Update main.yml #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: vm-NAP Processing Tests | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: vm-NAP | |
| auto-activate-base: false | |
| - name: Run vm-NAP Processing Tests | |
| run: | | |
| python vm-NAP_processing.py | |
| python vm-NAP_processing.py --help | |
| python vm-NAP_processing.py --debug --run_biotransformer --type_of_biotransformation='hgut' | |
| python vm-NAP_processing.py --debug --extra_compounds_table_file='input/extra_compounds-UTF8.tsv' --run_biotransformer | |
| python 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 vm-NAP_processing.py --debug --job_id False --sirius_input_file 'input/compound_identifications.tsv' | |
| python 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 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 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 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 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 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 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 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 | |