code_check.yml

# This is a template for a CI/CD workflow for your own Python package.
#
# Copy this template in to your repository and adapt it according to
# the TODOs. All relevant parts are marked with a `TODO` in the following.

name: code_check

env:
  # TODO for the user of this template: adapt the following variables to the names in your project.
  #
  # The template is designed for developing a Python package in the form:
  # project_template/
  # ├── package_src/
  # │   └── __init__.py
  # ├── tests/
  # │   └── __init__.py
  # The template can't know the name of the `package_src` and `tests` directories.
  # So, you have to add them here:

  # set the name of your Python package directory
  PY_PACKAGE_DIR: package_src

  # set the name of your unit test directory
  PY_UNIT_TEST_DIR: tests

# Controls when the workflow will run
on:
  # Triggers the workflow on push or pull request events but only for the "main" branch
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

jobs:

  pylint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.11"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        # note that pylint needs your project's dependencies to be installed
        pip install -r requirements.txt 
        pip install pylint
    - name: Analysing the code with pylint
      run: |
        pylint -d C0301,R0913,W1202 $(git ls-files '*.py') --ignored-modules "rdkit"
        
  pydocstyle:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.11"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pydocstyle
    - name: Analysing the code with pydocstyle
      run: |
        pydocstyle .
        
  black:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.11"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install black[jupyter]
    - name: Analysing the code with black
      run: |
        black --check .

  isort:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install isort
      - name: Analysing the code with isort
        run: |
          isort --profile black --check-only .

  test_basis:
    needs:
        - pylint
        - pydocstyle
        - black
        - isort
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install package
        run: |
          python -m pip install --upgrade pip
          pip install coverage
          pip install .
      - name: Run unit-tests
        run: |
          # TODO for the user of this template:
          #   You might have to adapt the call running the test coverage to fit your test backend.
          #   The default unittest framework is `unittest` from Python's standard library.
          #   For example, if you use `pytest` you need to comment/uncomment the lines below.
          #   For other backends and details see https://coverage.readthedocs.io/en/latest/index.html
          
          # Run test suite in the tests directory. 
          coverage run --source=$PY_PACKAGE_DIR,$PY_UNIT_TEST_DIR -m unittest discover $PY_UNIT_TEST_DIR
          # uncomment if you use pytest as test backend
          #coverage run --source=$PY_PACKAGE_DIR,$PY_UNIT_TEST_DIR -m pytest discover $PY_UNIT_TEST_DIR 
          # Create a coverage report. Fail if the coverage is below 80%.
          coverage report --fail-under=80