Refactor atom density class

[robinzyb]

No description provided.

[Copilot]

Pull Request Overview

This PR refactors the AtomDensity analysis to introduce a standalone function run_atom_density_analysis, updates tests to use this function, and revises documentation to reflect the new API.

• Tests now import and call run_atom_density_analysis, remove the class instantiation, and switch to assert_almost_equal for float comparisons.
• Documentation’s usage section shows how to build inputs, instantiate MDAnalysis objects, and call both the class and the new helper function.
• Added an “Old inputs” section recommending run_atom_density_analysis for users of the previous API.

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
tests/analysis/atom_density/test_atom_density.py	Switched to run_atom_density_analysis, updated fixture return, changed assertions to assert_almost_equal.
docs/analysis/atom_density.md	Expanded usage examples, added code snippet for MDAnalysis setup, introduced run_atom_density_analysis in legacy section.

Comments suppressed due to low confidence (2)

docs/analysis/atom_density.md:80

• Include necessary imports for Universe and Cell (e.g., from MDAnalysis import Universe and from MDAnalysis.core.universe import Cell) at the top of this snippet so users can run the example successfully.

xyz_file = inp.get("xyz_file")

docs/analysis/atom_density.md:145

• The variable input_dict is not defined; it should be inp_dict to match the example input object.

ad = run_atom_density_analysis(input_dict)

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 89.05109% with 15 lines in your changes missing coverage. Please review.

Project coverage is 26.18%. Comparing base (08f4688) to head (e0b389b).

Files with missing lines	Patch %	Lines
ectoolkits/analysis/atom_density.py	89.05%	15 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #48      +/-   ##
==========================================
- Coverage   26.79%   26.18%   -0.62%     
==========================================
  Files          23       23              
  Lines        3381     3468      +87     
==========================================
+ Hits          906      908       +2     
- Misses       2475     2560      +85     

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