Update main.yml #18
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| 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 | |