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main branch ruleset requires CodeQL/code-quality checks that never run, blocking all PR merges #185

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@d-morrison

The main branch ruleset (ruleset id 11765963) includes two rule types this repo has never configured any workflow to satisfy, which appears to permanently block every PR merge regardless of content:

  • code_scanning: requires a CodeQL analysis at security_alerts_threshold: high_or_higher, alerts_threshold: errors.
  • code_quality: requires a code quality analysis at severity: errors.

There is no CodeQL (or equivalent code-quality) workflow anywhere in .github/workflows/, and GET /repos/Morrison-Lab/rpt/code-scanning/alerts returns 404 no analysis found. With no analysis ever having run, GitHub can't confirm these rules are satisfied, so mergeStateStatus stays BLOCKED even when every required status check and the review are fully green.

Reproduced on #184: all 18 check runs SUCCESS, review verdict "Ready for merge", reviewDecision empty (0 required approvals), zero unresolved threads — yet mergeStateStatus: BLOCKED and gh pr merge would presumably refuse.

Since this is a repo/ruleset configuration gap rather than a per-PR issue, it likely blocks merging on this repo entirely until fixed. Two ways to resolve it:

  1. Add a CodeQL workflow (and whatever produces code_quality results, e.g. GitHub's code quality/Copilot-based analysis) so the required analyses actually run, or
  2. Remove the code_scanning / code_quality rules from the main ruleset if they weren't intentionally added (may have been copied from another repo's ruleset template).

This needs a repo admin — I can't safely modify branch ruleset/security settings myself.

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