main.yml

name: main
on:
  push:
    branches:
      - master
  pull_request:
    types:
      - opened
      - reopened
      - synchronize

jobs:
  build-and-test:
    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3


    - name: git setup
      # Set up git and export env vars to be used in later steps.
      #   Note the unconventional mechanism for exporting envs by appending to
      #   $GITHUB_ENV.
      id: git-setup
      run: |
        git config --global user.email "action@github.com"
        git config --global user.name "GitHub Action"
        echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
        echo "WORKDIR=$(pwd)" >> $GITHUB_ENV



    - name: cythonize and pip
      # Convert .pyx files to .cpp and package into sdist tarball.
      #
      # This only requires Cython, no other dependencies.
      run: |
        eval "$(conda shell.bash hook)"
        conda create -p ./cython-env -y cython python=${{ matrix.python-version }} numpy
        conda activate ./cython-env
        python setup.py clean cythonize sdist
        (cd dist && pip install pybedtools-*.tar.gz && cd $TMPDIR && python -c 'import pybedtools; print(pybedtools.__file__)')
        conda deactivate


    - name: conda env and install locally
      # Set up conda and install pybedtools into that env
      #
      # NOTE: Tests require *.so files that are created by installing the
      # package, otherwise we get:
      #
      #   ModuleNotFoundError: No module named 'pybedtools.cbedtools'
      #
      # We could install from the source repo dir. However this may inadvertently
      # rely on files that are in the source repo but not in the actual sdist
      # package. So we extract the sdist tarball to another location and install
      # from there.
      #
      # Tests below will operate in this newly-installed directory.
      run: |
        eval "$(conda shell.bash hook)"
        conda install mamba python=${{ matrix.python-version }} -y --channel conda-forge

        # Only install non-python dependencies (like bedtools & ucsc tools);
        # let pip take care of the rest.
        grep -Ev "genomepy|matplotlib" optional-requirements.txt > optional-requirements-conda.txt
        grep -E "genomepy|matplotlib" optional-requirements.txt > optional-requirements-python.txt
        mamba create -y -p ./test-env \
          --channel conda-forge \
          --channel bioconda \
          bedtools \
          python=${{ matrix.python-version }} \
          --file optional-requirements-conda.txt

        conda activate ./test-env
        pip install -r test-requirements.txt -r optional-requirements-python.txt

        mkdir -p /tmp/pybedtools-uncompressed
        cd /tmp/pybedtools-uncompressed
        tar -xf $WORKDIR/dist/pybedtools-*.tar.gz
        pip install -e /tmp/pybedtools-uncompressed/pybedtools-*

        # Trying import in the same directory will complain that cbedtools
        # can't be imported
        (cd / && python -c 'import pybedtools; print(pybedtools.__file__)')

    - name: tests
      # Run pytest and sphinx doctests
      run: |
        cd $WORKDIR
        eval "$(conda shell.bash hook)"
        conda activate ./test-env

        # Extract the package tarball built above, and use that for running the tests.
        cd /tmp/pybedtools-uncompressed/pybedtools-*
        pytest -v --doctest-modules
        pytest -v pybedtools/test/genomepy_integration.py
        cp -r $WORKDIR/docs .
        (cd docs && make clean doctest)


    - name: build-docs
      if: ${{ (matrix.python-version == 3.10) }}
      # Build docs and commit to gh-pages branch. Note that no push happens
      # unless we're on the master branch
      run: |
        if [ ${{ matrix.python-version }} != "3.11" ]; then
          eval "$(conda shell.bash hook)"
          conda activate ./test-env

          # Move to extracted tarball dir, see above notes
          cd /tmp/pybedtools-uncompressed/pybedtools-*
          (cd docs && make html)

          git clone \
            --single-branch \
            --branch gh-pages "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" \
            /tmp/docs

          rm -rf /tmp/docs/*
          cp -r docs/build/html/* /tmp/docs
          touch /tmp/docs/.nojekyll
          cd /tmp/docs
          git add .
          if git diff --cached --quiet; then
            echo "no changes, nothing to commit"
          else
            git commit -m 'update docs'
          fi
          cd $WORKDIR
        fi


    - name: docs artifact
      # Upload built docs as an artifact for inspection, even on PRs
      uses: actions/upload-artifact@v3
      with:
        name: docs
        path: /tmp/docs


    - name: push docs to gh-pages branch
      # Push docs to gh-pages if this test is running on master branch
      if: ${{ (github.ref == 'refs/heads/master') && (matrix.python-version == 3.8) }}
      run: |
        cd /tmp/docs
        git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" gh-pages
        cd $WORKDIR