bactrack/.github/workflows/python-package.yml at main · yyang35/bactrack · GitHub

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name: Python package

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11"]

    steps:
    - uses: actions/checkout@v3

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        python-version: ${{ matrix.python-version }}
        environment-file: .pre-commit-config.yaml
        activate-environment: bactrack
        auto-activate-base: false

    - name: Install System Dependencies
      run: sudo apt-get update && sudo apt-get install -y libopencv-dev libgl1-mesa-glx libegl1-mesa libgtk2.0-dev libgtk-3-dev libatlas-base-dev gfortran python3-pyqt5

    - name: Run Tests
      run: |
        source /usr/share/miniconda/etc/profile.d/conda.sh
        conda activate bactrack
        conda list
        pytest --cov=bactrack --cov-report xml:coverage.xml

    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v2
      with:
        token: 7ae0e45d-e732-4768-9c09-ec1cb81e712e
        file: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
        fail_ci_if_error: false
        verbose: true