tests.yml

name: Run unit tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8", "3.12"]
    steps:
    - uses: actions/checkout@v2
    - uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install .[rest_api,tests]
    - name: Run regular unit tests
      run: |
        pytest protmapper/tests --cov=protmapper
    - name: Run CLI smoketests
      run: |
        protmapper protmapper/tests/cli_input.csv output.csv --no_methionine_offset --no_orthology_mapping --no_isoform_mapping
        protmapper protmapper/tests/cli_input_peptide.csv output.csv --peptide