NF Portal Utilities • 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.

[!WARNING] For the last relatively stable version of nfportalutils, please install at https://github.com/nf-osi/nfportalutils/releases/tag/v0.9500-presynapser.

Currently, the package is in a refactoring period where usage is complex because of the coexistence of both synapser and separate synapseclient import. This will be updated when everything is 100% refactored to synapser.

[!NOTE] Underlying dependencies tested for this package are synapser==1.3.0 and synapseclient==3.1.1. There are known breaking issues for MacOS and Windows with the newer versions for now.

Docs

👉 Package documentation!

Installation

You should first install synapser following the instructions here.

Then you can install nfportalutils with:

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

Additional Notes 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.

Additional Notes for Contributors

Contrib workflow

Branch off 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.