Predefined subtype support, configurable optimisation weights, AnnData-based I/O, testing suite - #6

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robinfallegger wants to merge 64 commits into

earmingol:mainfrom

robinfallegger:predefined-subclusters

Commits on Aug 7, 2026

Add find_stack_level() helper for warning attribution
robinfallegger
committed
69e419e
moved preprocessing steps out of the setup_reference function, and replaced with errors and warnings instead (more user customisation)
robinfallegger
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c14448a
setup_spatial: changed MT/HLA/RPL removal to warning (up to user to remove)
robinfallegger
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4b70adf
added non-negative check skip option
robinfallegger
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f90516a
use automatic stack level finder for warnings
robinfallegger
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cf7fe21
make reference input validation function public
robinfallegger
committed
7541ca6

Commits on Aug 10, 2026

Commits on Aug 11, 2026

Commits on Aug 13, 2026

Commits on Aug 14, 2026

Commits on Aug 25, 2026

fixed type error in plan_subtype_refinement
robinfallegger
committed
281827a
added changelog
robinfallegger
committed
511f38b