ci.yaml

name: ci

on:
  push:
    branches:
    - master
    tags:
      - '*'
  pull_request:
    branches:
    - '*'
  schedule:
    - cron: '0 0 * * 1'  # weekly
  workflow_dispatch:
jobs:
  test:
    runs-on: ubuntu-24.04
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
        subdivision:
          - "test_auxiliary_lib"
          - "test_dataframe"
          - "test_frozen_instrumentation"
          - "test_genome_instrumentation"
          - "test_juxtaposition"
          - "test_phylogenetic_inference/test_estimators"
          - "test_phylogenetic_inference/test_pairwise"
          - "test_phylogenetic_inference/test_population"
          - "test_phylogenetic_inference/test_priors"
          - "test_phylogenetic_inference/test_tree"
          - "test_serialization"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators"
          - "test_stratum_retention_viz"
          - "test_test_drive"

    steps:
    - uses: actions/checkout@v1
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo sed -i 's/azure\.//' /etc/apt/sources.list
        sudo apt-get update -o Acquire::Retries=3
        sudo apt-get install -y ffmpeg -o Acquire::Retries=3
        python -m pip install --upgrade pip setuptools
        pip install tox tox-gh-actions
    - name: Test with tox
      run: |
        export HSTRAT_TESTS_SUBDIVISION=${{ matrix.subdivision }}
        tox

  cli-smoke:
    runs-on: ubuntu-24.04
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install Python dependencies
      uses: py-actions/py-dependency-install@v4
      with:
        path: "requirements-dev/requirements-testing.txt"
    - name: Run examples
      run: |
        python3 -m hstrat
        python3 -m hstrat.dataframe.surface_build_tree --help
        python3 -m hstrat.dataframe.surface_unpack_reconstruct --help
        python3 -m hstrat.dataframe.surface_postprocess_trie --help
        python3 -m hstrat._auxiliary_lib._alifestd_as_newick_asexual --help
        python3 -m hstrat._auxiliary_lib._alifestd_downsample_tips_asexual --help
        python3 -m hstrat._auxiliary_lib._alifestd_try_add_ancestor_list_col --help

  examples:
    runs-on: ubuntu-24.04
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install Python dependencies
      uses: py-actions/py-dependency-install@v4
      with:
        path: "requirements-dev/requirements-jit.txt"
    - name: Install Python dependencies
      uses: py-actions/py-dependency-install@v4
      with:
        path: "requirements-dev/requirements-testing.txt"
    - name: Run examples
      run: ./examples/run_all.sh

  test-cli:
    runs-on: ubuntu-24.04
    strategy:
      fail-fast: false
      matrix:
        head:
          # - "" exceeds memory on actions runner
          - "--head 10_000"
          - "--head 1_000_000"
          - "--sample 10_000 --seed 1"
          - "--sample 1_000_000 --seed 1"
    steps:
    - name: Cleanup pre-installed tools
      run: |
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf /opt/ghc
        sudo rm -rf "/usr/local/share/boost"
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install Python dependencies
      uses: py-actions/py-dependency-install@v4
      with:
        path: "requirements-dev/requirements-jit.txt"
    - name: Install Python dependencies
      uses: py-actions/py-dependency-install@v4
      with:
        path: "requirements-dev/requirements-testing.txt"
    - run: python3 -m pip freeze
    - name: Run tests
      env:
        HSTRAT_TESTS_CLI_HEAD: "${{ matrix.head }}"
        HSTRAT_TESTS_CLI_STDOUT: "/dev/null"
      run: ./tests-cli/run_all.sh

  build-script:
    runs-on: ubuntu-24.04
    steps:
    - uses: actions/checkout@v1
    - run: |
        sudo sed -i 's/azure\.//' /etc/apt/sources.list
        sudo apt-get update -o Acquire::Retries=3
        sudo apt-get install -y python3-pybind11 -o Acquire::Retries=3
    - run: ./build.sh

  coverage:
    runs-on: ubuntu-24.04
    strategy:
      fail-fast: false
      matrix:
        subdivision:
          - "test_auxiliary_lib"
          - "test_dataframe"
          - "test_frozen_instrumentation"
          - "test_genome_instrumentation"
          - "test_juxtaposition"
          - "test_phylogenetic_inference/test_estimators"
          - "test_phylogenetic_inference/test_pairwise"
          - "test_phylogenetic_inference/test_population"
          - "test_phylogenetic_inference/test_priors"
          - "test_phylogenetic_inference/test_tree"
          - "test_serialization"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo"
          - "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators"
          - "test_stratum_retention_viz"
          - "test_test_drive"
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        sudo sed -i 's/azure\.//' /etc/apt/sources.list
        sudo apt-get update -o Acquire::Retries=3
        sudo apt-get install -y ffmpeg -o Acquire::Retries=3
        python -m pip install --upgrade pip setuptools
        python -m pip install -r requirements-dev/py310/requirements-testing.txt
    - name: Log coverage configuration
      run: coverage debug sys
    - name: Run tests with coverage report
      run: coverage run -m pytest tests/test_hstrat/${{ matrix.subdivision }}
    - uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }} # required
        flags: tests # optional
        fail_ci_if_error: true # optional (default = false)
        verbose: true # optional (default = false)

  tidy:
    runs-on: ubuntu-24.04
    steps:
    - name: Install apt dependencies
      run: sudo apt-get install -y rename
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip setuptools
        python -m pip install -r requirements-dev/py310/requirements-testing.txt
    - name: Test isort tidyness
      uses: jamescurtin/isort-action@master
      with:
          requirementsFiles: "requirements-dev/py310/requirements-testing.txt"
    - name: Test Black tidyness
      uses: psf/black@27d20144a7517594e24a1649451177b2a11284be
      with:
          version: "22.10.0"
    - uses: editorconfig-checker/action-editorconfig-checker@main
    - name: Test editorconfig tidyness
      run: editorconfig-checker
    - name: Test tidy/ tidyness
      run: ./tidy/test_tidy.sh

  paper:
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Build draft PDF
        uses: openjournals/openjournals-draft-action@master
        with:
          journal: joss
          # This should be the path to the paper within your repo.
          paper-path: joss/paper.md
      - name: Upload
        uses: actions/upload-artifact@v4
        with:
          name: paper
          # This is the output path where Pandoc will write the compiled
          # PDF. Note, this should be the same directory as the input
          # paper.md
          path: joss/paper.pdf

  # regression test for https://github.com/mmore500/hstrat/commit/c276530
  packaging-bdist:
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Build bdist
        run: |
          python3 -m venv env
          source env/bin/activate
          python3 -m pip install -r requirements-dev/requirements-release.txt
          python3 setup.py bdist_wheel
          tree dist
          deactivate
      - name: Upgrade pip
        run: python3 -m pip install pip --upgrade
      - name: Install from bdist
        run: python3 -m pip install dist/*.whl
      - name: Test install
        run: |
          find . -type f -name '*.py' -exec rm {} \;
          find . -type f -name '*.pyi' -exec rm {} \;
          python3 -c "import hstrat; print(hstrat.__version__)"

  # regression test for https://github.com/mmore500/hstrat/commit/c276530
  packaging-sdist:
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Build sdist
        run: |
          python3 -m venv env
          source env/bin/activate
          python3 -m pip install -r requirements-dev/requirements-release.txt
          python3 setup.py sdist
          tree dist
          deactivate
      - name: Upgrade pip
        run: python3 -m pip install pip --upgrade
      - name: Install from sdist
        run: python3 -m pip install dist/*.tar.gz
      - name: Test install
        run: |
          find . -type f -name '*.py' -exec rm {} \;
          find . -type f -name '*.pyi' -exec rm {} \;
          python3 -c "import hstrat; print(hstrat.__version__)"

  # regression test for https://github.com/mmore500/hstrat/commit/c276530
  packaging-source:
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Upgrade pip
        run: python3 -m pip install pip --upgrade
      - name: Install from source
        run: python3 -m pip install .
      - name: Test install
        run: |
          rm -rf *
          cd
          python3 -c "import hstrat; print(hstrat.__version__)"

  deploy-ghcr:
    name: Docker Image Deploy
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Set Tags
        id: set_tags
        run: |
          if [[ "${GITHUB_REF_NAME}" != *merge ]]; then
            echo "TAGS=latest,${GITHUB_REF_NAME}" >> $GITHUB_ENV
          else
            echo "TAGS=latest" >> $GITHUB_ENV
          fi
      - name: Build and Push to GitHub Container Registry
        uses: docker/build-push-action@v1
        with:
          push: ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/v') }}
          tags: ${{ env.TAGS }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}
          repository: mmore500/hstrat
          registry: ghcr.io
          add_git_labels: true

  build_wheels:
    name: Build wheels on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-24.04, windows-latest, macos-14]

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: "recursive"
      - name: Set up Ubuntu Dependecies
        if: matrix.os == 'ubuntu-24.04'
        run: |
          sudo sed -i 's/azure\.//' /etc/apt/sources.list
          sudo apt-get update -o Acquire::Retries=3
          sudo apt-get install -y python3.12-dev python3-dev python3-pybind11 -o Acquire::Retries=3
      - name: Build wheels
        uses: pypa/cibuildwheel@v2.21.3
        env:
          CIBW_TEST_COMMAND: python3 -m hstrat.dataframe.surface_unpack_reconstruct --help
          CIBW_TEST_SKIP: "*313-* pp* *win* *i686* *musllinux*"
          CIBW_SKIP: "*-win32"
      - uses: actions/upload-artifact@v4
        with:
          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
          path: ./wheelhouse/*.whl

  build_sdist:
    name: Build source distribution
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: "recursive"
      - name: Build sdist
        run: pipx run build --sdist

      - uses: actions/upload-artifact@v4
        with:
          name: cibw-sdist
          path: dist/*.tar.gz

  deploy-test:
    runs-on: ubuntu-24.04
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install -r requirements-dev/py310/requirements-release.txt
    - name: Build package
      run: python setup.py egg_info --tag-build="${{github.run_number}}" sdist bdist_wheel
    - name: Test publish package
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
        repository-url: https://test.pypi.org/legacy/
    - name: Install from test PyPI
      run: |
        rm -rf *
        python3 -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ hstrat
    - name: Test install
      run: |
        python3 -c "import hstrat; print(hstrat.__version__)"

  deploy:
    if: startsWith(github.ref, 'refs/tags/v')
    needs:
      - build_sdist
      - build_wheels
      - build-script
      - coverage
      - cli-smoke
      - deploy-test
      - examples
      - packaging-bdist
      - packaging-sdist
      - packaging-source
      - test
      - test-cli
      - tidy
    runs-on: ubuntu-24.04
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.10
      uses: actions/setup-python@v2
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip setuptools
        python -m pip install -r requirements-dev/py310/requirements-release.txt
    - uses: actions/download-artifact@v4
      with:
        # unpacks default artifact into dist/
        # if `name: artifact` is omitted, the action will create extra parent dir
        pattern: cibw-*
        path: dist
        merge-multiple: true
    - name: Publish package
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}