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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #471 +/- ##
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Coverage 86.05% 86.05%
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Files 15 15
Lines 1276 1276
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Hits 1098 1098
Misses 178 178
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When dispersion optimization fails,
fit_alpha_mlecallsgrid_fit_alphawithout forwarding its regularization settings. The grid therefore enables Cox-Reid correction and disables the dispersion prior regardless of the requested objective. In particular, MAP fallback silently drops its prior.Forward
prior_disp_var,cr_reg, andprior_regso fallback continues minimizing the configured objective. Default gene-wise fallback behavior and the unsuccessful convergence flag are unchanged.The regression forces optimizer failure for BFGS and L-BFGS-B across all four Cox-Reid/prior combinations. It compares the result with an independently minimized negative-binomial log-PMF plus the requested penalties. Six cases fail before the fix; all eight pass afterward.
Validation: full upstream suite passes (73 tests); Ruff lint, formatting, and mypy pass.