Update HISTORY/NEWS and R version for 2.1.0 release (#4289)

* Update HISTORY/NEWS and R version for 2.1.0 release

* Add fake release for current minor release if needed
Allows deprecations to occur during release process

* Get around lifecycle trying to be clever, because it's not

* Change wording in comment

---------

Co-authored-by: Paul Hoffman <paul.hoffman@tiledb.com>

Author: jp-dark

apis/python/HISTORY.md

@@ -10,19 +10,27 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ### Changed
 
-- \[[#4284](https://github.com/single-cell-data/TileDB-SOMA/pull/4284)\] Update [TileDB core to 2.29.1](https://github.com/TileDB-Inc/TileDB/releases/tag/2.29.1).
-
 ### Deprecated
 
-- \[[#4275](https://github.com/single-cell-data/TileDB-SOMA/pull/4275)\] Deprecate allowing a dimension in `shape` for a new `SOMASpaseNDArray` to be defaulted to `1` with `None` in the `create` method. In the future, the shape must be a sequence of positive integers.
-- \[[#4275](https://github.com/single-cell-data/TileDB-SOMA/pull/4275)\] Deprecate leaving `domain=None` when creating a `SOMADataFrame`, `SOMAPointCloudDataFrame`, or `SOMAGeometryDataFrame`. In the future, the domain must be fully specified on creation.
-
 ### Removed
 
 ### Fixed
 
 ### Security
 
+## [Release 2.1.0]
+
+This release adds warnings for new deprecations in the allowed values for `shape` and `domain` in `create` methods and updates the TileDB core version to 2.29.1.
+
+### Changed
+
+- \[[#4284](https://github.com/single-cell-data/TileDB-SOMA/pull/4284)\] Update [TileDB core to 2.29.1](https://github.com/TileDB-Inc/TileDB/releases/tag/2.29.1).
+
+### Deprecated
+
+- \[[#4275](https://github.com/single-cell-data/TileDB-SOMA/pull/4275)\] Deprecate allowing a dimension in `shape` for a new `SOMASpaseNDArray` to be defaulted to `1` with `None` in the `create` method. In the future, the shape must be a sequence of positive integers.
+- \[[#4275](https://github.com/single-cell-data/TileDB-SOMA/pull/4275)\] Deprecate leaving `domain=None` when creating a `SOMADataFrame`, `SOMAPointCloudDataFrame`, or `SOMAGeometryDataFrame`. In the future, the domain must be fully specified on creation.
+
 ## [Release 2.0.0]
 
 This release is the first TileDB-SOMA release that follows our new versioning policy (see the [developer docs](../../dev_docs/POLICIES.md)). Highlights of this release include the addition of a "delete" feature, removal of deprecated function, an update to TileDB 2.28.1 and breaking changes to `ExperimentAxisQuery.to_anndata`.

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: 2.0.99.5
+Version: 2.1.99
 Authors@R: c(
     person(given = "Paul", family = "Hoffman",
            role = c("cre", "aut"), email = "tiledb-r@tiledb.com",

apis/r/NEWS.md

@@ -2,6 +2,22 @@
 
 ## Added
 
+## Changed
+
+## Deprecated
+
+## Removed
+
+## Fixed
+
+## Security
+
+# tiledbsoma 2.1.0
+
+This release adds support for ingestion of BPCells-backed `Seurat` objects in `write_soma()`, adds warnings for new deprecations, and updates the TileDB core version to 2.29.1.
+
+## Added
+
 - Add support for ingestion of BPCells-backed `Seurat` objects in `write_soma()` ([#4273](https://github.com/single-cell-data/TileDB-SOMA/pull/4273))
 
 ## Changed
@@ -13,12 +29,6 @@
 - Mark `SOMANDArrayBase$set_data_type()` for deprecation. ([#4279](https://github.com/single-cell-data/TileDB-SOMA/pull/4279))
 - Mark setting `domain` to `NULL` in `SOMADataFrame$create()` for deprecation. ([#4274](https://github.com/single-cell-data/TileDB-SOMA/pull/4274))
 
-## Removed
-
-## Fixed
-
-## Security
-
 # tiledbsoma 2.0.0
 
 This release is the first TileDB-SOMA release that follows our new versioning policy (see the [developer docs](../../dev_docs/POLICIES.md)). It introduces the new `DELETE` mode and deprecates removing elements from a `Collection` in `WRITE` mode. It also updates the core TileDB version to 2.28.1.

apis/r/R/utils-deprecations.R

@@ -6,8 +6,11 @@
 #' @inherit .deprecation_stage details
 #'
 #' @inheritParams lifecycle::deprecate_warn
-#' @inheritDotParams lifecycle::deprecate_warn id always
-#' @param env,user_env Needed for \code{\link[lifecycle:deprecate_warn]{lifecycle::deprecate_*}()}, do not modify
+#' @param ... Must be empty, and error will be thrown if anything is passed
+#' through the \dots
+#' @param env,user_env Needed for \
+#' code{\link[lifecycle:deprecate_warn]{lifecycle::deprecate_*}()},
+#' do not modify
 #'
 #' @return No return value, used for the side effects of signaling a
 #' deprecation or defunct stage
@@ -39,13 +42,16 @@
   with = NULL,
   ...,
   details = NULL,
+  id = NULL,
+  always = TRUE,
   env = rlang::caller_env(),
   user_env = rlang::caller_env(n = 2L)
 ) {
   stopifnot(
     rlang::is_character(what, n = 1L),
     is.null(x = with) || rlang::is_character(with)
   )
+  rlang::check_dots_empty0(...)
   switch(
     EXPR = .deprecation_stage(when = when) %||% "future",
     defunct = lifecycle::deprecate_stop(
@@ -60,7 +66,12 @@
       what = what,
       with = with,
       details = details,
-      ...,
+      # lifecycle tries to be clever when determining when to warn; however,
+      # it's actually pretty bad at it. It doesn't work well with R6 nor does
+      # it accurately track testthat usage. We need to force it
+      # to throw a deprecation warning
+      id = id %||% as.character(Sys.time()),
+      always = always,
       env = env,
       user_env = user_env
     )
@@ -130,6 +141,34 @@
     lib.loc = .pkgenv$libname,
     mustWork = TRUE
   )))
+  # Add fake release for current minor release if needed
+  mm <- unique(vapply(
+    X = releases$Version,
+    FUN = function(x) {
+      x <- unlist(strsplit(x = x, split = "\\."))
+      return(paste0(x[1:2], collapse = "."))
+    },
+    FUN.VALUE = character(length = 1L),
+    USE.NAMES = FALSE
+  ))
+  cmm <- unlist(strsplit(
+    x = as.character(utils::packageVersion(.pkgenv$pkgname)),
+    split = "\\."
+  ))
+  if (all(paste0(cmm[1:2], collapse = ".") > mm)) {
+    dates <- file.info(list.files(
+      base::system.file(package = .pkgenv$pkgname),
+      full.names = TRUE,
+      recursive = TRUE
+    ))$mtime
+    releases <- rbind(
+      releases,
+      data.frame(
+        Version = sprintf(fmt = "%s.%s.0", cmm[1L], cmm[2L]),
+        Date = format(as.POSIXlt(dates[which.max(dates)]), format = "%Y-%m-%d")
+      )
+    )
+  }
   # Check to see if the deprecation is scheduled for a future release
   # If so, exit out
   if (all(when > releases$Version)) {