ci.yml

name: CI

# Avoid running multiple jobs for the same branch
# in case of updates.
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

# Run on pull requests and push events to master only
on:
  pull_request:
    branches:
      - master
  push:
    branches:
      - master

permissions:
  contents: read

jobs:
  # Style Checking: Linux and Python version only.
  style:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    # Check for changes only on files changed by the PR/push
    - uses: tj-actions/changed-files@v45
      id: changed-files

    # Cache CI packages
    - uses: actions/cache@v4
      id: cache-precommit
      with:
        path: ~/.cache/pre-commit
        key: ${{ runner.os }}-precommit-hooks-v2-${{ hashFiles('**/.pre-commit-config.yaml') }}

    - name: Setup Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.9

    - name: Installing pre-commit
      run: |
        python -m pip install pre-commit

    - name: Installing pre-commit hooks (cached)
      if: steps.cache-precommit.outputs.cache-hit != 'true'
      run: |
        pre-commit install --install-hooks

    - name: Run style checking via pre-commit
      run: |
        pre-commit run --files ${{ steps.changed-files.outputs.all_changed_files }}

  # Cache pip & python dependencies for Linux runner
  # since it is used in most actions.
  # Adapted from: https://medium.com/ai2-blog/python-caching-in-github-actions-e9452698e98d
  linux_prep:
    needs: [style]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.11", "3.12"]

    steps:
    - uses: actions/checkout@v4

    - name: Setup Python
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - uses: actions/cache@v4
      id: cache-pip
      with:
        path: ${{ env.pythonLocation }}
        key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Install Python dependencies
      if: steps.cache-pip.outputs.cache-hit != 'true'
      run: |
        python -m pip install --upgrade --upgrade-strategy eager -r ci-dependencies.txt

  # Try building package:
  # - tarball on Linux
  # - wheels on all supported OSes and Linux, MacOS, and Windows
  build:
    needs: [style]
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.9

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Package tarball
      run: |
        python setup.py sdist --formats=gztar,zip

  build_wheels:
    needs: [style]
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-2019]
        python-version: ["3.9", "3.10", "3.11", "3.12"]

    runs-on: ${{ matrix.os }}

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Build wheel
      run: |
        python setup.py bdist_wheel

    # - name: Archive wheels
    #   uses: actions/upload-artifact@v2
    #   with:
    #     name: biopython_wheels
    #     path: |
    #       dist/*whl
    #
    # - name: Fetch archived wheels from previous jobs
    #   uses: actions/download-artifact@v2
    #   with:
    #     name: biopython_wheels
    #     path: dist


  # Run tests in parallel across Linux, MacOS, and Windows
  # hosts (thus the three steps and not the single matrix entry).
  #
  # Linux tests install all the dev dependencies, while MacOS and Windows
  # tests install only numpy (lightweight version).
  # NOTE: PyPy only runs on Linux with minimal dependencies because it's running slowly.
  #
  # Tests trigger only of the style and build steps succeed.
  #

  # Linux is where the thorough tests run. Install all dependencies and run all (offline) tests.
  test_linux:
    timeout-minutes: 15
    needs: [style, build, build_wheels, linux_prep]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.11", "3.12"]

    steps:

    # Start MySQL server: required for some tests.
    - run: |
        sudo /etc/init.d/mysql start

    - uses: actions/checkout@v4

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    # Retrieve cache to speed things up
    - uses: actions/cache@v4
      id: cache-pip
      with:
        path: ${{ env.pythonLocation }}
        key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}

    - name: Install dependencies
      if: steps.cache-pip.outputs.cache-hit != 'true'
      run: |
          python -m pip install --upgrade --upgrade-strategy eager -r ci-dependencies.txt

    - name: Debug Info
      run: |
        python -m pip list

    - name: Install from source
      run: |
        CC="gcc -fsanitize=address -fsanitize=undefined -g" python -m pip install .

    - name: Run test suite
      run: |
        cd Tests
        PYTHONMALLOC=debug LD_PRELOAD="$(realpath "$(gcc -print-file-name=libasan.so)") $(realpath "$(gcc -print-file-name=libstdc++.so)")" ASAN_OPTIONS="detect_leaks=0" python run_tests.py --offline
      shell: bash

  test_macos:
    timeout-minutes: 15
    needs: [style, build, build_wheels]
    runs-on: macos-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.12"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Install minimal Python dependencies
      run: |
        python -m pip install "numpy!=2.1.0"

    - name: Debug Info
      run: |
        python -m pip list

    - name: Install from source
      run: |
        python -m pip install .

    - name: Run test suite
      run: |
        cd Tests
        python run_tests.py --offline

  test_windows:
    timeout-minutes: 15
    needs: [style, build, build_wheels]
    runs-on: windows-2019
    strategy:
      matrix:
        # TODO - Try Python 3.11 again, was Python 3.11.0 was
        # failing when trying to delete SQlite databases.
        python-version: ["3.9", "3.10", "3.12"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Install minimal Python dependencies
      run: |
        python -m pip install "numpy!=2.1.0"

    - name: Debug Info
      run: |
        python -m pip list

    - name: Install from source
      run: |
        python -m pip install .

    - name: Run test suite
      run: |
        cd Tests
        python run_tests.py --offline

  test_pypy:
    timeout-minutes: 20  # a little more time
    needs: [style, build, build_wheels]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [pypy-3.9]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Install minimal Python dependencies
      run: |
        python -m pip install "numpy!=2.1.0"

    - name: Debug Info
      run: |
        python -m pip list

    - name: Install from source
      run: |
        python -m pip install .

    - name: Run test suite
      run: |
        cd Tests
        python run_tests.py --offline

  # Flag step
  check_tests:
    needs: [test_linux, test_macos, test_windows]
    runs-on: ubuntu-latest
    steps:
      - run: echo All tests passed.

  # Check and build (API) documentation if everything passes.
  docs:
    needs: [check_tests]
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.9

    - uses: actions/cache@v4
      id: cache-pip
      with:
        path: ${{ env.pythonLocation }}
        key: ${{runner.os}}-${{ env.pythonLocation }}-${{ matrix.python-version }}-v2-${{ hashFiles('setup.py') }}-${{ hashFiles('**/ci-dependencies.txt') }}

    - name: Install Python packaging tools
      run: |
        python -m pip install --upgrade pip setuptools wheel

    - name: Install dependencies
      if: steps.cache-pip.outputs.cache-hit != 'true'
      run: |
        python -m pip install --upgrade --upgrade-strategy eager -r .circleci/requirements-sphinx.txt

    - name: Debug Info
      run: |
        python -m pip list

    - name: Install from source
      run: |
        python -m pip install .

    - name: Make documentation
      run: |
        make -C Doc html
      shell: bash

  cleanup_wheels:
    if: always()
    needs: [build_wheels]
    runs-on: ubuntu-latest
    steps:
      - uses: geekyeggo/delete-artifact@v5
        with:
          name: biopython_wheels