Update references for LuciPHOr publications #29
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| # 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 3.11 | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest pytest-cov click | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| # Install the package in development mode | |
| pip install -e . | |
| - name: Install 7-Zip | |
| run: sudo apt-get update && sudo apt-get install -y p7zip-full | |
| - name: Extract test data files | |
| run: | | |
| # Extract compressed mzML file from zip archives | |
| cd data | |
| if [ -f 1.zip ]; then | |
| echo "Extracting 1.mzML from split zip archives..." | |
| ls -lh 1.* | |
| 7z x 1.zip | |
| ls -lh 1.mzML | |
| echo "Extraction complete" | |
| else | |
| echo "Warning: 1.zip not found in data directory" | |
| ls -la | |
| fi | |
| cd .. | |
| - name: Verify test data files | |
| run: | | |
| # Verify that required test data files exist | |
| if [ ! -f data/1_consensus_fdr_filter_pep.idXML ]; then | |
| echo "Error: idXML file not found" | |
| exit 1 | |
| fi | |
| if [ ! -f data/1.mzML ]; then | |
| echo "Error: mzML file not found" | |
| exit 1 | |
| fi | |
| echo "Test data files verified:" | |
| ls -lh data/1_consensus_fdr_filter_pep.idXML | |
| ls -lh data/1.mzML | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 onsite/ --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=__pycache__,.git,build,dist | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 onsite/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=__pycache__,.git,build,dist | |
| - name: Test package imports | |
| run: | | |
| # Test that the package and all modules can be imported | |
| python -c "import onsite; print('onsite package imported successfully')" | |
| python -c "from onsite import AScore; print('AScore imported successfully')" | |
| python -c "from onsite import calculate_phospho_localization_compomics_style; print('PhosphoRS imported successfully')" | |
| python -c "from onsite.lucxor import cli; print('LucXor CLI imported successfully')" | |
| - name: Test CLI commands availability | |
| run: | | |
| # Test that CLI commands are available | |
| onsite --help | |
| ascore --help || python -m onsite.ascore.cli --help | |
| phosphors --help || python -m onsite.phosphors.cli --help | |
| lucxor --help || python -m onsite.lucxor.cli --help | |
| - name: Run unit tests with coverage | |
| run: | | |
| # Run all unit tests with pytest and generate coverage report | |
| pytest tests/ -v --tb=short --color=yes --cov=onsite --cov-report=xml --cov-report=term | |
| - name: Test AScore with real data | |
| run: | | |
| # Test AScore algorithm with real data | |
| python -m onsite.ascore.cli \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_ascore_output.idXML \ | |
| --fragment-mass-tolerance 0.05 \ | |
| --fragment-mass-unit Da \ | |
| --threads 1 \ | |
| --add-decoys | |
| # Verify output file was created | |
| if [ -f test_ascore_output.idXML ]; then | |
| echo "AScore output file created successfully" | |
| ls -lh test_ascore_output.idXML | |
| else | |
| echo "Warning: AScore output file not created (may be expected if no phosphorylated peptides)" | |
| fi | |
| - name: Test PhosphoRS with real data | |
| run: | | |
| # Test PhosphoRS algorithm with real data | |
| python -m onsite.phosphors.cli \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_phosphors_output.idXML \ | |
| --fragment-mass-tolerance 0.05 \ | |
| --fragment-mass-unit Da \ | |
| --threads 1 \ | |
| --add-decoys | |
| # Verify output file was created | |
| if [ -f test_phosphors_output.idXML ]; then | |
| echo "PhosphoRS output file created successfully" | |
| ls -lh test_phosphors_output.idXML | |
| else | |
| echo "Warning: PhosphoRS output file not created (may be expected if no phosphorylated peptides)" | |
| fi | |
| - name: Test LucXor with real data | |
| run: | | |
| # Test LucXor algorithm with real data | |
| python -m onsite.lucxor.cli \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_lucxor_output.idXML \ | |
| --fragment-method HCD \ | |
| --fragment-mass-tolerance 0.5 \ | |
| --fragment-error-units Da \ | |
| --threads 1 \ | |
| --min-num-psms-model 50 | |
| # Verify output file was created | |
| if [ -f test_lucxor_output.idXML ]; then | |
| echo "LucXor output file created successfully" | |
| ls -lh test_lucxor_output.idXML | |
| else | |
| echo "Warning: LucXor output file not created (may be expected if no phosphorylated peptides)" | |
| fi | |
| - name: Test unified CLI with real data | |
| run: | | |
| # Test unified onsite CLI command | |
| onsite ascore \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_unified_ascore.idXML \ | |
| --fragment-mass-tolerance 0.05 \ | |
| --fragment-mass-unit Da \ | |
| --threads 1 \ | |
| --add-decoys | |
| onsite phosphors \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_unified_phosphors.idXML \ | |
| --fragment-mass-tolerance 0.05 \ | |
| --fragment-mass-unit Da \ | |
| --threads 1 \ | |
| --add-decoys | |
| onsite lucxor \ | |
| -in data/1.mzML \ | |
| -id data/1_consensus_fdr_filter_pep.idXML \ | |
| -out test_unified_lucxor.idXML \ | |
| --fragment-method HCD \ | |
| --fragment-mass-tolerance 0.5 \ | |
| --threads 1 \ | |
| --min-num-psms-model 50 | |
| - name: Upload test outputs as artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-outputs | |
| path: | | |
| test_*.idXML | |
| retention-days: 7 | |
| - name: Upload coverage to artifacts | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: coverage.xml | |
| retention-days: 7 | |