chore(pt): cleanup deadcode

[wanghan-iapcm]

• Clean up unused methods in region.py and preprocess.py #3791
• mainly preprocess and region
• deepmd/pt/infer/deep_eval.py:595:0: DC02 Function eval_model is never used. used by test_unused_params, which seems not easy to remove

Summary by CodeRabbit

• New Features

  • No new features introduced; significant code simplifications made.

• Bug Fixes

  • No specific bug fixes identified; however, the removal of outdated functions may enhance overall stability.

• Refactor

  • Removed the Region3D class and associated functions to streamline preprocessing logic.
  • Eliminated the get_atom_axis function to simplify atom axis determination.
  • Removed the _to_face_distance function, suggesting a refactor in distance calculations.

• Tests

  • Removed the TestLegacyRegion class, reducing the scope of testing related to the Region3D functionality.

[coderabbitai]

Walkthrough

Walkthrough

The changes include the removal of the get_atom_axis function from transform_output.py, the complete elimination of the Region3D class and several related functions from preprocess.py, and the removal of the private function _to_face_distance from region.py. Additionally, the TestLegacyRegion class has been removed from the test file test_region.py, which contained tests related to the Region3D functionality. These modifications indicate a significant refactoring and simplification of the codebase, particularly concerning the handling of atom coordinates and related functionalities.

Changes

File Path	Change Summary
deepmd/pt/model/model/transform_output.py	Removed get_atom_axis function.
deepmd/pt/utils/preprocess.py	Removed Region3D class and related functions: normalize_coord, compute_serial_cid, compute_pbc_shift, build_inside_clist, append_neighbors, build_neighbor_list. Only compute_smooth_weight remains.
deepmd/pt/utils/region.py	Removed _to_face_distance function.
source/tests/pt/model/test_region.py	Removed TestLegacyRegion class and its associated tests related to Region3D.

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Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between ba9f02f and 3bbef71.

Files selected for processing (4)

• deepmd/pt/model/model/transform_output.py (0 hunks)
• deepmd/pt/utils/preprocess.py (0 hunks)
• deepmd/pt/utils/region.py (0 hunks)
• source/tests/pt/model/test_region.py (0 hunks)

Files not reviewed due to no reviewable changes (4)

• deepmd/pt/model/model/transform_output.py
• deepmd/pt/utils/preprocess.py
• deepmd/pt/utils/region.py
• source/tests/pt/model/test_region.py

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.31%. Comparing base (64e6e52) to head (3bbef71).
Report is 198 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4142      +/-   ##
==========================================
+ Coverage   83.03%   83.31%   +0.28%     
==========================================
  Files         532      533       +1     
  Lines       52187    52051     -136     
  Branches     3030     3030              
==========================================
+ Hits        43331    43365      +34     
+ Misses       7911     7737     -174     
- Partials      945      949       +4     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[njzjz]

• deepmd/pt/infer/deep_eval.py:595:0: DC02 Function eval_model is never used. used by test_unused_params, which seems not easy to remove

It can be moved to tests