fix: preserve atom order in map_atom_types

[rathodkunj2005]

Summary

• map each existing atom type entry through atom_names instead of expanding grouped atom_numbs
• add a regression test for interleaved atom order ([H, O, H])

Fixes #984.

Verification

• python -m pytest test_system_set_type.py -q (from tests/): 3 passed in 0.20s
• python -m ruff check dpdata/system.py tests/test_system_set_type.py: All checks passed!
• issue reproducer now prints [0, 1, 0]

Summary by CodeRabbit

• Bug Fixes

  • Improved atom-type remapping so it now preserves the current atom order when converting to a new type map.
  • Ensured remapped atom types are generated consistently from existing atom-type indices.

• Tests

  • Added coverage verifying atom-type remapping returns the expected order for a simple in-memory system.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 5ac78019-0bea-4bc0-80b5-b0d3960d54b8

📥 Commits

Reviewing files that changed from the base of the PR and between 5de0229 and 139e559.

📒 Files selected for processing (2)

• dpdata/system.py
• tests/test_system_set_type.py

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📝 Walkthrough

Walkthrough

Fixed System.map_atom_types in dpdata/system.py to compute mapped atom types directly from the existing atom_types index sequence via atom_names, instead of rebuilding from grouped atom_names/atom_numbs, preserving current atom order. Added a corresponding unit test.

Changes

map_atom_types Fix

Layer / File(s)	Summary
Order-preserving atom type mapping dpdata/system.py, tests/test_system_set_type.py	map_atom_types now indexes atom_names using existing atom_types entries and maps through type_map, preserving atom order; a new test validates the corrected mapping.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Estimated code review effort

Not applicable beyond the metadata line above.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly matches the main fix: preserving atom order in map_atom_types.
Linked Issues check	✅ Passed	The code now maps self.data["atom_types"] directly through atom_names, matching #984 and the expected interleaved order.
Out of Scope Changes check	✅ Passed	The changes stay focused on the atom-type remapping fix and its regression test.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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[codspeed-hq]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 2 untouched benchmarks

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_{Comparing rathodkunj2005:fix-map-atom-types-order (139e559) with master (5de0229)}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.87%. Comparing base (5de0229) to head (139e559).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1007      +/-   ##
==========================================
- Coverage   86.87%   86.87%   -0.01%     
==========================================
  Files          89       89              
  Lines        8268     8266       -2     
==========================================
- Hits         7183     7181       -2     
  Misses       1085     1085              

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