main.yml

name: build

on:
  push:
    branches: [ main ]

jobs:
  build-linux:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python 3.10
      uses: actions/setup-python@v4
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y libcurl4-openssl-dev
        python -m pip install --upgrade pip
        pip install wheel
        pip install pytest-cov flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph .
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test and add coverage
      run: |
        pytest --cov --disable-warnings decoupler
    - name: Upload coverage reports to Codecov
      run: |
        curl -Os https://uploader.codecov.io/latest/linux/codecov
        chmod +x codecov
        ./codecov -t ${CODECOV_TOKEN}
        
  build-macOS:

    runs-on: macOS-latest

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python 3.10
      uses: actions/setup-python@v4
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        brew install openssl
        export LDFLAGS="-L/usr/local/opt/openssl@3/lib"
        export CPPFLAGS="-I/usr/local/opt/openssl@3/include"
        export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig"
        python -m pip install --upgrade pip
        pip install wheel
        pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil igraph .
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test
      run: |
        pytest --disable-warnings .