Closes #31. `_alpha_significance` degraded to `(nothing, empty DataFrame)`, and five distinct conditions collapsed onto that one value: the R runtime being held by a pipeline, R/vegan being absent, the groups sharing no sample IDs, R's own `tryCatch` yielding `NA_real_`, and a genuine result in which no pair reached significance. Only the last is a finding. The other four were rendered the way a null result is rendered, which publishes a negative result that was never computed. Two refinements to the issue, both measured rather than assumed: - The omnibus annotation was NOT a false negative. `_significance_stars(nothing)` already returned "n/a". The silent negative was one function away, in `_add_pairwise_annotations!`, which returned early on an empty DataFrame and so drew no brackets - exactly how "no pair reached significance" looks. - The issue describes two conditions; there are five. `:test_failed` (R returning NA for the statistic itself) was not previously distinguished at all. `AlphaSignificance` makes `status` the primary field and the p-value subordinate to it: `:computed` is the only status under which the numbers may be read as evidence. A chart whose pairwise tests did not run now carries an explicit notice instead of silently drawing nothing, and the omnibus caption says "not run" with the reason rather than printing "n/a" beside a test name. On criterion 5, whether to retry rather than degrade: the bounded wait stays. `r_runtime.jl` already argues it - a pipeline can hold R for hours and an interactive handler must not hang behind it. The defect was never the degradation, it was that the degradation was silent. `:r_busy` is transient and its wording invites a retry; `:r_unavailable` is a deployment fault and reads differently. The test that stood here asserted `isnothing(p) && nrow(pairs) == 0` - the ambiguous shape itself - so it passed the defect and would have passed a wrong fix. It now asserts that a not-computed result cannot be mistaken for a computed one. Both mutants were killed before this was believed: reverting the `:r_busy` branch to the old shape reds 4 assertions, and restoring the silent early return reds the surface test. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01X3hgXxWm6umMgZkjYyHnnm

Commits

Commits on Sep 22, 2026

fix: separate a significance test that did not run from a null result