lint/deps

[Adafede]

No description provided.

[Copilot]

Pull request overview

This PR refactors the CLI into a dedicated CliManager, updates packaging and tooling configuration (pyproject, uv.lock, pre-commit, CI), and makes a set of small robustness and documentation fixes across validation logic and tests.

Changes:

• Introduced a CliManager for argument parsing and wired it into the main CLI entrypoint, while re-exporting primary classes from the top-level package.
• Updated dependency metadata (including switching dev dependencies to [dependency-groups]), refreshed locked versions, and expanded/modernized pre-commit hooks.
• Improved error messages, logging text, and tests (including more robust regex matching for error messages and minor doc/typo cleanups).

Reviewed changes

Copilot reviewed 19 out of 28 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
uv.lock	Regenerated lock file with updated dependency versions and metadata (including new dev-dependency layout).
tests/test_processing/test_validation_manager/test_validate_reaction_smarts.py	Reformatted validator calls for readability; no behavior changes.
tests/test_processing/test_validation_manager/test_unescape_string.py	Added blank line after imports to satisfy style.
tests/test_processing/test_validation_manager/test_remove_ketcher_flavor_smarts.py	Added commas and minor formatting to assertions for style consistency.
tests/test_processing/test_validation_manager/test_cleanup_reaction_smarts.py	Adjusted call formatting and trailing commas; logic unchanged.
tests/test_processing/test_validation_manager/test_cleanup_ids.py	Switched to re.escape in pytest.raises(..., match=...) for more robust error-message matching and reformatted JSON mocks.
tests/test_processing/test_validation_manager/test_canonicalize_smiles.py	Reordered imports to group third-party vs. local and added spacing.
tests/test_processing/test_validation_manager/test_canonicalize_smarts.py	Same as above, plus trailing commas in nested function calls for style.
tests/test_processing/test_mite_parser.py	Reordered imports and added commas for style; behavior unchanged.
tests/test_processing/test_file_manager.py	Added blank line between third-party and local imports.
tests/test_processing/test_data_classes.py	Added blank line after imports for style.
tests/test_processing/example_indir_mite/example_valid.json	Ensured file ends with a newline (formatting only).
pyproject.toml	Simplified license-files declaration, reordered classifiers, removed argparse/jsonschema from dependencies, added mite-schema>=1.8.4, and replaced extras with [dependency-groups].dev.
mite_extras/processing/validation_manager.py	Tidied error strings (commas, wording, f-strings) and improved multi-line call formatting; logic preserved.
mite_extras/processing/mite_parser.py	Fixed a docstring typo and corrected f-string quoting when wrapping parse errors.
mite_extras/processing/file_manager.py	Improved log messages (grammar/typos) while keeping behavior the same.
mite_extras/processing/data_classes.py	Added trailing commas, clarified error messages, fixed a typo in a docstring, and slightly refactored validator calls without changing semantics.
mite_extras/main.py	Updated logger formatter call syntax and switched CLI parsing to use the new CliManager.
mite_extras/cli/cli_manager.py	New Pydantic-based CLI manager encapsulating argparse setup and argument parsing for input/output dirs and log verbosity.
mite_extras/init.py	Re-exported CliManager, FileManager, and MiteParser from the top-level package for easier consumption.
README.md	Trimmed trailing whitespace, fixed a “versiom” → “version” typo, but introduced a new “NOW” vs “NWO” acronym typo in the acknowledgements.
CODE_OF_CONDUCT.md	Added a trailing newline; no content change.
CHANGELOG.md	Corrected typos and minor formatting in change descriptions.
.pre-commit-config.yaml	Modernized the hook set (ruff, uv, pyupgrade, deptry, tombi, typos, etc.) and expanded checks; added a typos hook with a broad exclude pattern.
.github/workflows/publish_pypi.yml	Whitespace-only update; behavior unchanged.
.github/workflows/ci.yml	Kept the existing pip install .[dev] step while adjusting a subsequent run: pytest line; this now conflicts with the removal of the dev extra from pyproject.

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[Copilot]

The CI step pip install .[dev] will now fail because the dev extra is no longer defined in pyproject.toml (it has been replaced by a [dependency-groups] section), so pip cannot resolve this extra; please either restore a [project.optional-dependencies].dev extra or change the install step to use the new dependency-group mechanism (or a plain pip install . plus an explicit dev requirements spec).

Suggested change

	pip install .[dev]
	pip install .
	pip install pytest

[Adafede]

@mmzdouc ready!

[mmzdouc]

Hey @Adafede I am not sure if we should add Python 3.13 to the workflow matrix because of requires-python = ">=3.12.0,<3.13.0" in pyproject.toml.
I would propose to update the Python version when we are updating RDKit, and for that, we need the capacity to fix 30+ failing entries 😓

[Adafede]

Hey @Adafede I am not sure if we should add Python 3.13 to the workflow matrix because of requires-python = ">=3.12.0,<3.13.0" in pyproject.toml. I would propose to update the Python version when we are updating RDKit, and for that, we need the capacity to fix 30+ failing entries 😓

Good, removed it!