[MNT] Configure mypy in pre-commit for type checking

[alyssadai]

• Closes Add mypy pre-commit hook for type checking #403

Changes proposed in this pull request:

• Configure mypy as part of pre-commit for type checking (see https://mypy.readthedocs.io/en/stable/command_line.html#the-mypy-command-line)
• Expand return types for more complex data model utilities, for readability
• Slightly refactor error handling to avoid implicit None return type
• Fix type errors related to inference of None type objects (where such objects cannot actually be None due to preceding checks) by using direct indexing

Housekeeping:

• Explicitly capture warning in test for failed pipeline catalog checking, to remove it from pytest warnings summary

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

Summary by Sourcery

Enhance the codebase by adding type annotations to several functions and integrate mypy into the pre-commit hooks to ensure type checking is performed.

Enhancements:

• Add type annotations to various functions in the codebase to improve type safety and code clarity.

Build:

• Integrate mypy into the pre-commit configuration to enforce type checking.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces mypy for static type checking by adding type annotations to function return types across several modules, refactoring error handling in the transform_age function, updating dictionary access methods for better error handling, and integrating mypy into the pre-commit hooks.

Class diagram showing updated type annotations

classDiagram
    class pheno_utils {
        +map_categories_to_columns(data_dict: dict) dict[str, list]
        +map_tools_to_columns(data_dict: dict) dict[str, list]
        +transform_age(value: str, heuristic: str) float
        +get_transformed_values(columns: list, row: pd.Series, data_dict: dict) list[float | str]
        +find_undefined_cat_col_values(data_dict: dict, pheno_df: pd.DataFrame) dict[str, list]
        +find_unused_missing_values(data_dict: dict, pheno_df: pd.DataFrame) dict[str, list]
    }
    class model_utils {
        +get_subject_instances(dataset: models.Dataset) dict[str, models.Subject]
        +get_imaging_session_instances(jsonld_subject: models.Subject) dict[str, models.ImagingSession]
    }
    class file_utils {
        +load_tabular(input_p: Path, input_type: str) pd.DataFrame
        +load_json(input_p: Path) Any
    }
    note for pheno_utils "Added type hints for dictionary and list return types"
    note for model_utils "Added specific type hints for subject and session dictionaries"
    note for file_utils "Updated return types for data loading functions"

Loading

File-Level Changes

Change	Details	Files
Add type annotations to function return types for better type checking and clarity.	Changed return type of map_categories_to_columns to dict[str, list]. Changed return type of map_tools_to_columns to dict[str, list]. Changed return type of get_transformed_values to list[float	str]. Changed return type of find_undefined_cat_col_values to dict[str, list]. Changed return type of find_unused_missing_values to dict[str, list]. Changed return type of get_subject_instances to dict[str, models.Subject]. Changed return type of get_imaging_session_instances to dict[str, models.ImagingSession]. Changed return type of load_tabular to pd.DataFrame. Changed return type of load_json to Any.
Refactor error handling in transform_age function for better readability and efficiency.	Removed unnecessary variable is_recognized_heuristic. Reorganized error handling to raise ValueError directly when heuristic is not recognized.	bagel/utilities/pheno_utils.py
Update dictionary access to use direct indexing instead of get method for better error handling.	Changed participants assignment to use direct indexing. Changed existing_subject assignment to use direct indexing. Changed existing_img_session assignment to use direct indexing.	bagel/cli.py
Add mypy to pre-commit hooks for static type checking.	Added mypy configuration to .pre-commit-config.yaml with specific arguments for type checking.	.pre-commit-config.yaml

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#403	Configure mypy pre-commit hook for type checking	✅
#403	Configure mypy to ignore untyped functions	✅
#403	Fix any type errors that are detected	✅

Possibly linked issues

• Add mypy pre-commit hook for type checking #403: The PR adds mypy pre-commit hook, addressing the issue's requirement for type checking.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.54%. Comparing base (9125b91) to head (0ca5554).
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #423      +/-   ##
==========================================
- Coverage   98.54%   98.54%   -0.01%     
==========================================
  Files          18       18              
  Lines        1101     1100       -1     
==========================================
- Hits         1085     1084       -1     
  Misses         16       16              

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[rmanaem]

🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.4.1 🚀