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WalkthroughThe changes in this pull request involve several files related to the rebranding of the project from "quantms-ms2rescore" to "quantms-rescoring." The Changes
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipe/meta.yaml (1)
Line range hint
23-33: Consider dependency version management strategySeveral dependencies have fixed versions (ms2rescore=3.0.3, deepLC=2.2.38, psm-utils=0.8.3, scipy=1.13.1, protobuf=3.19.6). This might lead to compatibility issues when other packages need different versions.
Consider:
- Using version ranges instead of fixed versions where possible
- Documenting the reason for fixing specific versions
- Adding a requirements.txt for development dependencies
.github/workflows/python-package.yml (1)
46-46: Consider expanding test coverageThe command change from 'quantmsutilsc' to 'rescoring' is correct, but consider:
- Adding more comprehensive CLI tests beyond just --help
- Testing with Python 3.11 since it's now stable
pyproject.toml (1)
Line range hint
33-33: Consider updating Python version constraintsThe current Python version constraint
>=3.8,<3.11might be too restrictive. Consider:
- Adding support for Python 3.11 since it's now stable
- Documenting the reason for the upper bound constraint
.github/workflows/python-app.yml (1)
49-49: Consider optimizing processes for CI environmentThe command uses 2 processes (
--processes 2) for parallel processing. While this is a reasonable default, consider the following for CI optimization:
- GitHub-hosted runners have 2 cores by default
- Processing overhead might affect CI performance
Consider either:
- Using a single process for more predictable CI behavior:
-rescoring ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05 +rescoring ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 1 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05
- Or using an environment variable to make it configurable:
-rescoring ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05 +rescoring ms2rescore --psm_file TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --spectrum_path TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes ${{ env.CI_PROCESSES || 1 }} --ms2pip_model HCD2021 --feature_generators 'ms2pip,deeplc' --id_decoy_pattern ^rev --test_fdr 0.05
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📒 Files selected for processing (4)
.github/workflows/python-app.yml(1 hunks).github/workflows/python-package.yml(1 hunks)pyproject.toml(1 hunks)recipe/meta.yaml(1 hunks)
🔇 Additional comments (4)
recipe/meta.yaml (1)
13-13: Verify pin_subpackage configuration
The change from 'quantms-utils' to 'quantms-rescoring' in run_exports is consistent with the project rebranding. However, we should verify this doesn't break existing dependencies.
✅ Verification successful
Pin subpackage configuration is appropriate
The change from 'quantms-utils' to 'quantms-rescoring' in the pin_subpackage configuration is correct and consistent with the rest of the codebase. The environment.yml and meta.yaml files show proper alignment with the project's dependencies and naming. No references to 'quantms-utils' were found in the package configuration files that would conflict with this change.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for any remaining references to quantms-utils
rg -l 'quantms-utils' --type yaml --type python
Length of output: 78
Script:
#!/bin/bash
# Search for any remaining references to quantms-utils across all files
rg -l 'quantms-utils'
# Also check for any conda/build configuration files
fd -e yaml -e yml
Length of output: 105
Script:
#!/bin/bash
# Check content of all yaml files for any references to quantms-utils
cat environment.yml recipe/conda_build_config.yaml recipe/meta.yaml
Length of output: 1444
pyproject.toml (2)
Line range hint 37-47: Ensure dependency version consistency
Please verify that the dependency versions match across pyproject.toml and meta.yaml:
✅ Verification successful
Dependencies are consistent across pyproject.toml and meta.yaml
All shared dependencies have matching versions across both files:
- ms2rescore: 3.0.3
- deepLC: 2.2.38
- psm-utils: 0.8.3
- scipy: 1.13.1
- protobuf: 3.19.6 (only specified in meta.yaml)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Extract and compare dependency versions from both files
echo "=== pyproject.toml dependencies ==="
rg "^(ms2rescore|deepLC|psm-utils|scipy|protobuf) = " pyproject.toml
echo "=== meta.yaml dependencies ==="
rg "^ - (ms2rescore|deepLC|psm-utils|scipy|protobuf)=" recipe/meta.yaml
Length of output: 481
51-51: Verify entry point consistency
The script entry point change is aligned with the rebranding. Let's verify the implementation exists.
✅ Verification successful
Entry point is correctly implemented
The main() function exists in quantmsrescore/rescoring.py and is properly implemented as a CLI entry point using Click. The function correctly wraps the CLI command group and handles system exits appropriately.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify the main function exists in the correct location
ast-grep --pattern 'def main():' quantmsrescore/rescoring.py
Length of output: 62
Script:
#!/bin/bash
# Let's first check if the file exists and then examine its content
fd rescoring.py
# If file exists, let's look at its content
fd rescoring.py -x cat {}
Length of output: 600
.github/workflows/python-app.yml (1)
49-49: Verify the new command installation and documentation
The command has been updated from quantmsutilsc to rescoring as part of the rebranding.
Let's verify the command installation and documentation:
✅ Verification successful
Command installation and documentation are properly configured
The verification shows that:
- The
rescoringcommand is properly defined inpyproject.tomlunder[tool.poetry.scripts]section - The package has been rebranded to
quantms-rescoringin all configuration files - The command is documented in the codebase with proper help text and options
- The implementation in
quantmsrescore/ms2rescore.pysupports all the parameters used in the workflow
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if the new command is properly documented and installed
# Check if the command is mentioned in documentation files
echo "Checking documentation for new command..."
rg -l "rescoring ms2rescore" --type md
# Check if the command is defined in project configuration
echo "Checking command definition in project files..."
rg -l "rescoring = " pyproject.toml
Length of output: 291
Script:
#!/bin/bash
# Let's check the actual content of pyproject.toml and documentation
echo "Checking pyproject.toml content..."
cat pyproject.toml
echo -e "\nChecking for any documentation files..."
fd -e md
echo -e "\nChecking README.md content..."
cat README.md
echo -e "\nChecking for any usage documentation in Python files..."
rg -A 5 "rescoring" --type py
Length of output: 11323
Summary by CodeRabbit
New Features
quantmsutilsctorescoringfor improved command-line interaction.Documentation
Chores