ci_tools.yml

name: Uni-Dock Tools CI/CD
on:
  push:
    branches: [ fix_unidock_ut ]
  pull_request:
    branches: [ main ]

jobs:
  flake8:
    continue-on-error: true
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python  ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8

    - name: Run flake8 formating
      run: |
        flake8 unidock_tools/unidock_tools --exit-zero

  pylint:
    continue-on-error: true
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python  ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pylint

    - name: Run pylint formating
      run: |
        pylint unidock_tools/unidock_tools --exit-zero

  mypy:
    continue-on-error: true
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python  ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install mypy

    - name: Run mypy check
      id: mypy_check
      run: |
        mypy unidock_tools/unidock_tools --ignore-missing-imports

  ut:
    if: ${{ always() }}
    needs: [flake8, pylint]
    runs-on: nvidia
    strategy:
      matrix:
        python-version: ["3.9"]
    container: 
      image: docker.io/dptechnology/unidock:latest
      options: --gpus all
    steps:
    - name: checkout repo
      uses: actions/checkout@v3

    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        miniconda-version: "latest"
        python-version: ${{ matrix.python-version }}

    - name: install dependency
      run: |
        conda create -n mgltools mgltools -c bioconda -y
        conda install -n test -c conda-forge -y openbabel
        conda run -n test pip install --upgrade pip
        conda run -n test pip install pytest

    - name: install package
      working-directory: ./unidock_tools
      run: |
        export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
        python setup.py install

    - name: perform unit-test
      run: |
        export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
        pytest unidock_tools/tests/ut -v