Addition of a project using the BIOM format #222
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| # heavily adapted from scikit-bio's CI | |
| # https://github.com/biocore/scikit-bio/blob/31123c6471dc62f45a55bfdff59c61a4850be367/.github/workflows/ci.yml#L1 | |
| name: biom-format CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| env: | |
| latest_python: "3.11" | |
| supported_pythons: '["3.7", "3.8", "3.9", "3.10", "3.11"]' | |
| miniforge_version: "22.9.0-2" | |
| 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" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r ci/requirements.lint.txt | |
| conda list | |
| - name: Run linter | |
| shell: bash -l {0} | |
| run: make lint | |
| doc: | |
| name: Build Documentation (${{ needs.conf.outputs.latest_python }}, ubuntu-latest) | |
| needs: ["conf", "lint"] | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.latest_python }} | |
| miniforge-version: ${{ env.miniforge_version }} | |
| miniforge-variant: ${{ env.miniforge_variant }} | |
| environment-file: ci/conda_host_env.yml | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r ci/requirements.doc.txt | |
| pip install . | |
| conda list | |
| - name: Make docs | |
| shell: bash -l {0} | |
| run: make doc | |
| test-all: | |
| name: Test (${{ matrix.python_version }}, ${{ matrix.os }}, ${{ fromJSON('["pypi", "conda"]')[matrix.use_conda] }}) | |
| needs: ["conf", "lint"] | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| python_version: ${{ fromJSON(needs.conf.outputs.supported_pythons) }} | |
| use_conda: [true, false] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| 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 }} | |
| shell: bash -l {0} | |
| run: | | |
| conda install -q --yes -c conda-forge --file ci/conda_requirements.txt | |
| pip install . --no-deps | |
| conda list | |
| - name: Install dependencies (pip) | |
| if: ${{ !matrix.use_conda }} | |
| shell: bash -l {0} | |
| run: | | |
| pip install . | |
| conda list | |
| - name: Run unit tests | |
| shell: bash -l {0} | |
| run: make test | |
| test-aarch64: | |
| name: Test (${{ needs.conf.outputs.latest_python }}, qemu::aarch64-centos) | |
| needs: ["conf", "lint", "doc", "test-all"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # 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 }} |