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.

The package interops with the Python synapse client via reticulate. You will have to set up both (see #Installation). Outside of the tested versions, there may be some issues. The tested versions are: - Python Synapse Client == 4.3.1 - reticulate == 1.39.0

Docs

👉 Package documentation!

Installation

This presumes you have already set up R with RStudio.

1. Install reticulate following guide at https://rstudio.github.io/reticulate/index.html#installation.
2. Install synapseclient==4.3.1 following https://rstudio.github.io/reticulate/articles/python_packages.html, which will use a default environment “r-reticulate”.
3. Lastly, install nfportalutils. At startup, nfportalutils imports synapseclient from the default “r-reticulate”.

• As regular users: remotes::install_github("nf-osi/nfportalutils", build_vignettes = TRUE) or remotes::install_github("nf-osi/nfportalutils@some-branch", build_vignettes = TRUE)
• For developers, presumably working with devtools:
  • Clone the repo, checkout your desired development branch.
  • Make sure the package repo root is working directory, then in R run devtools::install().

4. Browse some vignettes: browseVignettes("nfportalutils").

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.