Implement apptainer parameter for use_rang ref #110 [no ci] (#156)

* Not using ... ref #110

* Update doc

* Correct docs

* Change the default CRAN_mirror

* Revert "Change the default CRAN_mirror"

This reverts commit 98e03b0.

* Apptainer

* MF

R/use_rang.R

@@ -13,6 +13,7 @@
 #' @param verbose logical, whether to print out messages
 #' @param force logical, whether to overwrite files (`inst/rang/update.R`, `Makefile`, `.here`) if they
 #' exist.
+#' @param apptainer logical, whether to use apptainer. `FALSE` indicates using Docker
 #' @return path, invisibly
 #' @details The infrastructure being added to your path consists of:
 #' * `inst/rang` directory in the project root
@@ -24,7 +25,7 @@
 #' you might need to edit this manually.
 #' @export
 use_rang <- function(path = ".", add_makefile = TRUE, add_here = TRUE,
-                     verbose = TRUE, force = FALSE) {
+                     verbose = TRUE, force = FALSE, apptainer = FALSE) {
     if (isFALSE(dir.exists(path))) {
         stop("'path' does not exist")
     }
@@ -35,11 +36,18 @@ use_rang <- function(path = ".", add_makefile = TRUE, add_here = TRUE,
     } else {
         .vcat(verbose, "`inst/rang` exists.")
     }
+    if (apptainer) {
+        source_update_file <- "update_apptainer.R"
+        make_file <- "apptainer/Makefile"
+    } else {
+        source_update_file <- "update.R"
+        make_file <- "Makefile"
+    }
     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)
+        file.copy(system.file(source_update_file, 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)
+        file.copy(system.file(make_file, 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))) {
@@ -80,7 +88,7 @@ use_rang <- function(path = ".", add_makefile = TRUE, add_here = TRUE,
 #' [The Turing Way: Research Compendia](https://the-turing-way.netlify.app/reproducible-research/compendia.html)
 #' Gorman, KB, Williams TD. and Fraser WR (2014). Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3):e90081. \doi{10.1371/journal.pone.0090081}
 #' @export
-create_turing <- function(path, add_rang = TRUE, add_makefile = TRUE, add_here = TRUE, verbose = TRUE, force = FALSE) {
+create_turing <- function(path, add_rang = TRUE, add_makefile = TRUE, add_here = TRUE, verbose = TRUE, force = FALSE, apptainer = FALSE) {
     if (isTRUE(dir.exists(path))) {
         stop("`path` exists.")
     }
@@ -91,7 +99,7 @@ create_turing <- function(path, add_rang = TRUE, add_makefile = TRUE, add_here =
     dir.create(file.path(path, "figures"))
     dir.create(file.path(path, "data_clean"))
     if (isTRUE(add_rang)) {
-        use_rang(path, add_makefile = add_makefile, add_here = add_here, verbose = verbose, force = force)
+        use_rang(path, add_makefile = add_makefile, add_here = add_here, verbose = verbose, force = force, apptainer = apptainer)
     }
     invisible(path)
 }

inst/Makefile

@@ -1,18 +1,18 @@
 ## Autogenerated by rang, you might want to change the handle
 handle=yourproject
-.PHONY: update build dockerlaunch dockerbash dockerdaemon dockerstop export rebuild
+.PHONY: update build launch bash daemon stop export rebuild
 
 update:
 	Rscript inst/rang/update.R
 build: Dockerfile
 	docker build -t ${handle}img .
-dockerlaunch:
+launch:
 	docker run --rm --name "${handle}container" -ti ${handle}img
-dockerbash:
+bash:
 	docker run --rm --name "${handle}container" --entrypoint bash -ti ${handle}img
-dockerdaemon:
+daemon:
 	docker run -d --rm --name "${handle}container" -ti ${handle}img
-dockerstop:
+stop:
 	docker stop ${handle}container
 export:
 	docker save ${handle}img | gzip > ${handle}img.tar.gz

inst/apptainer/Makefile

@@ -0,0 +1,16 @@
+## Autogenerated by rang, you might want to change the handle
+handle=yourproject
+.PHONY: update build apptainerlaunch apptainerbash apptainerdaemon apptainerstop export
+
+update:
+	Rscript inst/rang/update.R
+build: container.def
+	apptainer build "${handle}img.sif" container.def
+launch:
+	apptainer run "${handle}img.sif" R
+bash:
+	apptainer shell "${handle}img.sif"
+daemon:
+	apptainer instance start "${handle}img.sif" "${handle}container"
+stop:
+	apptainer instance stop "${handle}container"

inst/update.R

@@ -15,7 +15,7 @@ rang <- resolve(here::here(),
 
 ## You might want to edit `post_installation_steps` or `cache`
 dockerize(rang, output_dir = here::here(), verbose = TRUE, cache = TRUE,
-          post_installation_steps = c(recipes[['make']], recipes[['texlive']], recipes[['clean']]),
+          post_installation_steps = c(recipes[["make"]], recipes[["texlive"]], recipes[["clean"]]),
           insert_readme = FALSE,
           copy_all = TRUE,
           cran_mirror = cran_mirror)

inst/update_apptainer.R

@@ -0,0 +1,21 @@
+library(rang)
+library(here)
+
+cran_mirror <- "https://cloud.r-project.org/"
+
+## Please note that the project scanning result should be checked manually.
+## 1. Github packages must be added manually
+## as_pkgrefs(here::here())
+## 2. You might also want to change the `snapshot_date` to a fix date, when
+## the project is finalized.
+
+rang <- resolve(here::here(),
+                snapshot_date = NA,
+                verbose = TRUE)
+
+## You might want to edit `post_installation_steps` or `cache`
+apptainerize(rang, output_dir = here::here(), verbose = TRUE, cache = TRUE,
+             post_installation_steps = c(recipes[["make"]], recipes[["texlive"]], recipes[["clean"]]),
+             insert_readme = FALSE,
+             copy_all = TRUE,
+             cran_mirror = cran_mirror)

tests/testthat/test_use_rang.R

@@ -93,3 +93,19 @@ test_that("Existing components .here", {
     content <- readLines(file.path(tempdir, ".here"))
     expect_unequal(content, dummy) ## got overwritten
 })
+
+test_that("Apptainer", {
+    tempdir <- .generate_temp_dir()
+    dir.create(tempdir)
+    msg <- capture_messages(use_rang(tempdir, apptainer = TRUE))
+    expect_true(any(grepl("infrastructure", msg)))
+    tempdir <- .generate_temp_dir()
+    dir.create(tempdir)
+    expect_silent(use_rang(tempdir, verbose = FALSE, apptainer = TRUE))
+    expect_true(dir.exists(file.path(tempdir, "inst/rang")))
+    expect_true(file.exists(file.path(tempdir, "inst/rang/update.R")))
+    expect_true(file.exists(file.path(tempdir, ".here")))
+    expect_true(file.exists(file.path(tempdir, "Makefile")))
+    expect_true(any(grepl("apptainer", readLines(file.path(tempdir, "inst/rang/update.R")))))
+    expect_true(any(grepl("apptainer", readLines(file.path(tempdir, "Makefile")))))
+})