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fix(diagnostics,summary): NA-safe criteria, AM acceptance, summary contracts - #213

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MaartenMarsman merged 1 commit into
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audit/34-diagnostics-summary
Oct 21, 2026
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MaartenMarsman merged 1 commit into
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audit/34-diagnostics-summary

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Brief 34 of the August 2026 audit. Report: dev/review-2026-08/reports/34-diagnostics-summary.md

Constituent changes:

  • fix(summary): name the indicators field exactly in verdicts.bgmCompare
  • fix(diagnostics): make E-BFMI and the warmup flag NA-safe
  • fix(diagnostics): report the AM tuner acceptance probability
  • fix(summary): row names, contrast-major difference rows, and no dead slab Rhat
  • test(diagnostics,summary): pin the six repaired contracts
  • fix(diagnostics): let the energy trend criterion abstain on a constant trace

Part of the 12-PR stack replacing #200 (one PR per audit brief). Squash-merge in stack order starting from PR 29, then run dev/review-2026-08/restack.sh to rebase the remaining PRs. The combined tip of the stack is bit-identical to the tree that passed the stage gates: full suite 0 fail / 9276 pass, R CMD check --as-cran 0 errors, 0 warnings, 3 benign NOTEs.

Replaces #206, which GitHub closed when its base branch was retired after the #205 merge.

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codecov Bot commented Oct 19, 2026 •

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.09%. Comparing base (bfbb564) to head (a1c9afd).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #213      +/-   ##
===========================================
+ Coverage    92.83%   93.09%   +0.26%     
===========================================
  Files          115      115              
  Lines        18823    18852      +29     
===========================================
+ Hits         17474    17551      +77     
+ Misses        1349     1301      -48     

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@MaartenMarsman
MaartenMarsman force-pushed the audit/34-diagnostics-summary branch 2 times, most recently from 8e92802 to 691d0b6 Compare October 21, 2026 07:57
…ntracts

Brief 34 of the August 2026 audit. Report: dev/review-2026-08/reports/34-diagnostics-summary.md

Constituent changes:
- fix(summary): name the indicators field exactly in verdicts.bgmCompare
- fix(diagnostics): make E-BFMI and the warmup flag NA-safe
- fix(diagnostics): report the AM tuner acceptance probability
- fix(summary): row names, contrast-major difference rows, and no dead slab Rhat
- test(diagnostics,summary): pin the six repaired contracts
- fix(diagnostics): let the energy trend criterion abstain on a constant trace
@MaartenMarsman
MaartenMarsman force-pushed the audit/34-diagnostics-summary branch from 691d0b6 to a1c9afd Compare October 21, 2026 08:16
@MaartenMarsman
MaartenMarsman merged commit b07ab91 into develop Oct 21, 2026
7 of 8 checks passed
@MaartenMarsman
MaartenMarsman deleted the audit/34-diagnostics-summary branch October 21, 2026 09:00
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