python-package-conda.yml

# 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: "3.12"
  supported_pythons: '["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]'
  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@v4
      - 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@v4
      - 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", "windows-latest"]
        python_version: ${{ fromJSON(needs.conf.outputs.supported_pythons) }}
        use_conda: [true, false]
    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python_version }}
          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 (${{ needs.conf.outputs.latest_python }}, qemu::aarch64-centos)
    needs: ["conf", "lint", "doc", "test-all"]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        # setup-buildx-action uses the git context directly
        # but checklist wants the .git directory
      - name: Set up QEMU
        id: qemu
        uses: docker/setup-qemu-action@v1
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v1
      - name: Build and test for linux-aarch64
        id: docker_build
        uses: docker/build-push-action@v2
        with:
          context: .
          # ^ to use the local checkout, not the git context
          file: aarch64.Dockerfile
          cache-from: type=gha
          cache-to: type=gha,mode=max
          build-args: |
            PYTHON_VERSION=${{ env.latest_python }}