fix: Fix pre-commit errors

[lsetiawan]

This pull request includes updates to dependencies, configuration files, and a notebook script to improve compatibility, maintainability, and code quality. Below is a summary of the most important changes grouped by theme:

Dependency Updates:

• Updated the pre-commit hooks to use newer versions of tools such as prettier, ruff, mypy, codespell, validate-pyproject, check-jsonschema, and sp-repo-review for improved functionality and bug fixes. [1] [2] [3]

CI Workflow Improvements:

• Updated the codecov-action in .github/workflows/ci.yml to version v5.3.1 for better coverage reporting.
• Adjusted the runs-on syntax in .github/workflows/codeql.yml for clarity and maintainability.

Notebook Script Enhancements:

• Replaced np.random.seed with np.random.default_rng for better random number generation practices in docs/notebooks.ipynb.
• Added matplotlib.lines.Line2D import at the beginning of the notebook for better code organization.

Configuration File Adjustments:

• Standardized the logging level in pyproject.toml by changing log_cli_level to uppercase INFO.
• Removed the src key from the ruff configuration in pyproject.toml to simplify the setup.

Minor Syntax Changes:

• Standardized the cron schedule format in .github/workflows/codeql.yml by using double quotes.This pull request includes various updates across multiple files to improve code consistency, address deprecations, and enhance maintainability. Key changes include updates to workflow configuration, dependency adjustments, and code improvements in documentation and source files.

Workflow Configuration Updates:

• .github/workflows/codeql.yml: Reformatted the runs-on property for better readability and replaced single quotes with double quotes in the schedule cron expression for consistency. [1] [2]

Dependency and Configuration Adjustments:

• .pre-commit-config.yaml: Updated the Prettier hook to use a different repository (rbubley/mirrors-prettier) and downgraded the version to v3.5.3 for compatibility.
• pyproject.toml: Standardized the logging level to uppercase (INFO) and removed the src directory from the Ruff linter configuration's src property. [1] [2]

Documentation Code Improvements:

• docs/notebooks.ipynb: Replaced np.random.seed with np.random.default_rng for better random number generation practices and optimized imports by moving Line2D to the top of the file. [1] [2]

Related PRs

• chore: update pre-commit hooks #28

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (2f3a1c3) to head (468e9bc).
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main       #34   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files            2         2           
  Lines            6         6           
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  Hits             6         6           

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