Use 'future.seed' and 'progressr' in the future framework#177
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ycl6 wants to merge 1 commit intojinworks:mainfrom
Open
Use 'future.seed' and 'progressr' in the future framework#177ycl6 wants to merge 1 commit intojinworks:mainfrom
ycl6 wants to merge 1 commit intojinworks:mainfrom
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ycl6
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A PR with similar changes has been submitted before to CellChat v1 to fix and improve a few issues that seems to have persisted into the v2 version.
This PR changes how some functions deal with sequential and parallel processes.
Following the suggestion in sqjin/CellChat#424 and discussion in sqjin/CellChat#140 regarding the missing
future.seedsetting, I dropped the detection of number of cores and theifelseswitch betweenpbapply::pbsapplyandfuture.apply::future_sapplyfor sequential and parallel computing respectively, and opted to use theprogressrpackage for progress updates, which is the recommended way in thefutureframework.I also parallelise the calculation of
Pboot(default with 100 permutations) in thecomputeCommunProbfunction, which was running sequentially previously. The update should significantly speed upcomputeCommunProb().