[r] Prepare for 1.15.0rc3 (#3257)

* [r] Prepare for 1.15.0rc3 * backport #3252
single-cell-data · Oct 29, 2024 · 0ddfb3c · 0ddfb3c
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diff --git a/apis/r/DESCRIPTION b/apis/r/DESCRIPTION
@@ -6,7 +6,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
     like those commonly used for single cell data analysis. It is documented at
     <https://github.com/single-cell-data>; a formal specification available is at
     <https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.
-Version: 1.14.99.6
+Version: 1.14.99.7
 Authors@R: c(
     person(given = "Aaron", family = "Wolen",
            role = c("cre", "aut"), email = "aaron@tiledb.com",

diff --git a/apis/r/NEWS.md b/apis/r/NEWS.md
@@ -8,6 +8,9 @@
 * Implement missing `domain` argument to `SOMADataFrame` `create` [#3032](https://github.com/single-cell-data/TileDB-SOMA/pull/3032)
 * Remove unused `fragment_count` accessor [#3054](https://github.com/single-cell-data/TileDB-SOMA/pull/3054)
 * Bulk-sync `main` to `release-1.15` in prep for 1.15.0rc3
+* New-shape mods [#2407](https://github.com/single-cell-data/TileDB-SOMA/issues/2407)
+* Run `clang-format` for C++ source and `styler::style_pkg()` for R source
+* Fix context/config bug [#3252](https://github.com/single-cell-data/TileDB-SOMA/pull/3252)
 
 # tiledbsoma 1.14.5
 

diff --git a/apis/r/R/TileDBObject.R b/apis/r/R/TileDBObject.R
@@ -39,12 +39,35 @@ TileDBObject <- R6::R6Class(
       private$.tiledb_platform_config <- platform_config
 
       # Set context
-      tiledbsoma_ctx <- tiledbsoma_ctx %||% SOMATileDBContext$new()
-      if (!inherits(x = tiledbsoma_ctx, what = "SOMATileDBContext")) {
-        stop("'tiledbsoma_ctx' must be a SOMATileDBContext object", call. = FALSE)
+      if (!is.null(x = tiledbsoma_ctx)) {
+        if (!inherits(x = tiledbsoma_ctx, what = 'SOMATileDBContext')) {
+          stop(
+            "'tiledbsoma_ctx' must be a SOMATileDBContext object",
+            call. = FALSE
+          )
+        }
+        # TODO: Deprecate tiledbsoma_ctx in favor of soma_context
+        # warning("'tiledbsoma_ctx' is deprecated, use 'soma_context' instead")
+        # Set the old context
+        private$.tiledbsoma_ctx <- tiledbsoma_ctx
+        private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
+        # Also plumb through to the new context
+        if (!is.null(soma_context)) {
+          warning(
+            "Both 'soma_context' and 'tiledbsoma_ctx' were provided,",
+            "using 'soma_context' only"
+          )
+        } else {
+          # why we named the parameter and function the same thing is beyond me
+          soma_context <- tiledbsoma::soma_context(
+            config = unlist(tiledbsoma_ctx$to_list())
+          )
+        }
+      } else {
+        tiledbsoma_ctx <- SOMATileDBContext$new()
+        private$.tiledbsoma_ctx <- tiledbsoma_ctx
+        private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
       }
-      private$.tiledbsoma_ctx <- tiledbsoma_ctx
-      private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
 
       # TODO: re-enable once new UX is worked out
       # soma_context <- soma_context %||% soma_context()