Parameter dataclass refactoring#56

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kaghi wants to merge 34 commits intomainfrom

parameter-dataclass-refactoring

Commits on Jan 22, 2026

Initial refactor attempt

daharoni
authored and
sneakers-the-rat
committed
small fixes based on tests errors

daharoni
authored and
sneakers-the-rat
committed
add option to include legacy bug for comparing to old deconv code

daharoni
authored and
sneakers-the-rat
committed
black formatting

daharoni
authored and
sneakers-the-rat
committed
refactor pipeline

daharoni
authored and
sneakers-the-rat
committed
black format

daharoni
authored and
sneakers-the-rat
committed
add yappi and snakeviz for function level profiling

daharoni
authored and
sneakers-the-rat
committed
precompute square of Wt matrix

daharoni
authored and
sneakers-the-rat
committed
optimize all instances of self.Wt.T @ self.Wt

daharoni
authored and
sneakers-the-rat
committed
add result plotting of pipeline after profile run

daharoni
authored and
sneakers-the-rat
committed
optimize more by doing row-scalling of Mw

daharoni
authored and
sneakers-the-rat
committed
run all tests, split plotting step to separate job, fix pdm cache
sneakers-the-rat
committed
actually ignore test outputs
sneakers-the-rat
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rm pytest args that are redundant with pyproject.toml config
sneakers-the-rat
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match default for wt_trunc_thres
sneakers-the-rat
committed
do not default to verbose pytest output
sneakers-the-rat
committed

Commits on Jan 29, 2026

Added InputParams and UpdateParams class and am in the process of incorporating in DeconvBin.
kaghi
committed

Commits on Jan 30, 2026

Added solver function and have addressed downstream changes incorporating self._solver.
kaghi
committed

Commits on Feb 7, 2026

Added a new file as part of deconvolution module that moves the spike inference steps in the Deconv class to their own file (thres_and_solv.py). Started by refactoring max_thres. Other functions I …
kaghi
committed

Commits on Feb 11, 2026

Fixing bugs with variable name assignment issues in DeconvBin class
kaghi
committed

Commits on Feb 13, 2026

Fixing more bugs. Running into error with construction of G matrix where it doesn't initialize. I keep getting this:
kaghi
committed

Commits on Feb 16, 2026

Fixed more bugs during testing. Still have some issues with more bugs.
kaghi
committed

Commits on Feb 17, 2026

Commits on Feb 18, 2026

Commits on Feb 19, 2026

Debugging test_pipeline.py assertion error with F1 score
kaghi
committed

Commits on Feb 21, 2026

Fixed formatting issue of deconv.py
kaghi
committed

Commits on Mar 11, 2026

Testing pipeline with refactored code.
kaghi
committed