python-app.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python application

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

permissions:
  contents: read

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.10
      uses: actions/setup-python@v3
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        python setup.py install
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test with pytest
      run: |
        pytest
    - name: Download test data
      run: |
        wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML
        wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML
    - name: Test percolator ms2rescore
      run: |
        quantmsutilsc ms2rescore -p TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML -s TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML -n 2 -pipm "HCD2021" -fg "ms2pip,deeplc" --id_decoy_pattern "^rev" -t 0.05
    - name: Test makapot ms2rescore
      run: |
        quantmsutilsc ms2rescore -p TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML -s TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML -n 2 -pipm "HCD2021" -fg "ms2pip,deeplc" --id_decoy_pattern "^rev" -t 0.05 --rescoring_engine "mokapot"