nfportalutils

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

:point_right: 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.