Dirichilet Multinomial differential abundance method (#1956) #41
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| name: CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths-ignore: ["web/**", "**.md", "README.rst"] | |
| pull_request: | |
| branches: [ main ] | |
| paths-ignore: ["web/**", "**.md", "README.rst"] | |
| env: | |
| latest_python: "3.12" | |
| supported_pythons: '["3.8", "3.9", "3.10", "3.11", "3.12"]' | |
| miniforge_version: "23.11.0-0" | |
| miniforge_variant: "Mambaforge" | |
| jobs: | |
| conf: | |
| # This job is needed to route the global environment variables into | |
| # a context that's available for matrix (and name, but that's unimportant) | |
| name: Prepare Test Plan | |
| runs-on: ubuntu-latest | |
| outputs: | |
| latest_python: ${{ steps.set-vars.outputs.latest_python }} | |
| supported_pythons: ${{ steps.set-vars.outputs.supported_pythons }} | |
| steps: | |
| - name: Report Plan | |
| id: set-vars | |
| run: | | |
| echo "latest_python=$latest_python" >> $GITHUB_OUTPUT | |
| echo "supported_pythons=$supported_pythons" >> $GITHUB_OUTPUT | |
| lint: | |
| name: Lint code (${{ needs.conf.outputs.latest_python }}, ubuntu-latest) | |
| needs: conf | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies | |
| run: | | |
| pip install -r ci/requirements.lint.txt | |
| conda list | |
| - name: Run Ruff | |
| run: | | |
| ruff check --output-format=github . | |
| doc: | |
| name: Build Documentation (${{ needs.conf.outputs.latest_python }}, ubuntu-latest) | |
| needs: ["conf", "lint"] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies | |
| run: | | |
| pip install -r ci/requirements.doc.txt | |
| pip install . | |
| conda list | |
| - name: Make documentation | |
| run: make doc | |
| # save built documentation (HTML) for deployment | |
| - name: Substitute URLs | |
| if: github.event_name == 'push' | |
| run: python doc/suburl.py | |
| - name: Save documentation | |
| if: github.event_name == 'push' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docpack | |
| path: doc/build/html/ | |
| # full-scale test (including Cython) with latest Python | |
| test-cython: | |
| name: Test Cython (${{ needs.conf.outputs.latest_python }}, ${{ matrix.os }}) | |
| needs: conf | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| USE_CYTHON: TRUE | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies | |
| run: | | |
| pip install . | |
| conda list | |
| - name: Run unit tests | |
| env: | |
| WITH_COVERAGE: "TRUE" | |
| run: make test | |
| # upload coverage reports to Codecov (only under Linux) | |
| - name: Generate coverage reports | |
| if: runner.os == 'Linux' | |
| run: | | |
| cd ci && coverage lcov --rcfile ../.coveragerc | |
| - name: Upload coverage reports to Codecov | |
| if: runner.os == 'Linux' | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: scikit-bio/scikit-bio | |
| # test under AArch64 (ARM64) architecture | |
| test-cython-aarch64: | |
| name: Test Cython (${{ needs.conf.outputs.latest_python }}, qemu::aarch64-centos) | |
| needs: conf | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # setup-buildx-action uses the git context directly | |
| # but checklist wants the .git directory | |
| - name: Set up QEMU | |
| id: qemu | |
| uses: docker/setup-qemu-action@v1 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build and test for linux-aarch64 | |
| id: docker_build | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| # ^ to use the local checkout, not the git context | |
| file: aarch64.Dockerfile | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| build-args: | | |
| PYTHON_VERSION=${{ env.latest_python }} | |
| # test under all combinations of environments (Python versions, operating systems, PyPI vs Conda) | |
| test-all: | |
| name: Test (${{ matrix.python_version }}, ${{ matrix.os }}, ${{ fromJSON('["pypi", "conda"]')[matrix.use_conda] }}) | |
| runs-on: ${{ matrix.os }} | |
| needs: ["conf", "test-cython", "lint"] | |
| # not testing Cython here, whether the Cython compiles to C is tested above | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| python_version: ${{ fromJSON(needs.conf.outputs.supported_pythons) }} | |
| use_conda: [true, false] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies (conda) | |
| if: ${{ matrix.use_conda }} | |
| run: | | |
| conda install -q --yes -c conda-forge --file ci/conda_requirements.txt | |
| pip install . --no-deps | |
| conda list | |
| - name: Install dependencies | |
| if: ${{ !matrix.use_conda }} | |
| run: | | |
| pip install . | |
| conda list | |
| - name: Run unit tests | |
| env: | |
| WITH_COVERAGE: "TRUE" | |
| run: make test | |
| # deploy the current development documentation to the website | |
| # only when event is push and all tests have passed | |
| deploy-doc: | |
| name: Deploy documentation | |
| if: github.event_name == 'push' | |
| needs: ["doc", "test-all", "test-cython-aarch64"] | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| # load documentation built by job "doc" | |
| - name: Load documentation | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docpack | |
| path: docpack | |
| # checkout website repo | |
| - name: Check out website | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: scikit-bio/scikit-bio.github.io | |
| path: website | |
| ssh-key: ${{ secrets.SSH_DEPLOY_KEY }} | |
| # synchronize documentation to website's docs/dev directory | |
| - name: Update documentation | |
| run: rsync -av --delete docpack/ website/docs/dev | |
| # push website back to repo | |
| - name: Push website | |
| run: | | |
| cd website | |
| git config user.name "${{ github.actor }}" | |
| git config user.email "${{ github.actor_id }}+${{ github.actor }}@users.noreply.github.com" | |
| git add -A | |
| git commit -m "Update from ${{ github.server_url }}/${{ github.repository }}/commit/${{ github.sha }}" | |
| git push |