Bioc parallel#120

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jamespeapen wants to merge 29 commits intohuishenlab:masterfrom

jamespeapen:biocParallel

Commits on Nov 24, 2025

refactor(getArrayABsignal): extract preprocessArrays to own file
jamespeapen
committed
refactor(getCompartments): extract common compartment worker
jamespeapen
committed
refactor(scCompartments): directly call getCompartments without getATACABsignal
jamespeapen
committed
!fix(sc|arrayCompartments): add missing args and reorder for consistency
jamespeapen
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!fix(arrayCompartments): rename getArrayABsignal to arrayCompartments
jamespeapen
committed
docs(scCompartments): specify that inputs are RNA or ATAC
jamespeapen
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refactor: reorganize the arg order in top level functions
jamespeapen
committed
feat(threads): add BiocParallel worker checking functions
jamespeapen
committed
wip: add args for parallelization for scCompartments/arrayCompartments
jamespeapen
committed
wip: parallelize precomputeBootstrapMeans
jamespeapen
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wip: parallelize inference and bootstrapping,
jamespeapen
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chore(flake): update with parallelly
jamespeapen
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docs: add parallelization details
jamespeapen
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docs(vignettes): update call calls with BPPARAM
jamespeapen
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add logging
jamespeapen
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fix(getCompartments): remove bpparams setting
jamespeapen
committed
fix(logging): use futil.logger and move most to debug level
jamespeapen
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fix(bootstrap): don't show progress bar in the bootstrap step
jamespeapen
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fix(parallel): correctly calculate total when outer/inner is 1
jamespeapen
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fix(bootstrap): only message about slow bootstrap if bootstrapping
jamespeapen
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fix(logging): move bootstrap message after computing message
jamespeapen
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docs(parallel): add info on load balancing different configs
jamespeapen
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feat(parallel): check if user BPPARAM settings are optimal
jamespeapen
committed
fix(bootstrapping): don't warn about slow serial bootstrapping
jamespeapen
committed

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Bioc parallel#120

Bioc parallel#120
jamespeapen wants to merge 29 commits intohuishenlab:masterfrom
jamespeapen:biocParallel

Commits on Nov 24, 2025

refactor(getArrayABsignal): extract preprocessArrays to own file

refactor(getCompartments): extract common compartment worker

refactor(scCompartments): directly call getCompartments without getATACABsignal

!fix(sc|arrayCompartments): add missing args and reorder for consistency

!fix(arrayCompartments): rename getArrayABsignal to arrayCompartments

docs(scCompartments): specify that inputs are RNA or ATAC

refactor: reorganize the arg order in top level functions

feat(threads): add BiocParallel worker checking functions

wip: add args for parallelization for scCompartments/arrayCompartments

wip: parallelize precomputeBootstrapMeans

wip: parallelize inference and bootstrapping,

chore(flake): update with parallelly

docs: add parallelization details

docs(vignettes): update call calls with BPPARAM

add logging

fix(getCompartments): remove bpparams setting

fix(logging): use futil.logger and move most to debug level

fix(bootstrap): don't show progress bar in the bootstrap step

fix(parallel): correctly calculate total when outer/inner is 1

fix(bootstrap): only message about slow bootstrap if bootstrapping

fix(logging): move bootstrap message after computing message

docs(parallel): add info on load balancing different configs

feat(parallel): check if user BPPARAM settings are optimal

fix(bootstrapping): don't warn about slow serial bootstrapping

Commits on Dec 19, 2025

fix(parallel): add missing SerialParam import

chore(parallel): fix 'chromosme' typo

docs(parallel): add check_optim

chore(DESCRIPTION): add missing parallelly

test: remove message tests since they're now handled by futile.logger

Bioc parallel#120jamespeapen wants to merge 29 commits intohuishenlab:masterhuishenlab/compartmap:masterfrom jamespeapen:biocParalleljamespeapen/compartmap:biocParallelCopy head branch name to clipboard

Commits

Commits on Nov 24, 2025

Commits on Dec 19, 2025

Bioc parallel#120
jamespeapen wants to merge 29 commits intohuishenlab:masterfrom
jamespeapen:biocParallel