test.yml

# This worklflow will perform unit test and check linting.
# - Test linting with flake8
# - Test the code with pytest.
# 
# Maintainers:
#   - name: Nisha Sharma
#   - email: nisha.sharma@uni-jena.de

name: test

on:
  workflow_call:

jobs:
  test:
    runs-on: ubuntu-latest
    services:
        postgres:
            image: postgres:latest
            env:
                POSTGRES_USER: postgres
                POSTGRES_PASSWORD: postgres
                POSTGRES_DB: nmr_predict
                POSTGRES_SERVER: pgsql
            ports:
                - 5432:5432
            options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
    strategy:
      matrix:
        python-version: ["3.10"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: 'Create env file'
      run: |
        touch .env
        echo POSTGRES_USER="postgres" >> .env
        echo POSTGRES_PASSWORD="password" >> .env
        echo POSTGRES_SERVER="pgsql" >> .env
        echo POSTGRES_PORT=5432 >> .env
        echo POSTGRES_DB=nmr_predict >> .env
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip3 install --upgrade setuptools pip
        pip3 install --no-cache-dir -r requirements.txt
        pip3 install rdkit
        python3 -m pip uninstall -y imantics
        pip3 install imantics==0.1.12
        pip3 install openbabel-wheel
        git clone "https://github.com/rinikerlab/lightweight-registration.git" lwreg
        chmod +x lwreg
        pip3 install --editable ./lwreg/.
        pip install flake8 pytest
    - name: Analysing the code with pylint
      run: |
        flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files 'app/*.py') .
    - name: Run test
      run: |
        python3 -m pytest -p no:warnings --ignore=lwreg/lwreg/test-cli.py --ignore=lwreg/lwreg/test_lwreg.py --ignore=lwreg/lwreg/test_dbutils.py