Devnotes • nemo

R pkg dev

Command	Comment	Shortcut
`devtools::check()`	build and check the pkg	`Cmd + Shift + E`
`devtools::load_all()`	load the pkg	`Cmd + Shift + L`
`devtools::document()`	document the pkg	`Cmd + Shift + D`
`pak::local_install(upgrade = FALSE)`	install the pkg into the first library of `.libPaths()`	`Cmd + Shift + B`

conda

Command	Comment
`conda install foo -c bar`	install pkg `foo` from channel `bar`
`conda create --file env.yml --prefix ./bar`	install conda pkgs listed in `env.yml` into the `./bar` directory
`conda info -e`	list conda environments installed on this machine
`rattler-build build -r recipe.yaml --output-dir ${HOME}/tmp`	build conda pkg from a recipe file
`rattler-build upload anaconda -o tidywf --api-key <xxx> ${HOME}/tmp/r-<pkg>.conda`	upload conda pkg to anaconda

pkgdown

Command	Comment
`pkgdown::build_site()`	builds entire site
`pkgdown::build_articles(quiet = FALSE)`	builds vignettes in debug mode
`pkgdown::build_article("foo")`	builds `foo` vignette only

Debugging R6 private methods

For private methods, reach into .__enclos_env__$private (flags that instance only):

devtools::load_all()
path <- system.file("extdata/tool1", package = "nemo")
t <- Tool$new(name = "tool1", pkg = "nemo", path = path)

debugonce(t$.__enclos_env__$private$build_d_write)
t$run(output_dir = tempdir(), format = "parquet") # breaks on first call

Call private methods standalone:

row <- t$list_files()[1, ]
row$tidy <- list(t$.__enclos_env__$private$dispatch_tidy(row$path, row$parser))
d_write <- t$.__enclos_env__$private$build_d_write(
  row,
  tempdir(),
  NULL,
  NULL,
  FALSE
)

Data Version Control

DVC keeps test/example data in remote storage, tracked in git. Run dvc pull before tests, examples or vignettes.

Each pkg has two Cloudflare R2 remotes:

pull: cloudflare_r2_<pkg> (public, no auth), the default in .dvc/config
push: cloudflare_r2_<pkg>_push (private), set in gitignored .dvc/config.local, with R2 creds passed via env vars

Command	Comments
`dvc init`	initialise dvc
`dvc remote add -d storage gdrive://<...>`	add GDrive remote
`dvc remote add -d my_r2 s3://<...>`	add Cloudflare R2 remote
`dvc remote modify my_r2 endpointurl https://<...>.r2.cloudflarestorage.com`	add Cloudflare R2 remote endpointurl
`dvc remote list`	list all remotes
`dvc check-ignore *`	check what is dvc-ignored
`dvc list https://github.com/tidywf/<pkg> inst/extdata`	list dvc’ed data
`dvc add path/to/folder`	adds `folder` (and its contents) to dvc
`dvc add path/to/file.txt`	adds `file.txt` to dvc
`dvc pull`	pulls dvc data from public remote (no auth)
`AWS_ACCESS_KEY_ID=... AWS_SECRET_ACCESS_KEY=... dvc push -r cloudflare_r2_<pkg>_push`	pushes dvc data to private R2 remote (needs auth)