python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-osx-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} | |
| path: dist | |
| retention-days: 1 | |
| sdist: | |
| needs: test_rust | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - name: Build wheel | |
| uses: PyO3/maturin-action@v1 | |
| with: | |
| command: sdist | |
| args: --out dist | |
| - name: Test dist | |
| run: | | |
| echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree | |
| python -m pip install dendropy | |
| python -m pip install dist/*.tar.gz --force-reinstall | |
| python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-sdist | |
| path: dist | |
| retention-days: 1 | |
| semantic_release_publish: | |
| name: Publish to GitHub | |
| needs: [build_linux, musllinux, windows, osx, sdist] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| cache: npm | |
| node-version: lts/Iron | |
| - run: npm install | |
| - run: npx semantic-release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| upload_pypi: | |
| name: Publish to PyPI | |
| needs: [semantic_release_publish] | |
| runs-on: ubuntu-latest | |
| environment: | |
| name: pypi | |
| url: https://pypi.org/p/phylodm | |
| permissions: | |
| id-token: write | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| path: dist | |
| pattern: wheels-* | |
| merge-multiple: true | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| upload_crates: | |
| name: Publish to crates.io | |
| needs: [semantic_release_publish] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: semantic-release | |
| - uses: actions-rust-lang/setup-rust-toolchain@v1 | |
| with: | |
| toolchain: stable | |
| - run: cargo publish --allow-dirty --token ${CRATES_TOKEN} | |
| env: | |
| CRATES_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }} |