allow partial copying and writing of AnnData objects #197
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| name: Continuous integration | |
| on: [push, pull_request] | |
| jobs: | |
| test_rust_code: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: stable | |
| override: true | |
| - name: Cache rust build | |
| uses: Swatinem/rust-cache@v2 | |
| - name: Test Rust package | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/anndata-hdf5 && cargo test --no-fail-fast | |
| cd ${GITHUB_WORKSPACE}/anndata && cargo test --no-fail-fast | |
| cd ${GITHUB_WORKSPACE}/anndata-test-utils && cargo test --no-fail-fast | |
| - name: benchmark | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/anndata-test-utils && cargo bench | |
| cd ${GITHUB_WORKSPACE} | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: benchmark | |
| path: target/criterion | |
| test_python_code: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| anndata_version: ['0.9.*', '0.10.*', '0.11.*', '0.12.*'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: stable | |
| override: true | |
| - name: Cache rust build | |
| uses: Swatinem/rust-cache@v2 | |
| - name: Build and test package | |
| run: | | |
| pip install --user --upgrade pip | |
| cd ${GITHUB_WORKSPACE}/python | |
| pip install --user .[test] anndata==${{ matrix.anndata_version }} | |
| pytest -v --durations=0 ${GITHUB_WORKSPACE}/python/tests | |
| build_doc: | |
| runs-on: ubuntu-latest | |
| needs: [test_python_code] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| profile: minimal | |
| toolchain: stable | |
| override: true | |
| - name: Cache rust build | |
| uses: Swatinem/rust-cache@v2 | |
| - name: Install dependency | |
| run: | | |
| pip install --user --upgrade pip | |
| pip install --user Pygments sphinx==8.* pandoc nbsphinx \ | |
| sphinx-autodoc-typehints sphinx_rtd_theme \ | |
| markupsafe | |
| - name: Build package | |
| run: cd ${GITHUB_WORKSPACE}/python && pip install --user . | |
| - name: Build doc | |
| run: | | |
| cd ${GITHUB_WORKSPACE} | |
| sphinx-build ${GITHUB_WORKSPACE}/python/docs _build/html | |
| - name: Upload doc | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: documentation | |
| path: ./_build/html | |
| upload_gh-page: | |
| name: Publish | |
| runs-on: ubuntu-latest | |
| needs: [build_doc] | |
| steps: | |
| - name: Download | |
| uses: actions/download-artifact@v4 | |
| - name: Upload doc | |
| uses: peaceiris/actions-gh-pages@v4 | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./documentation | |
| publish_branch: gh-pages | |
| force_orphan: true |