ci.yaml

name: ci

on: [push, pull_request, workflow_dispatch]

jobs:
  examples:
    runs-on: ubuntu-20.04
    strategy:
      fail-fast: False
      matrix:
        python-version:
          - "3.6"
          - "3.7"
          - "3.8"
          - "3.9"
          - "3.10"
          - "3.11"
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          sudo apt-get install aptitude
          sudo aptitude install -y gcc-7 g++-7 gfortran-7
          sudo apt-get install libpython2.7  # required by paup
          python -m pip install --upgrade pip
      - name: Install paup
        run: |
          temp_dir=$(mktemp -d)
          wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
          gunzip ${temp_dir}/paup4a169_ubuntu64.gz
          chmod +x ${temp_dir}/paup4a169_ubuntu64
          sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
          echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
      - name: Install dendropy
        run: |
          python -m pip install .
      - name: Run examples
        run: |
          cd docs/source/examples
          # only allow known failures
          # and enforce removal of working examples from known failures
          for f in *.py; do
            echo "${f}"
            if timeout 60 python "${f}" && ! grep -q "${f}" backlogged-fail-whitelist.txt; then
              :
            elif grep -q "${f}" backlogged-fail-whitelist.txt; then
              :
            else
              echo FAIL "${f}"
              exit 1
            fi
          done
  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install ruff==0.0.292
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
      - name: Lint with ruff
        run: |
          # stop the build if there are Python syntax errors or undefined names
          ./lint.sh
  tests:
    runs-on: ubuntu-20.04
    strategy:
      fail-fast: False
      matrix:
        python-version:
          - "3.6"
          - "3.7"
          - "3.8"
          - "3.9"
          - "3.10"
          - "3.11"
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        continue-on-error: true
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          sudo apt-get install aptitude
          sudo aptitude install -y gcc-7 g++-7 gfortran-7
          sudo apt-get install libpython2.7  # required by paup
          python -m pip install --upgrade pip
          if [ -f .github/workflows/requirements.txt ]; then pip install -r .github/workflows/requirements.txt; fi
      - name: Install paup
        run: |
          temp_dir=$(mktemp -d)
          wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
          gunzip ${temp_dir}/paup4a169_ubuntu64.gz
          chmod +x ${temp_dir}/paup4a169_ubuntu64
          sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
          echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
      - name: Unit tests with setup.py
        run: |
          python setup.py pytest --addopts '-m "not smoke"'
      - name: Smoke tests with setup.py
        run: |
          python setup.py pytest --addopts "-m smoke"

  entrypoints:
    runs-on: ubuntu-20.04
    strategy:
      fail-fast: False
      matrix:
        python-version:
          - "3.6"
          - "3.7"
          - "3.8"
          - "3.9"
          - "3.10"
          - "3.11"
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        continue-on-error: true
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          sudo apt-get install aptitude
          sudo aptitude install -y gcc-7 g++-7 gfortran-7
          sudo apt-get install libpython2.7  # required by paup
          python -m pip install --upgrade pip
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
          python -m pip install .
      - name: Test sumtrees
        run: |
          which sumtrees
          sumtrees --help
          sumtrees  2>&1 | grep sumtrees || exit 1
      - name: Test sumlabels
        run: |
          which sumlabels
          sumlabels --help
          sumlabels 2>&1 | grep sumlabels || exit 1
      - name: Test dendropy-format
        run: |
          which dendropy-format
          dendropy-format --help
          dendropy-format 2>&1 | grep dendropy-format || exit 1
      - name: Test deprecated entrypoints
        run: |
          which sumtrees.py
          sumtrees.py --help
          sumtrees.py  2>&1 | grep sumtrees.py || exit 1
          which sumlabels.py
          sumlabels.py --help
          sumlabels.py  2>&1 | grep sumlabels.py || exit 1

  coverage:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@master
    - name: Setup Python
      uses: actions/setup-python@master
      with:
        python-version: 3.8
    - name: Install dependencies
      run: |
        sudo apt-get install aptitude
        sudo aptitude install -y gcc-7 g++-7 gfortran-7
        sudo apt-get install libpython2.7  # required by paup
        python -m pip install --upgrade pip
        temp_dir=$(mktemp -d)
        wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
        gunzip ${temp_dir}/paup4a169_ubuntu64.gz
        chmod +x ${temp_dir}/paup4a169_ubuntu64
        sudo mv ${temp_dir}/paup4a169_ubuntu64 /usr/local/bin/paup
        echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
    - name: Install coverage dependencies
      run: |
        python3 -m pip install pytest
        python3 -m pip install pytest-cov
    - name: Generate coverage report
      run: |
        python3 -m pytest tests/unittests --cov=tests --cov-report=xml
    - uses: codecov/codecov-action@v4
      with:
        token: ae13d715-bae4-4e6d-9dce-f47e7d7c7c01
        flags: unittests # optional
        fail_ci_if_error: true # optional (default = false)
        verbose: true # optional (default = false)
  packaging-bdist:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Install build tools
        run: python3 -m pip install pip setuptools wheel --upgrade
      - name: Build bdist
        run: |
          python3 setup.py bdist_wheel
          tree dist
      - 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 {} \;
          python3 -c "import dendropy; print(dendropy.__version__)"
  packaging-sdist:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Install build tools
        run: python3 -m pip install pip setuptools wheel --upgrade
      - name: Build sdist
        run: |
          python3 setup.py sdist
          tree dist
      - name: Install from sdist
        run: python3 -m pip install dist/*.tar.gz
      - name: Test install
        run: |
          find . -type f -name '*.py' -exec rm {} \;
          python3 -c "import dendropy; print(dendropy.__version__)"
  packaging-source:
    runs-on: ubuntu-latest
    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: |
          find . -type f -name '*.py' -exec rm {} \;
          python3 -c "import dendropy; print(dendropy.__version__)"
  docs:
    permissions:
      contents: write
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v2
      - name: Set up Python 3.9
        uses: actions/setup-python@v4
        continue-on-error: true
        with:
          python-version: 3.9
      - name: Upgrade pip
        run: python3 -m pip install pip --upgrade
      - name: Install from source
        run: python3 -m pip install .
      - name: Install documentation build dependencies
        run: python3 -m pip install -r docs/requirements.txt
      - name: Build documentation
        run: make -C docs html
      - name: Deploy docs
        if: github.ref == 'refs/heads/main'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: docs/build/html # The folder the action should deploy.
        # uses: jsmrcaga/action-netlify-deploy@v2.0.0
        # with:
        #   NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
        #   NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
        #   NETLIFY_DEPLOY_MESSAGE: "Prod deploy v${{ github.ref }}"
        #   NETLIFY_DEPLOY_TO_PROD: true
        #   install_command: "echo Skipping installing the dependencies"
        #   build_command: "echo Skipping building the web files"
        #   build_directory: docs/build/html
  deploy:
    runs-on: ubuntu-latest
    if: startsWith(github.ref, 'refs/tags/v')
    needs:
      - examples
      - lint
      - tests
    steps:
    - uses: actions/checkout@v1
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install setuptools wheel twine
    - run: python setup.py sdist bdist_wheel
    - name: Publish package
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}
  paper:
    runs-on: ubuntu-latest
    name: Paper Draft
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - 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