Migrate repository tooling to Ruff

[harryswift01]

Summary

This PR will migrate the repository's Python linting and formatting tooling to Ruff.

Changes

Migrate Python tooling to Ruff:

• Replace pyupgrade, isort, Black, and Pylint with Ruff.
• Update the pre-commit development dependencies to include Ruff and rstcheck.

Update pre-commit configuration:

• Add Ruff linting and formatting hooks.
• Retain rstcheck for Python docstrings.
• Retain the Sphinx documentation check as a pre-push hook.
• Exclude Amber input files and notebooks.

Clean up tooling configuration:

• Remove the obsolete Pylint and isort configuration from pyproject.toml.
• Remove the Pylint development dependency.

Impact

• Standardises Python linting and formatting with the organisation-wide Ruff tooling.
• Reduces the number of separate Python development tools and associated configuration.
• Keeps the existing documentation and repository-specific checks in place.

[coveralls]

Coverage Report for CI Build 33634787929

Coverage remained the same at 56.994%

Details

• Coverage remained the same as the base build.
• Patch coverage: No coverable lines changed in this PR.
• 248 coverage regressions across 18 files.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

248 previously-covered lines in 18 files lost coverage.

Top 10 Files by Coverage Loss	Lines Losing Coverage	Coverage
cli/antechamber.py	48	0.0%
cli/sander.py	45	0.0%
cli/parmed.py	34	0.0%
cli/pdb4amber.py	29	0.0%
cli/tleap.py	24	0.0%
helpers.py	17	0.0%
utils/searchprevious.py	13	26.92%
data/sander.py	8	72.97%
data/antechamber.py	6	74.19%
parsers/antechamber.py	4	87.88%

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Coverage Stats

Relevant Lines:	1251
Covered Lines:	713
Line Coverage:	56.99%
Coverage Strength:	3.42 hits per line

---

💛 - Coveralls

[jimboid]

Thanks for implementing this. An important change from pyupgrade and black to ruff. Although a lot of changes, most are just noise aligning from one opinionated tool to another. There a no changes in code behaviour, only syntactic changes. Thanks for sorting this out!