Add Type Hints to MDAnalysis.analysis.rms

[Agarwalchetan]

Description

This PR adds comprehensive type hints to the MDAnalysis.analysis.rms module as part of the ongoing effort to improve type safety, code documentation, and developer experience in MDAnalysis.

Changes Made

New Imports

• Added typing imports: Optional, Union, List, Dict, Any, Sequence, Tuple, TYPE_CHECKING
• Added numpy.typing.NDArray for array type hints
• Used TYPE_CHECKING guard for AtomGroup and Universe imports to avoid circular import issues at runtime

Function rmsd()

• Added type annotations for all parameters:
  • a: NDArray, b: NDArray - coordinate arrays
  • weights: Optional[NDArray] - optional weight array
  • center: bool, superposition: bool - boolean flags
• Added return type annotation: -> float

Function process_selection()

• Added type hint for select parameter: Union[str, Tuple[str, str], Dict[str, str]]
• Added return type annotation: -> Dict[str, Any]

Class RMSD

• Added class-level type annotations for instance attributes:
  • atomgroup, reference, groupselections, weights
  • weights_groupselections, tol_mass, ref_frame
• Added type hints to __init__() parameters including complex union types
• Added return type annotations to _prepare() and _single_frame() methods: -> None
• Added type assertions to help mypy with type inference in complex control flow

Class RMSF

• Added type hints to __init__() parameters
• Added return type annotations to _prepare(), _single_frame(), and _conclude() methods: -> None

Configuration

• Updated mypy.ini to enable type checking for MDAnalysis.analysis.rms module

PR Checklist

• Issue raised/referenced?
• Tests updated/added? (No new tests needed - type hints only)
• Documentation updated/added? (Type hints serve as inline documentation)
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS?

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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📚 Documentation preview 📚: https://mdanalysis--5179.org.readthedocs.build/en/5179/

[github-actions]

Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on GitHub Discussions so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.72%. Comparing base (bbcef1b) to head (61c8026).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5179      +/-   ##
===========================================
- Coverage    92.72%   92.72%   -0.01%     
===========================================
  Files          180      180              
  Lines        22472    22482      +10     
  Branches      3188     3188              
===========================================
+ Hits         20837    20846       +9     
- Misses        1177     1178       +1     
  Partials       458      458              

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