From 48737007fb8dbe9a782904e35985d93531625c22 Mon Sep 17 00:00:00 2001
From: Duncan Murdoch <murdoch.duncan@gmail.com>
Date: Mon, 9 Jan 2023 08:22:08 -0500
Subject: [PATCH 1/3] Change rgl.* calls to *3d

---
 R/neuronlist.R                   | 4 ++--
 man/nlapply.Rd                   | 4 ++--
 tests/testthat/test-hxsurf.R     | 2 +-
 tests/testthat/test-neuronlist.R | 2 +-
 tests/testthat/test-pop3d.R      | 6 +++---
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/neuronlist.R b/R/neuronlist.R
index 50361eed..c7644c8f 100644
--- a/R/neuronlist.R
+++ b/R/neuronlist.R
@@ -428,7 +428,7 @@ as.data.frame.neuronlist<-function(x, row.names = names(x), optional = FALSE, ..
 #' open3d()
 #' plot3d(kcs.reduced,col='red', lwd=2)
 #' plot3d(kcs20,col='grey')
-#' rgl.close()
+#' close3d()
 #'
 #' \dontrun{
 #' # example of using plyr's .inform argument for debugging error conditions
@@ -464,7 +464,7 @@ as.data.frame.neuronlist<-function(x, row.names = names(x), optional = FALSE, ..
 #' open3d()
 #' plot3d(kcs20[1:3])
 #' plot3d(xyzflip)
-#' rgl.close()
+#' close3d()
 #' }
 #'
 #' \dontrun{
diff --git a/man/nlapply.Rd b/man/nlapply.Rd
index 1a98c899..6bd5e785 100644
--- a/man/nlapply.Rd
+++ b/man/nlapply.Rd
@@ -144,7 +144,7 @@ kcs.reduced=nlapply(kcs20,function(x) subset(x,sample(nrow(x$points),50)))
 open3d()
 plot3d(kcs.reduced,col='red', lwd=2)
 plot3d(kcs20,col='grey')
-rgl.close()
+close3d()
 
 \dontrun{
 # example of using plyr's .inform argument for debugging error conditions
@@ -180,7 +180,7 @@ xyzflip=nmapply(function(...) {Sys.sleep(.2);mirror(...)}, kcs20,
 open3d()
 plot3d(kcs20[1:3])
 plot3d(xyzflip)
-rgl.close()
+close3d()
 }
 
 \dontrun{
diff --git a/tests/testthat/test-hxsurf.R b/tests/testthat/test-hxsurf.R
index 97441240..b8762f30 100644
--- a/tests/testthat/test-hxsurf.R
+++ b/tests/testthat/test-hxsurf.R
@@ -26,7 +26,7 @@ test_that("we can read hxsurf object", {
   plot3d(surf,alpha=0.2)
   nclear3d()
   plot3d(surf,col=rainbow,alpha=0.2)
-  rgl.close()
+  close3d()
   
   #For plotly..
   options(nat.plotengine='plotly')
diff --git a/tests/testthat/test-neuronlist.R b/tests/testthat/test-neuronlist.R
index d5746344..538f094f 100644
--- a/tests/testthat/test-neuronlist.R
+++ b/tests/testthat/test-neuronlist.R
@@ -240,7 +240,7 @@ test_that("basic interactive 3d functionality",{
   expect_equal(find.soma(selfun, db=Cell07PNs, rval='neuronlist'), 
                Cell07PNs[sel_soma])
   
-  rgl.close()
+  close3d()
 })
 
 context("neuronlist: set operations")
diff --git a/tests/testthat/test-pop3d.R b/tests/testthat/test-pop3d.R
index 8fa211e4..3d30ca89 100644
--- a/tests/testthat/test-pop3d.R
+++ b/tests/testthat/test-pop3d.R
@@ -2,11 +2,11 @@ context("npop3d")
 
 test_that("pop last plotted neurons",{
   nopen3d()
-  original.rgl.ids=rgl.ids()
+  original.rgl.ids=ids3d()
   plot3d(c("EBH11R", "EBH20L"), db=Cell07PNs)
   npop3d()
-  expect_equal(rgl.ids(), original.rgl.ids)
-  rgl.close()
+  expect_equal(ids3d(), original.rgl.ids)
+  close3d()
 })
 
 context("nview3d")

From 5cc85622a92ca083ba0031d74b892622f4ff0a8a Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 13 Jan 2023 11:19:15 +0000
Subject: [PATCH 2/3] rgl.pop -> pop3d

* as discussed in PR
---
 R/neuronlist_interactive_3d.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/neuronlist_interactive_3d.R b/R/neuronlist_interactive_3d.R
index 76829026..be1488ec 100644
--- a/R/neuronlist_interactive_3d.R
+++ b/R/neuronlist_interactive_3d.R
@@ -194,8 +194,8 @@ nlscan <- function(neurons, db=NULL,
     if(Wait){
       chc <- readline("Return to continue, b to go back, s to select, d [save to disk], t to stop, c to cancel (without returning a selection): ")
       if(chc=="c" || chc=='t'){
-        sapply(pl, rgl.pop, type='shape')
-        sapply(more_rgl_ids, rgl.pop, type='shape')
+        sapply(pl, pop3d, type='shape')
+        sapply(more_rgl_ids, pop3d, type='shape')
         break
       }
       if(chc=="s") {
@@ -211,8 +211,8 @@ nlscan <- function(neurons, db=NULL,
       Sys.sleep(sleep)
       i <- i+1
     }
-    sapply(pl, rgl.pop, type='shape')
-    sapply(more_rgl_ids, rgl.pop, type='shape')
+    sapply(pl, pop3d, type='shape')
+    sapply(more_rgl_ids, pop3d, type='shape')
   }
   if(is.null(chc) || chc=='c') return(NULL)
   if(!is.null(selected_file)) savetodisk(selected, selected_file)

From ad29cdc2b56090137e6b1f1d657b2c2fa4c352e4 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Mon, 23 Jan 2023 16:48:14 +0000
Subject: [PATCH 3/3] ignore codecov

---
 .Rbuildignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 38b100b9..c9361f7e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,4 @@ travisbuildchildren.sh
 ^pkgdown$
 ^\.github$
 ^depends.Rds$
+^codecov\.yml$