fix: select the minimum interstitial distance

[njzjz-bot]

Summary

• Filter the interstitial distance matrix to positive values and take the explicit minimum.
• Raise a clear error if a distance matrix contains no positive distances.
• Add deterministic regression coverage independent of set iteration order.

Tests

• python -m unittest tests.auto_test.test_interstitial_distance -v
• ruff check dpgen/auto_test/Interstitial.py tests/auto_test/test_interstitial_distance.py
• ruff format --check dpgen/auto_test/Interstitial.py tests/auto_test/test_interstitial_distance.py

Fixes #1902

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

Review profile: CHILL

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Run ID: ef39d844-fab2-4fe3-8b52-3cf30cfa7584

📥 Commits

Reviewing files that changed from the base of the PR and between d5ce577 and 3411c64.

📒 Files selected for processing (2)

• dpgen/auto_test/Interstitial.py
• tests/auto_test/test_interstitial_distance.py

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[codecov]

Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 49.82%. Comparing base (d5ce577) to head (3411c64).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
dpgen/auto_test/Interstitial.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1940      +/-   ##
==========================================
+ Coverage   49.80%   49.82%   +0.02%     
==========================================
  Files          83       83              
  Lines       14986    14994       +8     
==========================================
+ Hits         7464     7471       +7     
- Misses       7522     7523       +1     

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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\n\nBlocking finding: exact coincident atoms evade the minimum-distance filter.\n\nGitHub does not permit njzjz-bot to APPROVE or REQUEST_CHANGES on its own pull request, so the formal state is blocked by the self-review rule and this finding is submitted as COMMENT.\n\nCoding agent: Codex\nCodex version: codex-cli 0.151.0\nModel: gpt-5.6-sol\nReasoning 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

[njzjz-bot]

Independent re-review B

Re-reviewed the current head, including zero-overlap handling, upper-triangle selection, regression coverage, and successful CI. The implementation now retains valid off-diagonal zero overlaps. No further changes are required from this review.

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

[njzjz-bot]

Independent re-review C

No changes remain from this independent pass. GitHub does not allow njzjz-bot to formally approve its own PR, so this review is submitted as COMMENT rather than APPROVE.

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

[njzjz-bot]

Independent re-review A

No remaining correctness issues found at 3411c64. I checked upper-triangle pair selection, exact overlapping-atom handling, regression coverage, and passing CI. Because this PR is authored by njzjz-bot, GitHub does not permit this account to approve its own PR; this COMMENT means no changes remain from independent re-review A.

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