python.yml

name: fetal_brain_utils 

# on: [push, pull_request]
on:
  # trigger on pushes and PRs to main
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  build:

    runs-on: ubuntu-latest 
    steps:
    - uses: actions/checkout@v3
    - name: Checkout submodules
      shell: bash
      run: |
        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
        git submodule sync --recursive
        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
    - name: Set up Python 
      uses: actions/setup-python@v4
      with:
        python-version: 3.9 
    - name: Install dependencies and build package
      run: |
        python -m pip install --upgrade pip
        python -m pip install -e .
    - name: Lint with flake8
      run: |
        pip install flake8
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=B,C,E,F,W,T4,B9 --show-source --statistics --max-complexity=18 --max-line-length=100 --ignore=E203,E266,E501,W503,F403,F401,C901
    - name: Format with black
      run: |
        pip install black
        black *.py -l 100
        black fetal_brain_utils/*.py -l 100
        black tests/*.py -l 100
    - name: Test with pytest
      run: |
        pip install -U pytest
        python -m pytest