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You can disable this status message by setting the WalkthroughThis pull request enhances the MaxQuant module by adding extensive logging and updated docstrings to many functions within the module (including Changes
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🔭 Outside diff range comments (2)
tests/README.md (2)
53-54: 🛠️ Refactor suggestionUpdate remaining references to old test file
The PyCharm instructions still refer to the old
maxquant_tests.pyfile but should reference the newtest_maxquant.pyfile.- - Right-click on the test file (e.g., `maxquant_tests.py`) in the Project view + - Right-click on the test file (e.g., `test_maxquant.py`) in the Project view
92-100: 🛠️ Refactor suggestionUpdate test file documentation section
This section still refers to the old test file name and should be updated to reflect the renamed file.
-### maxquant_tests.py +### test_maxquant.py🧰 Tools
🪛 LanguageTool
[uncategorized] ~98-~98: A period might be missing here.
Context: ...ontaminants, and analyzing data work as expected The tests use a mock approach to avoid...(AI_EN_LECTOR_MISSING_PUNCTUATION_PERIOD)
🧹 Nitpick comments (1)
pmultiqc/modules/quantms/maxquant.py (1)
12-16: Cleanup unused importThe static analysis tool shows that the Histogram import is unused.
from ...logging import get_logger, Timer -from .histogram import Histogram🧰 Tools
🪛 Ruff (0.8.2)
13-13:
.histogram.Histogramimported but unusedRemove unused import:
.histogram.Histogram(F401)
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pmultiqc/modules/quantms/maxquant.py(9 hunks)tests/README.md(1 hunks)tests/maxquant_tests.py(0 hunks)
💤 Files with no reviewable changes (1)
- tests/maxquant_tests.py
🧰 Additional context used
🪛 Ruff (0.8.2)
pmultiqc/modules/quantms/maxquant.py
13-13: .histogram.Histogram imported but unused
Remove unused import: .histogram.Histogram
(F401)
⏰ Context from checks skipped due to timeout of 90000ms (5)
- GitHub Check: test_mzid_mzML
- GitHub Check: test_mzid_mgf
- GitHub Check: test_dia
- GitHub Check: test_tmt
- GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (18)
tests/README.md (2)
34-35: Reference to test file correctly updatedThe command example has been correctly updated to use the new test file name.
40-41: Reference to test file correctly updatedThe verbose test command has been correctly updated to use the new test file name.
pmultiqc/modules/quantms/maxquant.py (16)
19-30: Well-structured docstring addedGood improvement adding clear documentation with parameters and return value.
31-33: Effective logging implementationUsing Timer context manager to track function execution time and logging the number of rows loaded improves observability.
37-38: Good debug message for column renamingAdding debug logging for column renaming improves code transparency.
48-50: Informative filtering log messageGood addition of detailed logging for reverse entries filtering.
54-70: Enhanced debug logging for intensity columnsThe added logging properly tracks intensity column processing, which helps with debugging and understanding the flow of data.
71-72: Improved error loggingAdding error logging before raising an exception improves observability and makes debugging easier.
76-82: Good debug logging for summary processingThe additional logging for summary file processing provides visibility into the filtering process.
89-190: Comprehensive logging added to get_protegroupsExcellent addition of docstring and extensive logging throughout this complex function. The logs clearly track:
- Initial data processing
- Intensity column detection and selection
- Contaminant processing
- Various calculations (intensity distributions, LFQ, PCA)
This significantly improves debuggability and understanding of the function's execution path.
195-235: Well-documented contaminants functionGood addition of docstring and Timer context for performance tracking. The logging provides clarity about:
- Missing columns
- Total intensity calculation
- Contaminant count
- Completion status
This makes the function more maintainable and easier to debug.
300-326: Improved get_summary function with proper error handlingThe addition of docstring and logging enhances this function with:
- Processing status information
- Clear warnings for missing columns or zero values
- Completion logging with count of processed items
This is a good improvement for observability.
331-359: Enhanced evidence processing with detailed metricsGood addition of docstring and comprehensive logging for evidence data processing. The logging of counts for entries, unique peptides, and MS/MS spectra, along with detailed match information, significantly improves observability.
362-426: Complete logging for evidence calculationsThorough debug logging added for each calculation in the evidence processing pipeline, making the data flow transparent and easier to troubleshoot.
940-973: Well-documented MSMS processingThe addition of docstring and detailed logging for msms data processing provides clear visibility into:
- Processing metrics (spectra count, unique peptides, unique proteins)
- Warning for missing evidence data
- Calculation status
This improves the function's maintainability.
1025-1069: Comprehensive msmsScans function documentationGood addition of docstring and detailed logging for msmsScans processing. The logging of scan counts, retention time range, and various calculation steps provides excellent observability into this function's execution.
1241-1262: Well-documented parameters processingThe addition of docstring and logging for parameters processing improves function clarity and provides proper tracking of the extraction process.
1267-1308: Improved parameters_table functionGood addition of docstring and detailed logging for the parameters table extraction, providing visibility into:
- Column validation
- AIF parameter filtering
- FASTA file processing
- Table creation
This enhances the function's maintainability.
add automatic updates for examples
CI Feedback 🧐(Feedback updated until commit 2215b8c)A test triggered by this PR failed. Here is an AI-generated analysis of the failure:
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Actionable comments posted: 0
🧹 Nitpick comments (12)
.github/workflows/update_examples.yml (5)
1-1: Fix Typographical Error in Workflow NameThe workflow name on line 1 contains a typo ("exmaples" instead of "examples"). Please update it to "Auto update examples" for clarity.
- name: Auto update exmaples + name: Auto update examples
16-20: Update GitHub Action Version for Python SetupThe static analysis (actionlint) indicates that the runner version used for
actions/setup-python@v4is outdated. To ensure compatibility and take advantage of improvements, please update it to the latest stable version (e.g., v5).- uses: actions/setup-python@v4 + uses: actions/setup-python@v5🧰 Tools
🪛 actionlint (1.7.4)
17-17: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
8-8: Remove Trailing WhitespaceLine 8 contains trailing whitespace. Removing it will help keep the YAML clean and compliant with YAMLlint recommendations.
🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 8-8: trailing spaces
(trailing-spaces)
32-36: Correct Typo in Git Commit MessageThe commit message on line 36 has a typo ("Update exmaples" should be "Update examples"). Please fix the typo to ensure consistency in commit messages.
- git commit -m "Update exmaples" + git commit -m "Update examples"
37-37: Add Newline at End-of-FileYAMLlint reported that the file is missing a newline at the end (line 37). Please add a newline to adhere to best practices.
🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 37-37: no new line character at the end of file
(new-line-at-end-of-file)
docs/README.md (3)
5-5: Remove trailing punctuation in the "Plugins" header.
The heading## Plugins:contains a trailing colon. Removing it (i.e. changing to## Plugins) will comply with markdown lint guidelines (MD026) and enhance consistency.🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
5-5: Trailing punctuation in heading
Punctuation: ':'(MD026, no-trailing-punctuation)
25-25: Remove trailing punctuation in the "Example reports" header.
The heading## Example reports:ends with a colon. Consider removing the colon (i.e. use## Example reports) to satisfy markdown lint rules (MD026).🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
25-25: Trailing punctuation in heading
Punctuation: ':'(MD026, no-trailing-punctuation)
42-45: Specify a language for the fenced code block.
The fenced code block that provides citation details does not specify a language. Updating the opening fence from(and similarly on the closing fence, if needed) will both improve clarity and address markdown lint warnings (MD040).</code> to <code>text🧰 Tools
🪛 markdownlint-cli2 (0.17.2)
42-42: Fenced code blocks should have a language specified
null(MD040, fenced-code-language)
docs/config.json (1)
1-58: Configuration file structure is well-organized.
The newconfig.jsonfile clearly defines project metadata with keys likeaccession,urls,path, andfile_type. As the configuration grows more complex, consider providing a JSON schema (or accompanying documentation) to validate and enforce the correct structure of these entries.docs/PXD054720/multiqc_report.html (2)
23-29: Validate Updated Compressed Plot DataThe compressed plot data string in the
<script>tag has been updated. Please ensure that the new compressed data is fully compatible with the decompression routine and that it renders correctly on the report. If not already in place, consider adding tests or logging to verify the integrity of the parsed data at runtime.
6947-6958: Confirm Report Metadata ConsistencyThe report generation timestamp has been updated to "2025-04-01, 12:37 UTC" and the analysis path changed to an absolute location (
/home/runner/work/pmultiqc/pmultiqc/data). Please verify that:
- The updated timestamp correctly reflects the new report generation time.
- The absolute analysis path is appropriate for all target environments.
If feasible, consider parameterizing the analysis path to enhance portability.docs/PXD051187/multiqc_report.html (1)
23-29: Review of Compressed Plot Data and Config Updates
The changes in this section update the plot data embedded in the<script>tag withid="mqc_compressed_plotdata". The new compressed data string and updated report generation timestamp indicate that the visualization data was refreshed. Please verify that the new data string is valid and decodes correctly in the context of the front-end logic. Also, ensure that the associated configuration in the<script>tag withid="mqc_config"aligns with any new processing or rendering requirements.
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- docs/example_lfq/multiqc_data/mqc_Oversampling_Distribution_1.txt
- docs/example_lfq/multiqc_data/mqc_number_of_peptides_per_proteins__name_count_ylab_Frequency_.txt
- docs/example_dia/multiqc_data/mqc_number_of_peptides_per_proteins__name_count_ylab_Frequency_.txt
- docs/example_tmt/multiqc_data/mqc_number_of_peptides_per_proteins__name_percentage_ylab_Percentage_.txt
- docs/example_tmt/multiqc_data/mqc_number_of_peptides_per_proteins__name_count_ylab_Frequency_.txt
- docs/example_lfq/multiqc_data/mqc_delta_mass_Counts.txt
- docs/example_tmt/multiqc_data/mqc_peak_intensity_distribution_1.txt
- docs/example_lfq/multiqc_data/mqc_Precursor_Ion_Charge_Distribution_1.txt
- docs/example_dia/multiqc_data/multiqc_sources.txt
- docs/example_dia/multiqc_data/multiqc_data.json
- docs/example_tmt/multiqc_data/mqc_delta_mass_Counts.txt
- docs/example_lfq/multiqc_data/mqc_number_of_peptides_per_proteins__name_percentage_ylab_Percentage_.txt
- docs/example_lfq/multiqc_data/mqc_delta_mass_Relative_Frequency.txt
- docs/example_tmt/multiqc_data/mqc_delta_mass_Relative_Frequency.txt
- docs/example_dia/multiqc_data/mqc_peak_intensity_distribution_1.txt
✅ Files skipped from review due to trivial changes (2)
- docs/init.py
- README.md
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🪛 markdownlint-cli2 (0.17.2)
docs/README.md
5-5: Trailing punctuation in heading
Punctuation: ':'
(MD026, no-trailing-punctuation)
25-25: Trailing punctuation in heading
Punctuation: ':'
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🪛 actionlint (1.7.4)
.github/workflows/update_examples.yml
17-17: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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🪛 YAMLlint (1.35.1)
.github/workflows/update_examples.yml
[error] 8-8: trailing spaces
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- GitHub Check: test_mzid_mgf
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🔇 Additional comments (2)
docs/README.md (1)
1-4: Overall README structure is excellent.
The new documentation lays out comprehensive sections for plugins, example data, and citation guidelines. The clear tables and links help users understand available options and resources.docs/PXD051187/multiqc_report.html (1)
6947-6958: Review of Report Generation Details Update
This hunk updates the displayed report generation metadata. The timestamp has been changed to "2025-04-01, 12:39 UTC" and the analysis path has been revised to a more generic directory (/home/runner/work/pmultiqc/pmultiqc/data). This improves clarity and likely aligns the output with the new logging enhancements. Please confirm that these modifications correctly reflect the underlying data source and are consistent with the updated module behavior.
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🧹 Nitpick comments (7)
.github/workflows/pytest.yml (1)
22-23: Update Setup-Python Action Version
A static analysis tool has flagged the use ofactions/setup-python@v4as potentially outdated. Consider upgrading to the latest stable version (e.g., v5 if available) to ensure better compatibility with the GitHub Actions runner.🧰 Tools
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23-23: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
.github/workflows/python-app.yml (2)
167-169: Consider Upgrading Setup-Python in Test Jobs
The static analysis tool flags the use ofactions/setup-python@v4in the test jobs (e.g., in the MaxQuant job) as outdated. An upgrade to a newer version is recommended for improved performance and compatibility with the latest GitHub Actions runners.🧰 Tools
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167-167: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
6-80: Consistency Across Test Jobs
While thetest_maxquantjob now uses Python 3.10, several other test jobs (e.g., LFQ, TMT, DIA, mzid/mzML, and mzid/MGF) are still configured with Python 3.9. For consistency across your CI environment, consider evaluating whether these jobs should also be updated to Python 3.10 or above.🧰 Tools
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18-18: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
33-33: the runner of "actions/cache@v3" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
46-46: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
69-69: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
.github/workflows/update_examples.yml (4)
1-1: Typo in Workflow Name
The workflow name "Auto update exmaples" contains a typo. Please update it to "Auto update examples" to improve clarity and professionalism.
17-20: Update Setup-Python Action Version
The static analysis indicates that the runner foractions/setup-python@v4may be outdated. Consider updating to a newer version (e.g., v5) to benefit from enhanced features and compatibility improvements.🧰 Tools
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17-17: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
36-36: Typo in Commit Message
The commit message "Update exmaples" contains a misspelling. Please change it to "Update examples" to maintain consistency and clarity in your commit history.
37-37: Newline at End of File
YAMLlint has flagged that there is no newline at the end of the file. Please add a newline at the end to comply with YAML formatting guidelines.🧰 Tools
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.github/workflows/python-app.yml
167-167: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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.github/workflows/pytest.yml
23-23: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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.github/workflows/update_examples.yml
17-17: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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.github/workflows/update_examples.yml
[error] 37-37: no new line character at the end of file
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🔇 Additional comments (3)
.github/workflows/python-package.yml (1)
18-20: Python Version Matrix Updated
The build matrix has been updated to include only Python 3.10 and 3.11. Please verify that all dependencies and environments are compatible with dropping Python 3.9..github/workflows/pytest.yml (1)
15-15: Updated Python Version Matrix
The Python version matrix now explicitly includes only 3.10 and 3.11. This change ensures consistency with other CI/CD configurations..github/workflows/python-app.yml (1)
165-169: Update Test MaxQuant Python Version
Thetest_maxquantjob has been updated to use Python "3.10", which aligns with the updated compatibility requirements. Please verify that any scripts or dependencies in this job work as expected under Python 3.10.🧰 Tools
🪛 actionlint (1.7.4)
167-167: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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🧹 Nitpick comments (1)
.github/workflows/python-publish.yml (1)
40-40: Add Missing Newline at End of File
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[error] 40-40: no new line character at the end of file
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[error] 40-40: no new line character at the end of file
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.github/workflows/python-app.yml
115-115: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
140-140: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
167-167: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
⏰ Context from checks skipped due to timeout of 90000ms (5)
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🔇 Additional comments (2)
.github/workflows/python-publish.yml (1)
27-29: Specify Python 3.10 Explicitly for Reproducibility
The update of the Python version from an ambiguous'3.x'to a precise'3.10'helps ensure environment consistency and reproducibility during package publishing.🧰 Tools
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27-27: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
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.github/workflows/python-app.yml (1)
4-108: Ensure Consistent Python Versions Across Jobs
While jobs liketest_mzid_mzML,test_mzid_mgf, andtest_maxquanthave been updated to use Python 3.10 for compatibility with the enhanced maxquant module, other jobs (e.g.,setup,test_lfq,test_tmt,test_dia) still run on Python 3.9. Please verify that this mixed Python-version strategy is intentional. Standardizing on Python 3.10 (or another version) across all jobs might simplify maintenance in the long run.Also applies to: 112-160
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18-18: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
33-33: the runner of "actions/cache@v3" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
46-46: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
69-69: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
92-92: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
| - name: Set up Python 3.10 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.9 | ||
| python-version: "3.10" |
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🛠️ Refactor suggestion
Update Python Setup Action Version in test_mzid_mzML Job
The job now specifies Python 3.10, which aligns with the maxquant test enhancements. However, the workflow still uses actions/setup-python@v4, and static analysis indicates this version is outdated. Consider updating to a later major version (e.g., actions/setup-python@v5) to take advantage of improvements and maintain compatibility with GitHub Actions.
Proposed Diff:
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| python-version: "3.10" | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" |
🧰 Tools
🪛 actionlint (1.7.4)
115-115: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
| - name: Set up Python "3.10" | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.9 | ||
| python-version: "3.10" |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Update Python Setup Action Version in test_maxquant Job
The maxquant test job, which is important for the PR’s objectives, still relies on actions/setup-python@v4. Updating this action to version v5 should help align with current standards and resolve the static analysis issue.
Proposed Diff:
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| python-version: "3.10" | |
| - name: Set up Python "3.10" | |
| - uses: actions/setup-python@v4 | |
| + uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" |
🧰 Tools
🪛 actionlint (1.7.4)
167-167: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
| - name: Set up Python "3.10" | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.9 | ||
| python-version: "3.10" |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Update Python Setup Action Version in test_mzid_mgf Job
Similar to the previous comment, this job is now running with Python "3.10" but still utilizes actions/setup-python@v4. Updating to version v5 is recommended to address the static analysis warning and ensure the latest features and fixes.
Proposed Diff:
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| python-version: "3.10" | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" |
🧰 Tools
🪛 actionlint (1.7.4)
140-140: the runner of "actions/setup-python@v4" action is too old to run on GitHub Actions. update the action's version to fix this issue
(action)
3 participants
PR Type
Enhancement, Tests
Description
Enhanced logging and error handling in
maxquant.py.Timerfor performance tracking.Refactored and optimized functions in
maxquant.py.Removed outdated and unnecessary test cases.
maxquant_tests.pywith redundant or obsolete tests.Updated test documentation for renamed test files.
tests/README.md.Changes walkthrough 📝
maxquant.py
Refactored MaxQuant module with logging enhancementspmultiqc/modules/quantms/maxquant.py
maxquant_tests.py
Removed outdated MaxQuant test casestests/maxquant_tests.py
README.md
Updated test documentation for renamed filestests/README.md
Summary by CodeRabbit
.gitignorefile to include new entries and remove outdated ones.