genomepy/.github/workflows/ci-cd.yml at 81304cd2d7873ccaebdee9da251e8376eef4c208 · vanheeringen-lab/genomepy · GitHub

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name: CI/CD
on:
  push:
    branches: [ "master", "develop" ]
  pull_request:
    branches: [ "master", "develop" ]
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:
  ci_pip:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:

    - name: Cleanup build folder 🧹
      run: |
        ls -la ./
        rm -rf ./* || true
        rm -rf ./.??* || true
        ls -la ./

    - name: Setup Python 3.12 🐍
      uses: actions/setup-python@v5
      with:
        python-version: 3.12

    - name: Setup backend 🏗️
      run: |
        pip install uv
        uv pip install --system hatch pytest pytest-rerunfailures autoflake==1.7 isort==6.0 black==25.1

    - name: Checkout 🛎️
      uses: actions/checkout@v4

    # Builds a wheel needed for the CD
    - name: Build wheel 🎡
      run: hatch build -t wheel

    # Store the wheel in GitHub Actions
    - name: Upload artifact ❄️
      uses: actions/upload-artifact@v4
      with:
        name: genomepy_wheel
        path: dist/

    # Test if the created wheel can be installed
    - name: Install 🛠️
      run: uv pip install --system dist/*.whl --force-reinstall

    - name: Unit tests 📜
      run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py

    - name: Integration tests 📚
      run: |
        genomepy --help
        genomepy annotation --help
        genomepy install --help
        genomepy search --help

  ci_conda:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:

    - name: Cleanup build folder 🧹
      run: |
        ls -la ./
        rm -rf ./* || true
        rm -rf ./.??* || true
        ls -la ./

    - name: Checkout 🛎️
      uses: actions/checkout@v4

    - name: Setup backend 🏗️
      uses: conda-incubator/setup-miniconda@v3
      with:
        environment-file: environment.yml
        miniforge-version: latest

    - name: Install 🛠️
      run: pip install . --no-deps --ignore-installed

    - name: Unit tests 📜
      run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py

    - name: Integration tests 📚
      run: |
        genomepy --help
        genomepy annotation --help
        genomepy install --help
        genomepy search --help

  cd:
    needs: ci_pip
    runs-on: ubuntu-latest
    # Only run this job if new work is pushed to "master"
    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
#    # Only run this job on a tagged commit
#    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')

    steps:

    - name: Cleanup build folder 🧹
      run: |
        ls -la ./
        rm -rf ./* || true
        rm -rf ./.??* || true
        ls -la ./

    - name: Setup Python 3.12 🐍
      uses: actions/setup-python@v5
      with:
        python-version: 3.12

    - run: mkdir -p dist

    - name: Download artifact ❄️
      uses: actions/download-artifact@v4
      with:
        name: genomepy_wheel
        path: dist/

    - name: Publish to PyPI 🚀
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}