Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

5-5: Use is and is not for type comparisons, or isinstance() for isinstance checks

(E721)

5-5: Undefined name snakemake

(F821)

6-6: Use is and is not for type comparisons, or isinstance() for isinstance checks

(E721)

6-6: Undefined name snakemake

(F821)

7-7: Use is and is not for type comparisons, or isinstance() for isinstance checks

(E721)

7-7: Undefined name snakemake

(F821)

9-9: Undefined name snakemake

(F821)

9-9: Undefined name snakemake

(F821)

10-10: Undefined name snakemake

(F821)

10-10: Undefined name snakemake

(F821)

11-11: Undefined name snakemake

(F821)

11-11: Undefined name snakemake

(F821)

Test coverage is appropriate for parameter pickling functionality

The test implementation is well-designed and sufficient for its purpose:

• It covers all three major data structure types (pandas DataFrame, polars DataFrame, numpy ndarray)
• The test data includes mixed types (integers and floating-point) which validates type preservation
• The Snakefile demonstrates correct parameter passing and the test.py verifies both type preservation and data integrity
• The presence of expected-results (testnp.tsv, testpd.tsv, testpl.tsv) ensures output validation
• The simple test data is appropriate as complex structures would be serialized the same way

Additional test cases for different versions or error scenarios would be handled by the CI pipeline running against different dependency versions, and error cases are covered by Python's built-in type checking and serialization mechanisms.

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check for other test files that might contain related parameter pickling tests
fd -e py -e yaml -e json . tests/ --exec grep -l "params.*test[np]p|test[np]l|DataFrame|ndarray" {}

Length of output: 103

Script:

#!/bin/bash
# Let's try a different approach to find test files and configurations
# First, let's check the test directory structure
fd . tests/test_params_pickling/

# Then look for test configuration files
fd -e yaml -e json . tests/test_params_pickling/

# Finally, let's examine the Snakefile or workflow file
fd Snakefile . tests/test_params_pickling/

Length of output: 829

Script:

#!/bin/bash
# Let's also check the actual test implementation for parameter definitions
cat tests/test_params_pickling/Snakefile 2>/dev/null
cat tests/test_params_pickling/*.smk 2>/dev/null

Length of output: 471

Script:

#!/bin/bash
# Search for any other similar test patterns in the codebase
rg -g '!{node_modules,dist,build}' -l "DataFrame|ndarray" tests/

Length of output: 66

✓ Parameters are properly handled in test.py

The test script correctly:

• Validates parameter types (numpy array, polars DataFrame, pandas DataFrame)
• Writes each parameter to its corresponding output file with tab separation
• Uses consistent naming between rule params and script variables

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Verify the existence and content of the test script
if [ -f "tests/test_params_pickling/test.py" ]; then
    echo "test.py exists"
    # Check if it handles all parameters
    rg -A 5 "testpd|testnp|testpl" "tests/test_params_pickling/test.py"
else
    echo "test.py not found"
fi

Length of output: 518

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

146-151: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

5-5: Undefined name snakemake

(F821)

6-6: Undefined name snakemake

(F821)

7-7: Undefined name snakemake

(F821)

9-9: Undefined name snakemake

(F821)

9-9: Undefined name snakemake

(F821)

10-10: Undefined name snakemake

(F821)

10-10: Undefined name snakemake

(F821)

11-11: Undefined name snakemake

(F821)

11-11: Undefined name snakemake

(F821)