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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.