main.yml

name: vm-NAP Processing Tests

on: [push, pull_request]

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v2
      with:
        submodules: 'recursive'
      
    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        environment-file: environment.yml
        activate-environment: vm-NAP
        auto-activate-base: false

    - name: Check Python Version
      run: python --version

    - name: List installed Conda packages
      run: conda list
      
    - name: Check Current Working Directory and Path
      run: |
        echo "Current directory: $(pwd)"
        echo "Python Path: $PYTHONPATH"
        python -c "import sys; print(sys.path)"

    - name: Check if gnps_postprocessing is present
      run: |
        if [ -d "gnps_postprocessing" ]; then
          echo "gnps_postprocessing directory exists"
          ls -l gnps_postprocessing/
        else
          echo "gnps_postprocessing directory does not exist"
        fi
    - name: List installed Conda packages
      run: conda list
      
    - name: Run vm-NAP Processing Tests
      run: |
        python src/vm-NAP_processing.py 
        python src/vm-NAP_processing.py --help
        python src/vm-NAP_processing.py --debug --run_biotransformer --type_of_biotransformation='hgut'
        python src/vm-NAP_processing.py --debug --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer
        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
        python src/vm-NAP_processing.py --debug --job_id False --sirius_input_file 'input/compound_identifications.tsv'
        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --job_id='bbee697a63b1400ea585410fafc95723' --sirius_input_file 'input/compound_identifications.tsv'
    - name: Test with Extra Compounds and Custom Biotransformation Mode
      run: |
        python src/vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --debug
    - name: Test with GNPS Data, SyGMa, and BioTransformer
      run: |
        python src/vm-NAP_processing.py --debug --run_sygma --max_compounds_debug=10 --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --run_sygma --run_biotransformer --type_of_biotransformation='hgut' --sirius_input_file 'input/compound_identifications.tsv'
    - name: Test with Full GNPS Parameters and Debug Mode
      run: |
        python src/vm-NAP_processing.py --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='neg' --max_ppm_error=15 --min_cosine=0.7 --shared_peaks=4 --max_spec_charge=3 --debug --sirius_input_file 'input/compound_identifications.tsv'
    - name: Test with Extra Compounds, Custom Biotransformation, and SyGMa
      run: |
        python src/vm-NAP_processing.py --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer --mode='-k pred -b allHuman -s 2 -cm 3' --run_sygma --phase_1_cycle=2 --phase_2_cycle=1 --top_sygma_candidates=5 --debug
    - name: Test with Metadata Filtering and SIRIUS Parameters
      run: |
        python src/vm-NAP_processing.py --compound_name_to_keep 'a' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.8 --confidence_score=0.2 --db_links='KEGG' --debug
    - name: Test with Planar Structure and BioTransformer Standard Mode
      run: |
        python src/vm-NAP_processing.py --use_planar_structure_boolean=True --run_biotransformer --mode='standard' --type_of_biotransformation='hgut' --number_of_steps=2 --debug
    - name: Test with All Parameters Combined
      run: |
        python src/vm-NAP_processing.py --debug --max_compounds_debug=20 --run_sygma --job_id='bbee697a63b1400ea585410fafc95723' --ionisation_mode='pos' --max_ppm_error=10 --min_cosine=0.6 --shared_peaks=3 --max_spec_charge=2 --compound_name_to_keep 'a' --extra_compounds_table_file='input/extra_compounds.tsv' --sirius_input_file 'input/compound_identifications.tsv' --zodiac_score=0.7 --confidence_score=0.1 --db_links='HMDB' --use_planar_structure_boolean=True --run_sygma --phase_1_cycle=1 --phase_2_cycle=1 --top_sygma_candidates=10 --run_biotransformer --mode='-k pred -b superbio -a' --type_of_biotransformation='allHuman' --number_of_steps=1 > test_output.txt

    - name: Compare Output with Baseline
      run: |
        diff test_output.txt test/baseline_output.txt

    - name: Check for Differences
      run: |
        if ! diff test_output.txt test/baseline_output.txt; then
          echo "Differences found in the output compared to the baseline."
          exit 1
        fi