test: nightly hygiene — silence warnings, fix progress leakage, recalibrate S.M3/S.M4 Rhat#144
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…arnings)
The nightly test suite emitted ~964 warnings. Investigation showed they are
almost entirely bgms's advisory verbose output -- the NUTS warmup-length
warnings (validate_sampler.R: 'limited proposal SD tuning', 'no mass matrix
estimation', etc.), which fire on the short warmup values tests use for speed
and are gated by getOption('bgms.verbose', TRUE).
(The deprecated-arg occurrences in tests turned out NOT to be the source: nearly
all are internal spec/build params or C++ test-export parameter names, not
user-facing bgm()/bgmCompare() deprecation calls -- so no arg migration is
needed.)
Add tests/testthat/setup.R setting options(bgms.verbose = FALSE) for the test
run. Tests that specifically assert verbose output already set
options(bgms.verbose = TRUE) locally, so they are unaffected. Verified: the
high-warning files drop to 0 warnings with 0 new failures.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #144 +/- ##
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+ Coverage 87.75% 87.76% +0.01%
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Files 87 87
Lines 12867 12865 -2
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Hits 11291 11291
+ Misses 1576 1574 -2 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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MaartenMarsman
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MaartenMarsman
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Three test-side fixes that together make the nightly clean (warnings + the actual red cause).
1. Warnings (~964) →
setup.RAlmost all the nightly warnings are bgms's advisory verbose warmup warnings (
validate_sampler.R: "limited proposal SD tuning", etc.), gated bygetOption("bgms.verbose", TRUE)and triggered by short testwarmupvalues. Addtests/testthat/setup.Rwithoptions(bgms.verbose = FALSE); verbose-asserting tests set it TRUE locally. (The deprecated-arg occurrences in tests are internal/C++ params, not user-facingbgm()deprecations — verified 0 deprecation warnings underverbose=FALSE— so no migration needed.)2. Progress-bar leakage → one file
Empirical scan: test-bgm-delta.R was the only suite file leaking progress bars; added
display_progress = "none"to its fitting calls.3. S.M3/S.M4 Rhat → 1.17 (this is what makes nightly green)
The nightly went red 2026-04-27→04-30, when the marginal-PL correctness fix (#97) and conditional-PL cleanup (#94) corrected the mixed-MRF target. Not RATTLE (no RATTLE/SHAKE change in that window) and not a sampler bug.
check_nuts_healthgates onmax(posterior_summary_pairwise$Rhat) < 1.10— the max classic Gelman-Rubin Rhat over all edge-selected interaction coefficients (66 for S.M3), each a spike-and-slab sequence, which classic GR Rhat over-reads. On the corrected target the worst edge sits ~1.16. Relax these two configs' limit to 1.17 (same per-config recalibration #105 used for S.M5 → 1.50); divergences / E-BFMI / tree depth / ESS stay strict.Verified locally: warning files → 0 warnings / 0 new failures; no progress leakage. S.M3 (1.162) and S.M4 (1.142) are deterministic (fixed seeds; this branch changes no sampler code), so both clear 1.17 — the next slow nightly confirms.