python-app.yml

name: Run tests

on:
  push:
    branches: [ master ]
    paths: ['**.py', '**.yaml']
  pull_request:
    branches: [ master ]
    paths: ['**.py', '**.yaml']

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.11
      uses: actions/setup-python@v2
      with:
        python-version: 3.11
#    - uses: actions/cache@v2
#      with:
#        path: ~/.cache/pip
#        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
#        restore-keys: |
#          ${{ runner.os }}-pip-
    - name: Install Python dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest 
        pip install -r requirements.txt -r requirements_TCRdist.txt -r requirements_DeepRC.txt -r requirements_generative_models.txt
    - name: Install CompAIRR
      run: |
        git clone https://github.com/uio-bmi/compairr.git
        make -C compairr
#    - 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 with pytest
      env:
        PYTHONFAULTHANDLER: 1 
      run: python -m pytest