feat: Add non-interactive setup

R/eula.R

@@ -1,3 +1,5 @@
+AUTO_ACCEPT_ENV_VAR <- "AUTO_ACCEPT_EULA"
+
 #' Present EULA and Record agreement
 #'
 #' @return TRUE on success, FALSE on error
@@ -8,13 +10,35 @@ eula <- function() {
     return(invisible(TRUE))
   }
 
+  prompt_begin <- paste(
+    "The LoupeR executable is subject to the 10x End User Software License,",
+    "available at:\nhttps://10xgen.com/EULA \n\n"
+  )
+
+  if (auto_accepted_eula()) {
+    print(paste0(
+      prompt_begin,
+      "You have automatically accepted the EULA by setting the `",
+      AUTO_ACCEPT_ENV_VAR,
+      "` environment variable"
+    ))
+
+    eula_create()
+    return(invisible(TRUE))
+  }
+
   resp <- ""
-  while(!(resp %in% c("y", "yes", "n", "no"))) {
-    resp <- readline(prompt="The LoupeR executable is subject to the 10x End User Software License, available at:\nhttps://10xgen.com/EULA \n\nDo you accept the End-User License Agreement\n(y/yes or n/no): ")
+  while (!(resp %in% c("y", "yes", "n", "no"))) {
+    prompt <- paste0(
+      prompt_begin,
+      "Do you accept the End-User License Agreement\n(y/yes or n/no): ",
+    )
+
+    resp <- readline(prompt = prompt)
     resp <- tolower(resp)
   }
 
-  if(resp %in% c("n", "no")) {
+  if (resp %in% c("n", "no")) {
     return(FALSE)
   }
 
@@ -26,7 +50,7 @@ eula <- function() {
 #' Create Eula lock file
 #' @noRd
 eula_create <- function() {
-  dir.create(eula_data_dir(), showWarnings=FALSE, recursive = TRUE)
+  dir.create(eula_data_dir(), showWarnings = FALSE, recursive = TRUE)
   file.create(eula_lock_file())
 }
 
@@ -55,3 +79,13 @@ eula_data_dir <- function() {
 eula_lock_file <- function() {
   file.path(eula_data_dir(), "eula_agreement")
 }
+
+#' Check to see if we have auto accepted the eula
+#' @noRd
+auto_accepted_eula <- function() {
+  print("Xalling")
+  value <- Sys.getenv(AUTO_ACCEPT_ENV_VAR, unset = "false")
+  value <- trimws(tolower(value))
+
+  return(value %in% c("t", "true", "y", "yes"))
+}

tests/testthat/test-lib.R

@@ -5,57 +5,85 @@ create_default_seurat_obj <- function() {
   proj <- create_dim_reduction(count_mat, "proj1")
   cluster <- factor(seq(barcode_count))
 
-  obj <- Seurat::CreateSeuratObject(count_mat, assay="rna")
+  obj <- Seurat::CreateSeuratObject(count_mat, assay = "rna")
   obj[["proj1"]] <- proj
   obj[["cluster1"]] <- cluster
 
   obj
 }
 
-test_that("can run create_loupe_from_seurat", {
-  # create eula lock file to avoid interactive setup
-  eula_create()
+setup({
+  # install the eula automatically and non-interactively
+  do.call(Sys.setenv, setNames(list("true"), AUTO_ACCEPT_ENV_VAR))
+  eula()
+})
 
+test_that("can run create_loupe_from_seurat", {
   obj <- create_default_seurat_obj()
   x <- create_loupe_from_seurat(obj, executable_path = get_executable_path())
   expect(x, "create_loupe_from_seurat returns TRUE")
 })
 
 test_that("can run create_loupe with spaces in output_name", {
-  # create eula lock file to avoid interactive setup
-  eula_create()
-
   obj <- create_default_seurat_obj()
-  x <- create_loupe_from_seurat(obj, executable_path = get_executable_path(), output_name = "name with spaces")
+
+  x <- create_loupe_from_seurat(
+    obj,
+    executable_path = get_executable_path(),
+    output_name = "name with spaces"
+  )
+
   expect(x, "create_loupe_from_seurat returns TRUE")
 })
 
 test_that("can run create_loupe", {
-  # create eula lock file to avoid interactive setup
-  eula_create()
-
   barcode_count <- 5
   count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
   proj <- create_dense_mat(barcode_count, 2)
-  clusters <- list("f1" = factor(c("a", "c", "b", "a", "b"), levels=c("a", "b", "c"), ordered=TRUE))
   projections <- list("p1" = proj)
 
-  x <- create_loupe(count_mat, clusters = clusters, projections = projections, executable_path = get_executable_path())
+  cluster <- factor(
+    c("a", "c", "b", "a", "b"),
+    levels = c("a", "b", "c"),
+    ordered = TRUE
+  )
+  clusters <- list("f1" = cluster)
+
+  x <- create_loupe(
+    count_mat,
+    clusters = clusters,
+    projections = projections,
+    executable_path = get_executable_path()
+  )
+
   expect(x, "create_loupe returns TRUE")
 })
 
 test_that("can run create_loupe with integer projection matrix", {
-  # create eula lock file to avoid interactive setup
-  eula_create()
-
   barcode_count <- 5
   count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
-  proj <- matrix(as.integer(create_dense_mat(barcode_count, 2) * 10), nrow=barcode_count, ncol=2)
-  clusters <- list("f1" = factor(c("a", "c", "b", "a", "b"), levels=c("a", "b", "c"), ordered=TRUE))
+
+  proj <- matrix(
+    as.integer(create_dense_mat(barcode_count, 2) * 10),
+    nrow = barcode_count,
+    ncol = 2
+  )
+
+  cluster <- factor(
+    c("a", "c", "b", "a", "b"),
+    levels = c("a", "b", "c"),
+    ordered = TRUE
+  )
+  clusters <- list("f1" = cluster)
+
   projections <- list("p1" = proj)
 
-  x <- create_loupe(count_mat, clusters = clusters, projections = projections, executable_path = get_executable_path())
+  x <- create_loupe(
+    count_mat,
+    clusters = clusters,
+    projections = projections,
+    executable_path = get_executable_path()
+  )
+
   expect(x, "create_loupe returns TRUE")
 })
-
-