Skip to content

Utilities for NF Portal project and data management

License

MIT, MIT licenses found

Licenses found

MIT
LICENSE
MIT
LICENSE.md
Notifications You must be signed in to change notification settings

nf-osi/nfportalutils

nfportalutils

R-CMD-check

The goal of nfportalutils is to provide convenience functions for project and (meta)data management in the NF-OSI data portal scope. Currently, develop branch is default so package install and docs refer to code in this branch.

Docs

👉 Package documentation!

Installation

You can install nfportalutils from here:

remotes::install_github("nf-osi/nfportalutils")

The package interops with the Python synapse client via reticulate. You will have to download the Python synapse client first.

For Users

  • View function reference on docs site at Reference.
  • An alternative to viewing vignettes as Articles on the docs site is to download them with pkg install and load with e.g. vignette("annotate-nf-processed-data", package = "nfportalutils") to view.

For Contributors

General picture

  • Again, default development happens in develop.
  • But we have a side branch called develop-synapser where interop tries to transition to synapser. However, current coexistence makes development a bit tricky so consult first before trying new developments there.

Contrib workflow

  • Branch of develop and make changes
  • Run devtools::check(vignettes = FALSE) early and often, and definitely before submitting a PR
  • Make a pull request to develop; this will run R-CMD-CHECK and pkgdown
  • Request a reviewer if both checks pass
  • Reviewer requests changes or merges

Local development tips

  • Some vignettes need to be precomputed.
  • Again, run devtools::check(vignettes = FALSE) early and often.
  • At minimal, address any ERRORS and WARNINGS.
  • Yes, we do have a lot of NOTES that need to be resolved.
  • For custom indexing after adding/updating functions, edit the _pkgdown.yml.
  • Preview the pkg docs site locally with pkgdown::build_site().

Code of Conduct

Please note that the nfportalutils project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

About

Utilities for NF Portal project and data management

Resources

License

MIT, MIT licenses found

Licenses found

MIT
LICENSE
MIT
LICENSE.md

Code of conduct

Stars

Watchers

Forks

Packages

 
 
 

Languages