pluripotent

Repeatedly generate an embryonic repository with one command.

Like a pluripotent stem cell, this package will generate new cells/projects. These offspring repos are more specialized, and will exist to do real work (as opposed to exist to generate more stem cells).

The inst/metadata/file-to-copy.csv file describes the source and destination of transferred files. The two projects currently natively supported are:

• RAnalysisSkeleton which is our all-purpose data science project.

• cdw-skeleton-1 which is our public repo used to seed our CDW analysis projects.

A new project/repo called ‘beasley-poc-1’ can be generated in two ways:

1. Run this single chunk of code, after updating the project_name and destination_directory arguments.

   remotes::install_github(repo="OuhscBbmc/pluripotent")
   pluripotent::start_cdw_skeleton_1(
     project_name            = "beasley-poc-1",
     destination_directory   = "~/bbmc/cdw"
   )

2. The cdw-template-1 repo provides a platform to jump-start consistent repos for CDW projects. Once it’s used as a GitHub template, the utility/spawn.R file contains the following dynamic code that should run without modification.

   # Install remotes & pluripotent if not already installed.  pluripotent won't reinstall if it's already up-to-date.
   if( !requireNamespace("remotes") ) utils::install.packages("remotes")
   remotes::install_github("OuhscBbmc/pluripotent")
   
   # Discover repo name & parent directory.
   project_name          <- basename(normalizePath(".."))
   project_parent_path   <- normalizePath("..\\..")
   
   # Copy remote files to the current repo.
   pluripotent::start_cdw_skeleton_1(
   project_name          = project_name,
   destination_directory = project_parent_path
   )
   
   # Afterwards, close RStudio and open the *.Rproj file in the root directory.

   To spawn a cdw repo (i.e., a repo whose template is cdw-template-1):

   1. open utility/spawn.R directly in RStudio & run the whole file (i.e., ctrl+shift+r)
   2. after it completes, close RStudio
   3. commit & push the repo. A typical commit message is > populate repo files > > closes #1 (or whatever issue number corresponds to ‘initialize repo’)
   4. go up one directory (to the repo root) and open the *.Rproj file.
   5. Do Science 🥇

3. To update a config file that’s downloaded from the skeleton’s config file, run this instead of spawning a new repo. This scenario comes up when refitting older repos to newer standards.

   pluripotent::populate_config("config.yml", basename(getwd())

@andkov, as I’m describing this, I see the resemblance to a factory pattern in software. But the stem cell metaphor is both flowery and abstruse, which seems to be what you and I go for when we’re attaching metaphors.

Installation and Documentation

The development version can be installed from GitHub after installing the remotes package.

install.packages("pluripotent") # Run this line if the 'remotes' package isn't installed already.
remotes::install_github(repo="OuhscBbmc/pluripotent")

The package can be uninstalled from your local machine with remove.packages("pluripotent").

Build Status and Package Characteristics

GitHub	Travis-CI	AppVeyor	Coveralls
Main
Dev
	Ubuntu LTS	Windows Server	Test Coverage

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