Draft release 0.0.1 #22
Workflow file for this run
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: [release] | |
| 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: Install Pandas | |
| run: | | |
| conda activate vm-NAP | |
| - name: Install Submodule Dependencies | |
| run: | | |
| conda env update --name vm-NAP --file gnps_postprocessing/environment.yml | |
| - 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 | |