This PR changes the parallelization architecture, replacing foreach with a combination of future, doFuture, and BiocParallel. This PR addresses points brought up in #18, #31, and #32.
Pros:
BiocParallel is the recommended parallelization architecture for Bioconductor packages. It is a flexible wrapper for registering parallelization schemes and supports many backends. Adopting this package also means that users in the Bioconductor community will be more "at home" when manipulating/modifying the internals of this software
future and doFuture together provide an extremely flexible manner by which parallel evaluation can be performed across a variety of architectures and plans. The current implementation flexibly invokes either future::multiprocess or future::sequential, and provides the user the flexibility to specify their own preferred plan (via the new future_param argument to the biomarkertmle wrapper function).
The foreach loop is replaced in favor of a call to BiocParallel::bplapply, which provides a cleaner syntax for evaluating the relevant estimation procedure.
This PR changes the parallelization architecture, replacing
foreachwith a combination offuture,doFuture, andBiocParallel. This PR addresses points brought up in #18, #31, and #32.Pros:
BiocParallelis the recommended parallelization architecture for Bioconductor packages. It is a flexible wrapper for registering parallelization schemes and supports many backends. Adopting this package also means that users in the Bioconductor community will be more "at home" when manipulating/modifying the internals of this softwarefutureanddoFuturetogether provide an extremely flexible manner by which parallel evaluation can be performed across a variety of architectures and plans. The current implementation flexibly invokes eitherfuture::multiprocessorfuture::sequential, and provides the user the flexibility to specify their own preferredplan(via the newfuture_paramargument to thebiomarkertmlewrapper function).foreachloop is replaced in favor of a call toBiocParallel::bplapply, which provides a cleaner syntax for evaluating the relevant estimation procedure.Cons: