Sparse matrix rebase#52

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sneakers-the-rat wants to merge 17 commits intomainfrom

sparse-matrix-rebase

Commits on Jan 22, 2026

Initial refactor attempt

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

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

daharoni
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sneakers-the-rat
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black formatting

daharoni
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sneakers-the-rat
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refactor pipeline

daharoni
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sneakers-the-rat
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black format

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

daharoni
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sneakers-the-rat
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precompute square of Wt matrix

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

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

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

daharoni
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sneakers-the-rat
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run all tests, split plotting step to separate job, fix pdm cache
sneakers-the-rat
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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
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do not default to verbose pytest output
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make 'format' pdm script
sneakers-the-rat
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