feat: filter short-distance FP structures

[njzjz-bot]

Summary

• add min_distance/min_dist to fp_skip_bad_box screening;
• compute the nearest periodic interatomic distance using the minimum-image convention;
• document the criterion and add regression coverage alongside the existing cell checks.

Example:

"fp_skip_bad_box": "length_ratio:3;height_ratio:3;min_distance:1.0"

Tests

• cd tests/generator && /tmp/dpgen-test-env/bin/python -m unittest test_check_bad_box -v
• /tmp/dpgen-test-env/bin/python -m unittest tests.test_check_examples -v
• ruff check dpgen/generator/run.py dpgen/generator/arginfo.py tests/generator/test_check_bad_box.py
• ruff format --check dpgen/generator/run.py dpgen/generator/arginfo.py tests/generator/test_check_bad_box.py

Fixes #1816

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

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📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and 279fee7.

📒 Files selected for processing (3)

• dpgen/generator/arginfo.py
• dpgen/generator/run.py
• tests/generator/test_check_bad_box.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.84%. Comparing base (d5ce577) to head (279fee7).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1957      +/-   ##
==========================================
+ Coverage   49.80%   49.84%   +0.04%     
==========================================
  Files          83       83              
  Lines       14986    14995       +9     
==========================================
+ Hits         7464     7475      +11     
+ Misses       7522     7520       -2     

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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