Bug fixing #9
Bug fixing #9
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WalkthroughThis pull request updates the version number of the package from "0.0.3" to "0.0.4" in both Changes
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Actionable comments posted: 1
🔭 Outside diff range comments (1)
quantmsrescore/ms2rescore.py (1)
Line range hint
517-524: Fix inconsistent error handling for mokapotThe error message refers to "moakapot" (with an extra 'a'), which is inconsistent with the CLI option that uses "mokapot".
- if rescoring_engine == "moakapot": + if rescoring_engine == "mokapot": logging.warning( "Mokapot rescoring engine is not supported in this version. Please use Percolator." )
🧹 Nitpick comments (1)
quantmsrescore/ms2rescore.py (1)
266-268: Fix grammatical error in warning messageThe warning message has incorrect grammar.
- f"{spectrum.getNativeID()} spectra don't have spectra information!" + f"{spectrum.getNativeID()} spectrum doesn't have spectral information!"
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📒 Files selected for processing (3)
pyproject.toml(1 hunks)quantmsrescore/__init__.py(1 hunks)quantmsrescore/ms2rescore.py(5 hunks)
✅ Files skipped from review due to trivial changes (2)
- quantmsrescore/init.py
- pyproject.toml
⏰ Context from checks skipped due to timeout of 90000ms (5)
- GitHub Check: build (3.10)
- GitHub Check: build
- GitHub Check: build (3.9)
- GitHub Check: build
- GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (3)
quantmsrescore/ms2rescore.py (3)
8-8: LGTM!The addition of the
osmodule import is necessary for path manipulation operations and follows Python's import ordering conventions.
144-161: LGTM!The function signature updates improve code readability while maintaining the same functionality.
Also applies to: 294-294, 452-471
258-281: Consider memory usage when handling large mzML filesLoading all spectra into memory at once could be problematic for large files. Consider processing spectra in chunks or using a streaming approach.
Let's check if there are any large mzML files in the test data:
✅ Verification successful
Consider adding a warning log for large mzML files
The current implementation is appropriate for the specific task of filtering empty spectra. While memory usage could be a concern for very large files, implementing a streaming solution would significantly increase complexity. Consider adding a warning log when loading files larger than a certain threshold (e.g., 1GB) to inform users about potential memory requirements.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Find mzML files and their sizes find . -name "*.mzML" -exec du -h {} \;Length of output: 125
Script:
#!/bin/bash # Search for other instances of MSExperiment and MzMLFile usage rg "MSExperiment|MzMLFile" -B 2 -A 2 # Look for any comments about memory or performance rg -i "memory|performance|large file" -B 2 -A 2 # Check documentation files fd "README|CONTRIBUTING" --exec cat {}Length of output: 2619
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🔭 Outside diff range comments (1)
quantmsrescore/ms2rescore.py (1)
Line range hint
516-516: Fix typo in rescoring engine check.There's a typo in the condition checking for "moakapot" (should be "mokapot").
- if rescoring_engine == "moakapot": + if rescoring_engine == "mokapot":
🧹 Nitpick comments (2)
quantmsrescore/ms2rescore.py (2)
266-268: Fix grammatical error in warning message.The warning message has incorrect grammar.
- f"{spectrum.getNativeID()} spectra don't have spectra information!" + f"{spectrum.getNativeID()} spectrum doesn't have spectral information!"
283-283: Implement temporary file cleanup.The TODO comment indicates that temporary file cleanup is still needed. This should be implemented to prevent accumulation of temporary files.
Would you like me to provide an implementation for cleaning up the temporary file after processing?
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📒 Files selected for processing (1)
quantmsrescore/ms2rescore.py(5 hunks)
⏰ Context from checks skipped due to timeout of 90000ms (6)
- GitHub Check: build
- GitHub Check: build (3.10)
- GitHub Check: build
- GitHub Check: build (3.9)
- GitHub Check: Codacy Static Code Analysis
- GitHub Check: build
🔇 Additional comments (3)
quantmsrescore/ms2rescore.py (3)
8-8: LGTM!The addition of the
osmodule import is necessary for path manipulation operations.
144-161: LGTM! Improved code formatting.The function signature changes are purely formatting-related and improve readability while maintaining the same functionality.
Also applies to: 297-298, 455-474
258-284: LGTM! Good implementation of empty spectra handling.The new code properly handles empty spectra by:
- Detecting MS2 spectra without peaks
- Logging warnings for transparency
- Creating a cleaned spectra file
- Using the output directory for temporary files as previously suggested
Let's verify the impact of empty spectra handling:
✅ Verification successful
Empty spectra handling implementation is safe and well-designed
The implementation correctly handles empty MS2 spectra without affecting other parts of the codebase. The temporary file creation in the output directory and the pending cleanup TODO are acceptable trade-offs for maintainability and debugging purposes.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for any existing empty spectra handling in the codebase rg -A 3 "empty.*spectr" rg -A 3 "len\(.*peaks.*\).*==.*0"Length of output: 1209
Script:
#!/bin/bash # Check for mzML file processing and spectrum path handling rg -A 3 "MzMLFile\(\)" rg -A 3 "spectrum.*path" rg -A 3 "setSpectra"Length of output: 3787
Bug Fixing bigbio/quantms#471
Summary by CodeRabbit
Version Update
Improvements