test(dpmodel): collect ASE virtual atom regression

[njzjz-bot]

Closes #5664.

Summary

• retain the ASE virtual-atom edge filtering already added by feat(pt_expt): O(N) on-device NeighborGraph builders — vesin & nvalchemiops (PR-C) #5714
• move its intended dense/ASE parity regression into TestAseCarryAll so pytest actually collects it
• verify that neither graph centers nor neighbors can reference atype < 0

Why existing tests missed this

The production fix landed incidentally in the larger graph-builder PR #5714. Its dedicated virtual-atom regression was syntactically valid but placed after if __name__ == "__main__": unittest.main() while still indented, so pytest did not collect it. The other ASE/dense parity tests used only nonnegative atom types, allowing CI to pass without executing the original failure case.

Before this change, --collect-only reported four tests in test_from_ijs.py; after moving the guard, it reports five and includes test_ase_excludes_virtual_atoms_like_dense.

Validation

• pytest source/tests/common/dpmodel/test_from_ijs.py -v (5 passed)
• ruff format . (1663 files unchanged)
• ruff check . (passed)
• git diff --check (passed)

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.32%. Comparing base (6c3b985) to head (2da720d).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5855      +/-   ##
==========================================
- Coverage   78.58%   78.32%   -0.26%     
==========================================
  Files        1050     1050              
  Lines      120637   120638       +1     
  Branches     4356     4355       -1     
==========================================
- Hits        94801    94490     -311     
- Misses      24278    24586     +308     
- Partials     1558     1562       +4     

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[njzjz]

Possible reviewers based on changed lines, exact file history, and exact-file review history:

• @wanghan-iapcm — 2 commits on changed files; 11 reviews on exact changed files (source/tests/common/dpmodel/test_from_ijs.py).
• @OutisLi — 8 reviews on exact changed files (source/tests/common/dpmodel/test_from_ijs.py).

No review request was made automatically.

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh