Merge branch 'dev' into dev2

NEWS.md

@@ -1,4 +1,12 @@
 
+# GiottoClass 0.3.6 (2024/08/30)
+
+## bug fixes
+- fix `dimnames()` for some subobjects
+
+## enhancements
+- python packages to install through pip is now settable in `installGiottoEnvironment()`
+
 # GiottoClass 0.3.5 (2024/08/28)
 
 ## breaking changes

R/join.R

@@ -686,7 +686,6 @@ joinGiottoObjects <- function(gobject_list,
 
 
 
-
     ## spatial locations
     vmsg(.v = verbose, "3. spatial locations")
 

R/methods-names.R

@@ -1,12 +1,17 @@
 #' @include generics.R
 NULL
 
+# NOTE:
+# dimnames MUST be provided for rownames and colnames methods to be well
+# behaved
+
 #' @title Row and column names
 #' @name row-plus-colnames-generic
 #' @aliases colnames rownames
 #' @description Retrieve or set the row or column names of an object
 #' @param x object
 #' @return A character vector of row or col names
+#' @keywords internal
 #' @examples
 #' g <- GiottoData::loadSubObjectMini("exprObj")
 #'
@@ -19,6 +24,7 @@ NULL
 #' Retrieve or set the dimnames of an object
 #' @param x object
 #' @returns character
+#' @keywords internal
 #' @examples
 #' g <- GiottoData::loadSubObjectMini("exprObj")
 #'
@@ -60,7 +66,9 @@ setMethod("rownames", signature(x = "exprObj"), function(x) rownames(x[]))
 #' @export
 setMethod("rownames", signature(x = "dimObj"), function(x) rownames(x[]))
 
-
+#' @rdname row-plus-colnames-generic
+#' @export
+setMethod("rownames", signature(x = "metaData"), function(x) rownames(x[]))
 
 
 
@@ -71,3 +79,21 @@ setMethod("dimnames", signature(x = "exprObj"), function(x) dimnames(x[]))
 #' @rdname dimnames
 #' @export
 setMethod("dimnames", signature(x = "dimObj"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "spatLocsObj"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "metaData"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "enrData"), function(x) dimnames(x[]))
+
+#' @rdname dimnames
+#' @export
+setMethod("dimnames", signature(x = "dimObj"), function(x) dimnames(x[]))
+
+

R/methods-rbind.R

@@ -33,7 +33,7 @@ setMethod(
             stop("rbind: `spatLocsObj` with the same IDs cannot be joined", 
                  call. = FALSE)
         }
-        
+
         # if one is 3d, ensure both are 3d
         x3 <- .is_3d_spatlocs(x)
         y3 <- .is_3d_spatlocs(y)