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.
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-synapserwhere interop tries to transition tosynapser. However, current coexistence makes development a bit tricky so consult first before trying new developments there.
Contrib workflow
- Branch of
developand make changes - Run
devtools::check(vignettes = FALSE)early and often, and definitely before submitting a PR - Make a pull request to
develop; this will runR-CMD-CHECKandpkgdown - 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
ERRORSandWARNINGS. - Yes, we do have a lot of
NOTESthat 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.