IGF-HPC-Airflow/.github/workflows/python-app.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python application

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.7
      uses: actions/setup-python@v2
      with:
        python-version: 3.7
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - 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: Checkout other repo
      uses: actions/checkout@v2
      with:
        repository: imperial-genomics-facility/data-management-python
        ref: cellranger_v6
        path: data-management-python
    - name: Test with pytest
      run: |
        ls $GITHUB_WORKSPACE
        echo ${{ env.GITHUB_WORKSPACE }}
        echo $PYTHONPATH
        echo ${{ env.PYTHONPATH }}
        pytest test/
      env:
        GITHUB_WORKSPACE: $GITHUB_WORKSPACE
        PYTHONPATH: $PYTHONPATH
        PYTHONPATH: "${{ env.GITHUB_WORKSPACE }}/data-management-python:${{ env.PYTHONPATH }}"
        AIRFLOW__CORE__DAGBAG_IMPORT_TIMEOUT: 20
        AIRFLOW__SECRETS__BACKEND: airflow.secrets.local_filesystem.LocalFilesystemBackend
        AIRFLOW__SECRETS__BACKEND_KWARGS: '{"variables_file_path":"airflow_var/var.json","connections_file_path":"airflow_var/conn.json"}'