Sync db and dev branches

.gitignore

@@ -6,7 +6,7 @@ inst/doc
 .git_old
 .vscode/*
 .Rprofile
-docs
 codecov.yml
-pkgdown
 cell_rna*
+docs
+pkgdown

DESCRIPTION

@@ -42,7 +42,8 @@ Imports:
     reticulate (>= 1.25),
     stats,
     terra (>= 1.8-21)
-Suggests: 
+Suggests:
+    GiottoDB,
     Biobase,
     chihaya,
     DelayedArray,

R/aggregate.R

@@ -516,6 +516,17 @@
     feat_subset_ids = deprecated(),
     count_info_column = deprecated(),
     ...) {
+        is_db_x <- inherits(x@spatVector, "dbSpatial")
+        is_db_y <- inherits(y@spatVector, "dbSpatial")
+
+        if (xor(is_db_x, is_db_y)) {
+            stop(
+                "calculateOverlap: dbSpatial-backed and terra-backed inputs ",
+                "are not both supported",
+                call. = FALSE
+            )
+        }
+
         # deprecations
         feat_subset_values <- GiottoUtils::deprecate_param(
             feat_subset_ids, feat_subset_values,
@@ -538,6 +549,50 @@
             feat_count_column <- NULL
         }
 
+        # ------------------------------------------------------------------
+        # dbSpatial-backed path: keep results dbSpatial-native
+        # ------------------------------------------------------------------
+        if (isTRUE(is_db_x)) {
+            # GiottoDB defines the <dbSpatial,dbSpatial> method for this generic
+            if (!base::requireNamespace("GiottoDB", quietly = TRUE)) {
+                stop(
+                    "calculateOverlap: dbSpatial-backed inputs require the ",
+                    "GiottoDB package. Install it, or load it via `library(GiottoDB)`.",
+                    call. = FALSE
+                )
+            }
+
+            if (!methods::hasMethod(
+                "calculateOverlap",
+                signature = signature(x = "dbSpatial", y = "dbSpatial")
+            )) {
+                stop(
+                    "calculateOverlap: dbSpatial-backed giottoPolygon or ",
+                    "giottoPoints method missing. Load the GiottoDB package.",
+                    call. = FALSE
+                )
+            }
+
+            # The <dbSpatial,dbSpatial> method is defined in GiottoDB
+            res <- calculateOverlap(
+                x = x@spatVector,
+                y = y@spatVector,
+                poly_subset_ids = poly_subset_ids,
+                feat_subset_column = feat_subset_column,
+                feat_subset_values = feat_subset_values,
+                feat_count_column = feat_count_column,
+                verbose = verbose,
+                ...
+            )
+
+            if (isTRUE(return_gpolygon)) {
+                if (is.null(name_overlap)) name_overlap <- objName(y)
+                x@overlaps[[name_overlap]] <- res
+                return(x)
+            }
+            return(res)
+        }
+
         # return an overlap info object
         res <- calculateOverlap(
             x = x[],

R/data_input.R

@@ -28,11 +28,20 @@ readExprMatrix <- function(
         cores = determine_cores(),
         transpose = FALSE,
         feat_type = "rna",
-        expression_matrix_class = c("dgCMatrix", "DelayedArray"),
-        ...) {
+        expression_matrix_class = c(
+            "dgCMatrix",
+            "DelayedArray",
+            "dbSparseMatrix"
+        )) {
     # check if path is a character vector and exists
     if (!is.character(path)) stop("path needs to be character vector")
     if (!file.exists(path)) stop("the path: ", path, " does not exist")
+
+    expression_matrix_class <- match.arg(expression_matrix_class)
+    if (identical(expression_matrix_class, "dbSparseMatrix")) {
+        stop("File conversion to dbMatrix is not yet supported")
+    }
+
     data.table::setDTthreads(threads = cores)
 
     # read and convert