-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #127 from chainsawriot/userang
Add a usable version of `use_rang` for Rocker
- Loading branch information
Showing
15 changed files
with
424 additions
and
63 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: rang | ||
| Title: Reconstructing Reproducible R Computational Environments | ||
| Version: 0.2.2 | ||
| Version: 0.2.3 | ||
| Authors@R: | ||
| c(person("Chung-hong", "Chan", , "[email protected]", role = c("aut", "cre"), | ||
| comment = c(ORCID = "0000-0002-6232-7530")), | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| #' Setup rang for a directory | ||
| #' | ||
| #' This function adds the infrastructure in a directory (presumably with R scripts | ||
| #' and data) for (re)constructing the computational environment. | ||
| #' Specifically, this function inserts `inst/rang` into the directory, which contains | ||
| #' all components for the reconstruction. Optionally, `Makefile` and `.here` are also inserted | ||
| #' to ease the development of analytic code. | ||
| #' By default, (re)running this function does not overwrite any file. One can change this by setting | ||
| #' `force` to TRUE. | ||
| #' @param path character, path to the project root | ||
| #' @param add_makefile logical, whether to insert a barebone `Makefile` in the project root. | ||
| #' @param add_here logical, whether to insert a hidden `.here` file in the project root | ||
| #' @param verbose logical, whether to print out messages | ||
| #' @param force logical, whether to overwrite files (`inst/rang/update.R`, `Makefile`, `.here`) if they | ||
| #' exist. | ||
| #' @return path, invisibly | ||
| #' @details The infrastructure being added to your path consists of: | ||
| #' * `inst/rang` directory in the project root | ||
| #' * `update.R` file inside the directory | ||
| #' * `.here` in the project root (if `add_here` is TRUE) | ||
| #' * `Makefile` in the project root (if `add_makefile` is TRUE) | ||
| #' You might need to edit `update.R` manually. The default is to scan the whole project for | ||
| #' used R packages and assume they are either on CRAN or Bioconductor. If you have used other R packages, | ||
| #' you might need to edit this manually. | ||
| #' @export | ||
| use_rang <- function(path = ".", add_makefile = TRUE, add_here = TRUE, | ||
| verbose = TRUE, force = FALSE) { | ||
| if (isFALSE(dir.exists(path))) { | ||
| stop("'path' does not exist") | ||
| } | ||
| base_dir <- file.path(path, "inst/rang") | ||
| if (isFALSE(dir.exists(base_dir))) { | ||
| dir.create(base_dir, recursive = TRUE) | ||
| .vcat(verbose, "`inst/rang` created.") | ||
| } else { | ||
| .vcat(verbose, "`inst/rang` exists.") | ||
| } | ||
| if (isFALSE(file.exists(file.path(base_dir, "update.R"))) || isTRUE(force)) { | ||
| file.copy(system.file("update.R", package = "rang"), file.path(base_dir, "update.R"), overwrite = TRUE) | ||
| } | ||
| if (isTRUE(add_makefile) && (isFALSE(file.exists(file.path(path, "Makefile"))) || isTRUE(force))) { | ||
| file.copy(system.file("Makefile", package = "rang"), file.path(path, "Makefile"), overwrite = TRUE) | ||
| .vcat(verbose, "`Makefile` added.") | ||
| } | ||
| if (isTRUE(add_here) && (isFALSE(file.exists(file.path(path, ".here"))) || isTRUE(force))) { | ||
| file.create(file.path(path, ".here")) | ||
| .vcat(verbose, "`.here` added.") | ||
| } | ||
| .vcat(verbose, "The infrastructure for running `rang` in this project is now ready.") | ||
| .vcat(verbose, "You might want to edit this file: inst/rang/update.R") | ||
| .vcat(verbose, paste0("After that, run: setwd(\"", path,"\"); source(\"inst/rang/update.R\")")) | ||
| .vcat(verbose && add_makefile, "Or run in your shell: make update") | ||
| return(invisible(path)) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| ## Autogenerated by rang, you might want to change the handle | ||
| handle=yourproject | ||
| .PHONY: update build launch export rebuild | ||
|
|
||
| update: | ||
| Rscript inst/rang/update.R | ||
| build: Dockerfile | ||
| docker build -t ${handle}img . | ||
| dockerlaunch: | ||
| docker run --rm --name "${handle}container" -ti ${handle}img | ||
| export: | ||
| docker save ${handle}img | gzip > ${handle}img.tar.gz | ||
| rebuild: ${handle}img.tar.gz | ||
| docker load < ${handle}img.tar.gz |
Oops, something went wrong.