re-enable plotVelocityStream() with a warning; only test on non-macOS (…

…#89)

* re-enable plotVelocityStream() with a warning; only test on non-macOS

* conditional run of examples in man page

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.10
-Date: 2024-09-11
+Version: 1.15.11
+Date: 2024-09-12
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="[email protected]", comment = c(ORCID = '0000-0002-3564-4813')),
     person("Charlotte", "Soneson", role="aut", email="[email protected]", comment = c(ORCID = '0000-0003-3833-2169')),

NEWS.md

@@ -1,3 +1,7 @@
+# velociraptor 1.15.11
+
+* Re-enable `plotVelocityStream()` with a warning.
+
 # velociraptor 1.15.10
 
 * Temporarily disable `plotVelocityStream()` due to unexplained issue related to

R/plotVelocityStream.R

@@ -67,7 +67,9 @@
 #' 
 #' em <- embedVelocity(reducedDim(out, 1), out)[,1:2]
 #' 
-#' \dontrun{
+#' # https://github.com/kevinrue/velociraptor/issues/90
+#' 
+#' if (!basilisk.utils::isMacOSX()){
 #' plotVelocityStream(out, em)
 #' plotVelocityStream(out, em, color.streamlines = TRUE)
 #' }
@@ -92,10 +94,14 @@ plotVelocityStream <- function(
     "#22A884", "#43BF71", "#7AD151",
     "#BBDF27", "#FDE725"),
   arrow.angle = 8, arrow.length = 0.8) {
-  stop(
-    "This function is temporarily unavailable while we investigate an issue ",
-    "related to metR::geom_streamline()"
-  )
+  if (basilisk.utils::isMacOSX()){ # both Intel and Arm
+    warning(
+      "This function has been observed to run indefinitely on macOS. ",
+      "The issue is related to the metR::geom_streamline() layer but unsolved yet. ",
+      "Use with caution and consider terminating R if rendering the plot freezes your session.",
+      immediate. = TRUE
+    )
+  }
 
   if (!identical(ncol(sce), nrow(embedded))) {
     stop("'sce' and 'embedded' do not have consistent dimensions.")

tests/testthat/test-plotting.R

@@ -66,37 +66,30 @@ test_that("plotVelocity runs", {
     unlink(tf)
 })
 
-test_that("plotVelocityStream throws an error", {
-
-  expect_error(
-    plotVelocityStream(out2, em2),
-    "temporarily"
-  )  
-
+test_that("plotVelocityStream runs", {
+  # metR::geom_streamline() layer causes timeouts on macOS 
+  if (!basilisk.utils::isMacOSX()) {
+    skip_if_not_installed("ggplot2")
+    skip_if_not_installed("metR")
+
+    expect_error(plotVelocityStream("error", em2))
+    expect_error(plotVelocityStream(out2, "error"))
+    expect_error(plotVelocityStream(out2, em2[1:10, ]))
+    expect_error(plotVelocityStream(out2, em2, use.dimred = "error"))
+    expect_error(plotVelocityStream(out2, em2, use.dimred = FALSE))
+    expect_error(plotVelocityStream(out2, em2, color_by = "error"))
+    expect_error(plotVelocityStream(out2, em2, grid.resolution = "error"))
+    expect_error(plotVelocityStream(out2, em2, scale = "error"))
+    expect_error(plotVelocityStream(out2, em2, color.streamlines = "error"))
+
+    tf <- tempfile(fileext = ".png")
+    png(tf)
+    expect_warning(print(plotVelocityStream(out2, em2, color_by = "#44444422")))
+    print(plotVelocityStream(out2, em2))
+    print(plotVelocityStream(out3, em2, color_by = "type"))
+    print(plotVelocityStream(out2, em2, color.streamlines = TRUE))
+    dev.off()
+    expect_true(file.exists(tf))
+    unlink(tf)
+  }
 })
-
-# test_that("plotVelocityStream runs", {
-# 
-#     skip_if_not_installed("ggplot2")
-#     skip_if_not_installed("metR")
-#     
-#     expect_error(plotVelocityStream("error", em2))
-#     expect_error(plotVelocityStream(out2, "error"))
-#     expect_error(plotVelocityStream(out2, em2[1:10, ]))
-#     expect_error(plotVelocityStream(out2, em2, use.dimred = "error"))
-#     expect_error(plotVelocityStream(out2, em2, use.dimred = FALSE))
-#     expect_error(plotVelocityStream(out2, em2, color_by = "error"))
-#     expect_error(plotVelocityStream(out2, em2, grid.resolution = "error"))
-#     expect_error(plotVelocityStream(out2, em2, scale = "error"))
-#     expect_error(plotVelocityStream(out2, em2, color.streamlines = "error"))
-#     
-#     tf <- tempfile(fileext = ".png")
-#     png(tf)
-#     expect_warning(print(plotVelocityStream(out2, em2, color_by = "#44444422")))
-#     print(plotVelocityStream(out2, em2))
-#     print(plotVelocityStream(out3, em2, color_by = "type"))
-#     print(plotVelocityStream(out2, em2, color.streamlines = TRUE))
-#     dev.off()
-#     expect_true(file.exists(tf))
-#     unlink(tf)
-# })