Refactor py

[ypriverol]

PR Type

enhancement, tests, documentation

---

Description

• Implemented new classes for machine learning feature selection and cross-validation (FSMLMethod, MLCVModel).
• Introduced FSDataFrame class for efficient feature selection with support for sparse and dense matrices.
• Added multivariate and univariate feature selection methods with corresponding tests.
• Provided utility functions for data processing, including missing data handling and percentile rank conversion.
• Added example scripts for converting loom files to parquet and merging parquet files.
• Updated documentation to reflect new features and usage examples.

---

Changes walkthrough 📝

	Relevant files
Enhancement	9 files ml.py Implement ML Feature Selection and Cross-Validation Classes fslite/fs/ml.py Implemented FSMLMethod class for ML feature selection. Added MLCVModel class for cross-validation ML models. Integrated feature selection and evaluation metrics. +399/-0  fdataframe.py Introduce FSDataFrame for Feature Selection                            fslite/fs/fdataframe.py Introduced FSDataFrame class for feature selection. Implemented data handling with sparse and dense matrices. Added methods for feature scaling and selection. +311/-0  multivariate.py Add Multivariate Feature Selection Methods                              fslite/fs/multivariate.py Added FSMultivariate class for multivariate feature selection. Implemented correlation and variance-based selection methods. +217/-0  univariate.py Implement Univariate Feature Selection Methods                      fslite/fs/univariate.py Implemented FSUnivariate class for univariate feature selection. Added various univariate selection methods like ANOVA and correlation. +205/-0  methods.py Define Abstract Class for Feature Selection Methods            fslite/fs/methods.py Defined FSMethod abstract class for feature selection. Provided structure for derived feature selection methods. +193/-0  constants.py Add Constants for Feature Selection Methods                            fslite/fs/constants.py Added constants for feature selection methods. Defined valid methods for univariate, multivariate, and ML. +134/-0  loom2parquetchunks.py Add Script for Loom to Parquet Conversion                                examples/loom2parquetchunks.py Added script to convert loom files to parquet format. Implemented chunk processing for large datasets. +114/-0  utils.py Implement Utility Functions for Data Processing                    fslite/fs/utils.py Implemented utility functions for data processing. Added percentile rank conversion and missing data handling. +35/-15  loom2parquetmerge.py Add Script for Merging Parquet Files                                          examples/loom2parquetmerge.py Added script to merge parquet files. Implemented incremental concatenation to manage memory. +62/-0
Tests	5 files test_ml_methods.py Add Tests for ML Feature Selection Methods                              fslite/tests/test_ml_methods.py Added tests for ML methods using cross-validation. Verified feature scores and evaluation metrics. +177/-0  test_univariate_methods.py Add Tests for Univariate Feature Selection                              fslite/tests/test_univariate_methods.py Added tests for univariate feature selection methods. Verified feature selection accuracy and thresholds. +143/-0  test_fsdataframe.py Add Tests for FSDataFrame Initialization and Scaling          fslite/tests/test_fsdataframe.py Added tests for FSDataFrame initialization and scaling. Verified memory usage and data handling. +121/-0  test_multivariate_methods.py Add Tests for Multivariate Feature Selection                          fslite/tests/test_multivariate_methods.py Added tests for multivariate feature selection methods. Verified correlation and variance-based selection. +122/-0  test_fs_pipeline.py Add Tests for Feature Selection Pipeline                                  fslite/tests/test_fs_pipeline.py Added tests for feature selection pipeline. Verified pipeline execution and results. +72/-0
Documentation	1 files fs_pipeline_example.py Add Example for Feature Selection Pipeline                              fslite/pipeline/fs_pipeline_example.py Added example for feature selection pipeline. Demonstrated univariate, multivariate, and ML methods. +69/-0

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Action: build

Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to Python syntax errors detected by flake8: An IndentationError was found in the file ./examples/loom2parquetmerge.py at line 45, indicating an unexpected indent. A SyntaxError was found in the file ./fslite/tests/generate_big_tests.py at line 44, indicating an unmatched parenthesis.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 333: 2 E999 IndentationError: unexpected indent 334: 2 335: ##[error]Process completed with exit code 1.

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Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to a Python syntax error detected by flake8: An IndentationError was found in the file examples/loom2parquetmerge.py at line 45. The specific error is E999 IndentationError: unexpected indent, indicating that there is an incorrect indentation in the code.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: 1 E999 IndentationError: unexpected indent 333: 1 334: ##[error]Process completed with exit code 1.

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Failed stage: Lint with flake8 [❌]

Failed test name: ""

Failure summary: The action failed due to Python syntax errors detected by flake8: An IndentationError was found in the file examples/loom2parquetmerge.py at line 45. A SyntaxError for unmatched parentheses was found in the file fslite/tests/generate_big_tests.py at line 44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 333: 2 E999 IndentationError: unexpected indent 334: 2 335: ##[error]Process completed with exit code 1.

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Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: flake8

Failure summary: The action failed because the flake8 linter detected a Python syntax error: An IndentationError was found in the file examples/loom2parquetmerge.py at line 45. The specific error is E999 IndentationError: unexpected indent, indicating that there is an incorrect indentation in the code.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: 1 E999 IndentationError: unexpected indent 379: 1 380: ##[error]Process completed with exit code 1.

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Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: ""

Failure summary: The action failed due to syntax errors detected by flake8: An IndentationError was found in the file examples/loom2parquetmerge.py at line 45. A SyntaxError due to an unmatched parenthesis was found in the file fslite/tests/generate_big_tests.py at line 44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 379: 2 E999 IndentationError: unexpected indent 380: 2 381: ##[error]Process completed with exit code 1.

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In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

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Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: ""

Failure summary: The action failed due to syntax errors detected by flake8: An IndentationError was found in ./examples/loom2parquetmerge.py at line 45, indicating an unexpected indent. A SyntaxError was found in ./fslite/tests/generate_big_tests.py at line 44, indicating an unmatched parenthesis.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 379: 2 E999 IndentationError: unexpected indent 380: 2 381: ##[error]Process completed with exit code 1.

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✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
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In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

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• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

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Action: build

Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to Python syntax errors and an undefined name detected by flake8: ./examples/loom2parquetmerge.py:45:9: IndentationError due to an unexpected indent. ./fslite/fs/ml.py:143:19: F821 error due to an undefined name InvalidDataError. ./fslite/tests/generate_big_tests.py:44:14: SyntaxError due to an unmatched parenthesis.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 333: raise InvalidDataError( 334: ^ 335: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 336: 2 E999 IndentationError: unexpected indent 337: 1 F821 undefined name 'InvalidDataError' 338: 3 339: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build

Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to the following Python syntax errors and undefined names detected by flake8: E999 IndentationError: unexpected indent at line 45 in ./examples/loom2parquetmerge.py. F821 undefined name 'InvalidDataError' at line 143 in ./fslite/fs/ml.py. E999 SyntaxError: unmatched ')' at line 44 in ./fslite/tests/generate_big_tests.py.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 333: raise InvalidDataError( 334: ^ 335: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 336: 2 E999 IndentationError: unexpected indent 337: 1 F821 undefined name 'InvalidDataError' 338: 3 339: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build

Failed stage: Lint with flake8 [❌]

Failed test name: ""

Failure summary: The action failed due to the following Python syntax errors and undefined names detected by flake8: E999 IndentationError: unexpected indent in ./examples/loom2parquetmerge.py at line 45. F821 undefined name 'InvalidDataError' in ./fslite/fs/ml.py at line 143. E999 SyntaxError: unmatched ')' in ./fslite/tests/generate_big_tests.py at line 44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 333: raise InvalidDataError( 334: ^ 335: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 336: 2 E999 IndentationError: unexpected indent 337: 1 F821 undefined name 'InvalidDataError' 338: 3 339: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build-linux

Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to syntax and undefined name errors detected by flake8: E999 IndentationError: unexpected indent at ./examples/loom2parquetmerge.py:45 F821 undefined name 'InvalidDataError' at ./fslite/fs/ml.py:143 E999 SyntaxError: unmatched ')' at ./fslite/tests/generate_big_tests.py:44

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 379: raise InvalidDataError( 380: ^ 381: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 382: 2 E999 IndentationError: unexpected indent 383: 1 F821 undefined name 'InvalidDataError' 384: 3 385: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: flake8

Failure summary: The action failed due to syntax errors and undefined names detected by flake8: E999 IndentationError: unexpected indent at ./examples/loom2parquetmerge.py:45. F821 undefined name 'InvalidDataError' at ./fslite/fs/ml.py:143. E999 SyntaxError: unmatched ')' at ./fslite/tests/generate_big_tests.py:44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 379: raise InvalidDataError( 380: ^ 381: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 382: 2 E999 IndentationError: unexpected indent 383: 1 F821 undefined name 'InvalidDataError' 384: 3 385: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: flake8

Failure summary: The action failed due to syntax errors and an undefined name detected by flake8: E999 IndentationError: unexpected indent at ./examples/loom2parquetmerge.py:45:9 E999 SyntaxError: unmatched ')' at ./fslite/tests/generate_big_tests.py:44:14 F821 undefined name 'InvalidDataError' at ./fslite/fs/ml.py:143:19

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/fs/ml.py:143:19: F821 undefined name 'InvalidDataError' 379: raise InvalidDataError( 380: ^ 381: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 382: 2 E999 IndentationError: unexpected indent 383: 1 F821 undefined name 'InvalidDataError' 384: 3 385: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

CI Failure Feedback 🧐

Action: build

Failed stage: Lint with flake8 [❌]

Failure summary: The action failed due to Python syntax errors detected by flake8: IndentationError: unexpected indent in the file ./examples/loom2parquetmerge.py at line 45. SyntaxError: unmatched ')' in the file ./fslite/tests/generate_big_tests.py at line 44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 311: Downloading pyparsing-3.1.4-py3-none-any.whl (104 kB) 312: Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 313: Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) 314: Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) 315: Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) 316: Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) 317: Installing collected packages: pytz, tzdata, threadpoolctl, six, pyparsing, psutil, pillow, numpy, networkx, kiwisolver, joblib, fonttools, cycler, scipy, python-dateutil, memory-profiler, contourpy, scikit-learn, pandas, matplotlib 318: Successfully installed contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 memory-profiler-0.61.0 networkx-3.3 numpy-2.1.1 pandas-2.2.3 pillow-10.4.0 psutil-6.0.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tzdata-2024.2 319: ##[group]Run # stop the build if there are Python syntax errors or undefined names 320: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 321: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 322: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m 323: �[36;1mflake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics�[0m 324: shell: /usr/bin/bash -e {0} 325: env: 326: pythonLocation: /opt/hostedtoolcache/Python/3.10.15/x64 327: LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.15/x64/lib 328: ##[endgroup] 329: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 330: print(f"Concatenated parquet file written to {output_path}") 331: ^ 332: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 333: 2 E999 IndentationError: unexpected indent 334: 2 335: ##[error]Process completed with exit code 1.

---

✨ CI feedback usage guide:

---

The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.

[qodo-merge-pro]

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CI Failure Feedback 🧐

Action: build-linux

Failed stage: Lint with flake8 [❌]

Failed test name: flake8

Failure summary: The action failed due to syntax errors detected by flake8: An IndentationError was found in the file examples/loom2parquetmerge.py at line 45. A SyntaxError due to an unmatched parenthesis was found in the file fslite/tests/generate_big_tests.py at line 44.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 329: # 330: # $ conda activate base 331: # 332: # To deactivate an active environment, use 333: # 334: # $ conda deactivate 335: ##[group]Run conda install flake8 336: �[36;1mconda install flake8�[0m 337: �[36;1m# stop the build if there are Python syntax errors or undefined names�[0m 338: �[36;1mflake8 . --count --select=E9,F63,F7,F82 --show-source --statistics�[0m 339: �[36;1m# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide�[0m ... 367: mccabe pkgs/main/noarch::mccabe-0.7.0-pyhd3eb1b0_0 368: pycodestyle pkgs/main/linux-64::pycodestyle-2.12.1-py310h06a4308_0 369: pyflakes pkgs/main/linux-64::pyflakes-3.2.0-py310h06a4308_0 370: Proceed ([y]/n)? 371: Downloading and Extracting Packages: ...working... done 372: Preparing transaction: ...working... done 373: Verifying transaction: ...working... done 374: Executing transaction: ...working... done 375: ./examples/loom2parquetmerge.py:45:9: E999 IndentationError: unexpected indent 376: print(f"Concatenated parquet file written to {output_path}") 377: ^ 378: ./fslite/tests/generate_big_tests.py:44:14: E999 SyntaxError: unmatched ')' 379: 2 E999 IndentationError: unexpected indent 380: 2 381: ##[error]Process completed with exit code 1.

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✨ CI feedback usage guide:

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The CI feedback tool (/checks) automatically triggers when a PR has a failed check.
The tool analyzes the failed checks and provides several feedbacks:

• Failed stage
• Failed test name
• Failure summary
• Relevant error logs

In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR:

/checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}"

where {repo_name} is the name of the repository, {run_number} is the run number of the failed check, and {job_number} is the job number of the failed check.

Configuration options

• enable_auto_checks_feedback - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
• excluded_checks_list - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
• enable_help_text - if set to true, the tool will provide a help message with the feedback. Default is true.
• persistent_comment - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
• final_update_message - if persistent_comment is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

See more information about the checks tool in the docs.