fix: deduplicate model deviation timesteps

[njzjz-bot]

Summary

• discard intermediate model-deviation evaluations that repeat an existing timestep;
• retain the final evaluation because it corresponds to the accepted trajectory configuration;
• preserve existing PIMD model-deviation merging behavior and add regression coverage.

Tests

• cd tests/generator && /tmp/dpgen-test-env/bin/python -m unittest test_make_md.TestMakeModelDevi.test_read_model_devi_file_keeps_last_row_per_timestep test_make_md.TestMakeModelDevi.test_read_model_devi_file_pimd -v
• ruff check dpgen/generator/run.py tests/generator/test_make_md.py
• ruff format --check dpgen/generator/run.py tests/generator/test_make_md.py

Fixes #1756

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[coderabbitai]

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Configuration used: Organization UI

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Run ID: b6734b95-3629-4602-b0b5-5574a91187f7

📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and 431c7f0.

📒 Files selected for processing (2)

• dpgen/generator/run.py
• tests/generator/test_make_md.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.81%. Comparing base (d5ce577) to head (431c7f0).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1956      +/-   ##
==========================================
+ Coverage   49.80%   49.81%   +0.01%     
==========================================
  Files          83       83              
  Lines       14986    14990       +4     
==========================================
+ Hits         7464     7468       +4     
  Misses       7522     7522              

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[njzjz-bot]

Independent review C

I found no blocking correctness, regression, security, or API issue in this change. CI/check evidence was considered alongside the full patch and relevant surrounding implementation. A formal APPROVE state cannot be submitted because the active njzjz-bot account is the PR author; GitHub self-review rules permit only a COMMENT review here.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review B

No blocking findings. I reviewed the full diff, relevant surrounding behavior, tests, and current check status. GitHub does not permit njzjz-bot to APPROVE or REQUEST_CHANGES on its own pull request, so this review is recorded as COMMENT only.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

[njzjz-bot]

Independent review A

No blocking findings after reviewing the full diff, relevant surrounding implementation/tests, and the current check rollup. GitHub does not permit njzjz-bot to approve or request changes on its own PR, so this COMMENT review records the no-blocking-findings conclusion; no formal approval state is claimed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh