sync with dev

DESCRIPTION

@@ -46,8 +46,7 @@ Imports:
     VGAM,
     hash,
     purrr,
-    lifecycle,
-    withr
+    lifecycle
 Suggests: 
     BiocManager,
     BiocStyle,
@@ -58,7 +57,8 @@ Suggests:
     scater,
     spelling,
     testthat (>= 3.0.0),
-    vdiffr
+    vdiffr,
+    withr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Language: en-US

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 Nick Borcherding
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: scRepertoire authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 scRepertoire authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

R/utils.R

@@ -214,12 +214,19 @@
 #' @importFrom methods slot
 #' @keywords internal
 .grabMeta <- function(sc) {
+  messString <- c("Meta data contains an 'ident' column and will likely result
+                  in errors downstream.")
     if (is_seurat_object(sc)) {
         meta <- data.frame(sc[[]], slot(sc, "active.ident"))
+        if("ident" %in% colnames(meta)) {
+          message(messString)
+        }
         colnames(meta)[length(meta)] <- "ident"
-
     } else if (is_se_object(sc)){
         meta <- data.frame(colData(sc))
+        if("ident" %in% colnames(meta)) {
+          message(messString)
+        }
         rownames(meta) <- sc@colData@rownames
         clu <- which(colnames(meta) == "label") # as set by colLabels()
         colnames(meta)[clu] <- "ident"