[Feature request]: overhaul flepiconfig to current config schema, a to use yaml::write_yaml

[pearsonca]

Label

dependency, r-flepiconfig

Priority Label

medium priority

Describe the bug/issue

the flepiconfig package no longer reflects the current configuration structure. additionally, the package imports the yaml package, but uses manual file writing to create configurations.

Desired Solution

flepiconfig should be re-written (with a breaking-indicating version change) to reflect the current configuration approach. ideally, flepiconfig will also deal with correctly assembling configuration file structures, so that future changes to config schema won't have big impacts on users code leveraging flepiconfig2.0

[pearsonca]

upstream of this: need to separate flepiconfig as its own R package, update flepimop to depend on specific (current) version and then in a future version of flepimop, update its dependencies to reflect the updated (breaking) flepiconfig.

then need to provide information on how to revert to old version of flepiconfig if needed to run some particular old script.

basically, need to let people use the old flepiconfig version if they need to, but start switching new applications / users over to updated version.

[pearsonca]

There is one supporting infrastructure gap in yaml package: vubiostat/r-yaml#77 and/or vubiostat/r-yaml#123 - we really want to support the array style for user readability, and particularly some of our nested array syntax, while legal yaml, might not be convenient to output.

There is some work on a branch to support some of what we need, but I expect we will need to successully offer contributions against that project if we want to leverage it.