Update pre-commits and pytest configuration

[lang-m]

User description

• pre-commit: use ruff and ruff formatting to replace black, isort, flake8
• pre-commit: remove hard-coded Python version
• tests: convert all warnings to errors

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Type

enhancement, bug_fix

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Description

• Updated pre-commit hooks and configurations to use newer versions and streamline settings.
• Removed flake8 configurations from setup.cfg as the project transitions to using ruff for linting.
• Enhanced Python project settings in pyproject.toml to handle specific false positives and improve test configurations.
• Minor code and formatting improvements across various Python modules for better readability and maintenance.

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Changes walkthrough

	Relevant files
Configuration changes	3 files .pre-commit-config.yaml Update and streamline pre-commit configurations                    .pre-commit-config.yaml Updated versions for pre-commit hooks. Removed unused configurations. Added new hook configurations. +2/-5      pyproject.toml Enhance Python project configurations                                        pyproject.toml Added new configurations for tool.coverage.run and tool.pytest.ini_options. Updated tool.ruff settings to handle notebook specific false positives. +14/-7    setup.cfg Remove flake8 configurations                                                          setup.cfg Removed all flake8 configurations. +0/-28
Enhancement	1 files field.py Simplify dictionary comprehension in field.py                        discretisedfield/field.py Simplified dictionary comprehension in _r_dim_mapping property. +1/-1
Formatting	10 files __init__.py Minor formatting improvement in __init__.py                            discretisedfield/init.py Added a blank line for better code organization. +1/-0      __init__.py Minor formatting improvement in io/__init__.py                      discretisedfield/io/init.py Added a blank line for clarity. +1/-0      ovf2vtk.py Minor formatting improvement in ovf2vtk.py                              discretisedfield/io/ovf2vtk.py Added a blank line for clarity. +1/-0      __init__.py Minor formatting improvement in plotting/__init__.py          discretisedfield/plotting/init.py Added a blank line for clarity. +1/-0      hv.py Minor formatting improvement in hv.py                                        discretisedfield/plotting/hv.py Added a blank line for clarity. +1/-0      k3d_field.py Minor formatting improvement in k3d_field.py                          discretisedfield/plotting/k3d_field.py Added a blank line for clarity. +1/-0      mpl.py Minor formatting improvement in mpl.py                                      discretisedfield/plotting/mpl.py Added a blank line for clarity. +1/-0      mpl_field.py Minor formatting improvement in mpl_field.py                          discretisedfield/plotting/mpl_field.py Added a blank line for clarity. +1/-0      __init__.py Minor formatting improvement in tools/__init__.py                discretisedfield/tools/init.py Added a blank line for clarity. +1/-0      tasks.py Minor formatting improvement in tasks.py                                  tasks.py Added a blank line for clarity. +1/-0

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[github-actions]

PR Description updated to latest commit (20b7dff)

[github-actions]

PR Review

⏱️ Estimated effort to review [1-5]	3, because the PR includes a variety of changes across multiple configuration files and Python scripts. The changes involve updates to pre-commit hooks, removal of old linting configurations, and adjustments in testing configurations. Understanding the implications of these changes, especially in the context of continuous integration and code quality, requires a thorough review.
🧪 Relevant tests	No
🔍 Possible issues	Possible Bug: The change in discretisedfield/field.py modifies the behavior of the _r_dim_mapping method by removing the default return value of None for missing keys in the dictionary comprehension. This could lead to a KeyError if reversed_mapping does not contain a key found in self.mesh.region.dims.
🔒 Security concerns	No

Code feedback:

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relevant file	discretisedfield/field.py
suggestion	Consider restoring the default value of None in the dictionary comprehension to avoid potential KeyError. This can be done by modifying the line to include a default return value when the key is not found in the reversed_mapping. [important]
relevant line	return {dim: reversed_mapping.get(dim) for dim in self.mesh.region.dims}

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[github-actions]

PR Code Suggestions

Category	Suggestions
Bug	Add a default value in dictionary lookup to prevent potential None values. In the _r_dim_mapping method, the reversed_mapping.get(dim) call should include a default value to handle cases where dim is not present in reversed_mapping. This prevents the method from returning None for some dimensions, which could lead to unexpected behavior or errors in other parts of the code that rely on this mapping. discretisedfield/field.py [604] -return {dim: reversed_mapping.get(dim) for dim in self.mesh.region.dims} +return {dim: reversed_mapping.get(dim, dim) for dim in self.mesh.region.dims}
Enhancement	Update the revision number in pre-commit configuration to the latest version. Update the rev version for the pre-commit/pre-commit-hooks to v4.5.0 to match the new version specified in the PR. This ensures that all hooks use the latest versions for consistency and to leverage any new features or bug fixes in the hooks. .pre-commit-config.yaml [5] -rev: v4.4.0 +rev: v4.5.0
	Expand the list of ignored warnings in pytest configuration for clearer test outputs. It's beneficial to specify a more comprehensive list of warnings to ignore in the pytest configuration to avoid common false positives and focus on significant warnings during testing. pyproject.toml [112-115] filterwarnings = [ + "error", + "ignore:DeprecationWarning", + "ignore:UserWarning", + "ignore:((.|\n)*)Sentinel is not a public part of the traitlets API((.|\n)*)" +]
Best practice	Refine the pattern for omitting files in coverage configuration to improve accuracy. The omit configuration in [tool.coverage.run] should include more specific patterns to ensure that only test files are omitted from coverage reports, rather than excluding all files under the tests directory. This change helps in maintaining accurate test coverage metrics. pyproject.toml [73] -omit = ["discretisedfield/tests/*"] +omit = ["discretisedfield/tests/**/*.py"]
	Reintroduce the trailing whitespace hook for cleaner code. Consider reintroducing the trailing-whitespace hook in the pre-commit configuration. This hook is useful for maintaining clean code by automatically removing unnecessary trailing whitespaces, which are generally considered bad practice in many coding standards. .pre-commit-config.yaml [7-10] hooks: + - id: trailing-whitespace

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