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test(differential): the absence-path ml fit needs fittable counts #176

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Merged
hyperpolymath merged 2 commits into from
Oct 16, 2026
Merged

test(differential): the absence-path ml fit needs fittable counts #176

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test(differential): the absence-path ml fit needs fittable counts
hyperpolymath Oct 16, 2026
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Merge branch 'main' into fix/glmgampoi-test
hyperpolymath Oct 16, 2026
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11 changes: 9 additions & 2 deletions test/unit/test_differential.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -755,8 +755,15 @@ end
@test e isa GlmGamPoiUnavailable
@test occursin("renv::restore()", sprint(showerror, e))
# The override defers to base for everything else, so the default
# dispersion must still fit normally with it in place.
r = fit_nb([5 6; 7 3; 9 4; 4 8], ["A", "A", "B", "B"], [0.0, 0.0, 0.0, 0.0];
# dispersion must still fit normally with it in place. The
# injected-effect dataset, not the minimal matrix above:
# MEASURED with MASS::glm.nb, with 4 samples of small counts the
# alternating fit runs theta to its upper bound (status boundary)
# and one taxon's fit even produced NaNs (status failed), so that
# data never reaches status ok on any machine; the dataset
# "Negative-binomial fit recovers an injected effect" already
# proves fits.
r = fit_nb(effect, effect_groups, log.(tss_factors(effect, effect_samples));
levels=("A", "B"))
@test all(r.status .== "ok")
finally
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