Merge branch 'main' into kerl/query-shape

apis/python/setup.py

@@ -280,11 +280,16 @@ def run(self):
         "numba==0.56.4; python_version<'3.8'",
         "numpy>=1.18,<1.24; python_version<'3.8'",
         "pandas",
-        "pyarrow>=9.0.0",
+        # TODO: once we no longer support Python 3.7, remove this and pin to pyarrow >= 14.0.1
+        # https://github.com/single-cell-data/TileDB-SOMA/issues/1926
+        "pyarrow_hotfix",
+        # MacOS issue with import pyarrow before import tiledb at >= 13.0:
+        # https://github.com/single-cell-data/TileDB-SOMA/issues/1926#issuecomment-1834695149
+        "pyarrow>=9.0.0,<13.0.0",
         "scanpy>=1.9.2",
         "scipy",
         "somacore==1.0.4",
-        "tiledb~=0.23.4",
+        "tiledb~=0.24.0",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={

apis/python/src/tiledbsoma/__init__.py

@@ -96,6 +96,11 @@
 from somacore import AxisColumnNames, AxisQuery, ExperimentAxisQuery
 from somacore.options import ResultOrder
 
+# TODO: once we no longer support Python 3.7, remove this and pin to pyarrow >= 14.0.1
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1926
+# ruff: noqa
+import pyarrow_hotfix
+
 from ._collection import Collection
 from ._constants import SOMA_JOINID
 from ._dataframe import DataFrame

apis/r/DESCRIPTION

@@ -34,7 +34,7 @@ Imports:
     Matrix,
     stats,
     bit64,
-    tiledb (>= 0.21.3),
+    tiledb (>= 0.22.0),
     arrow,
     utils,
     fs,

apis/r/R/RcppExports.R

@@ -133,9 +133,11 @@ tiledbsoma_stats_dump <- function() {
 #' libtiledbsoma version
 #'
 #' Returns a string with version information for libtiledbsoma and the linked TileDB Embedded library.
+#' If argument `compact` is set to `TRUE`, shorter version of just the TileDB Embedded library
+#' version is returned,
 #' @noRd
-libtiledbsoma_version <- function() {
-    .Call(`_tiledbsoma_libtiledbsoma_version`)
+libtiledbsoma_version <- function(compact = FALSE) {
+    .Call(`_tiledbsoma_libtiledbsoma_version`, compact)
 }
 
 #' TileDB embedded version

apis/r/R/utils-tiledb.R

@@ -33,7 +33,7 @@ show_package_versions <- function() {
     cat("tiledbsoma:    ", toString(utils::packageVersion("tiledbsoma")), "\n",
         "tiledb-r:      ", toString(utils::packageVersion("tiledb")), "\n",
         "tiledb core:   ", as.character(tiledb::tiledb_version(compact=TRUE)), "\n",
-        "libtiledbsoma: ", libtiledbsoma_version(), "\n",
+        "libtiledbsoma: ", libtiledbsoma_version(compact=TRUE), "\n",
         "R:             ", R.version.string, "\n",
         "OS:            ", utils::osVersion, "\n",
         sep="")

apis/r/src/RcppExports.cpp

@@ -178,12 +178,13 @@ BEGIN_RCPP
 END_RCPP
 }
 // libtiledbsoma_version
-std::string libtiledbsoma_version();
-RcppExport SEXP _tiledbsoma_libtiledbsoma_version() {
+std::string libtiledbsoma_version(const bool compact);
+RcppExport SEXP _tiledbsoma_libtiledbsoma_version(SEXP compactSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
-    rcpp_result_gen = Rcpp::wrap(libtiledbsoma_version());
+    Rcpp::traits::input_parameter< const bool >::type compact(compactSEXP);
+    rcpp_result_gen = Rcpp::wrap(libtiledbsoma_version(compact));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -213,7 +214,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_tiledbsoma_tiledbsoma_stats_disable", (DL_FUNC) &_tiledbsoma_tiledbsoma_stats_disable, 0},
     {"_tiledbsoma_tiledbsoma_stats_reset", (DL_FUNC) &_tiledbsoma_tiledbsoma_stats_reset, 0},
     {"_tiledbsoma_tiledbsoma_stats_dump", (DL_FUNC) &_tiledbsoma_tiledbsoma_stats_dump, 0},
-    {"_tiledbsoma_libtiledbsoma_version", (DL_FUNC) &_tiledbsoma_libtiledbsoma_version, 0},
+    {"_tiledbsoma_libtiledbsoma_version", (DL_FUNC) &_tiledbsoma_libtiledbsoma_version, 1},
     {"_tiledbsoma_tiledb_embedded_version", (DL_FUNC) &_tiledbsoma_tiledb_embedded_version, 0},
     {NULL, NULL, 0}
 };

apis/r/src/rutilities.cpp

@@ -318,10 +318,19 @@ std::string tiledbsoma_stats_dump() {
 //' libtiledbsoma version
 //'
 //' Returns a string with version information for libtiledbsoma and the linked TileDB Embedded library.
+//' If argument `compact` is set to `TRUE`, a shorter version of just the TileDB Embedded library
+//' version is returned,
 //' @noRd
 // [[Rcpp::export]]
-std::string libtiledbsoma_version() {
-    return tiledbsoma::version::as_string();
+std::string libtiledbsoma_version(const bool compact = false) {
+    if (compact) {
+        auto v = tiledbsoma::version::embedded_version_triple();
+        std::ostringstream txt;
+        txt << std::get<0>(v) << "." << std::get<1>(v) << "." << std::get<2>(v);
+        return txt.str();
+    } else {
+        return tiledbsoma::version::as_string();
+    }
 }
 
 //' TileDB embedded version

apis/r/tools/get_tarball.R

@@ -1,8 +1,8 @@
 #!/usr/bin/env Rscript
 
 ## version pinning info
-tiledb_core_version <- "2.17.4"
-tiledb_core_sha1 <- "a1f648e"
+tiledb_core_version <- "2.18.2"
+tiledb_core_sha1 <- "9ae6e1a"
 
 if ( ! dir.exists("inst/") ) {
     stop("No 'inst/' directory. Exiting.", call. = FALSE)

apis/system/tests/test_version_match.py

@@ -17,6 +17,6 @@ def test_version_match(self):
         library("tiledb")
         version = tiledb_version()
         stopifnot(as.integer(version["major"]) == {major})
-        stopifnot(as.integer(version["minor"]) == {minor})
+        stopifnot(as.integer(version["minor"]) >= {minor})
         """
         )

libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake

@@ -58,8 +58,8 @@ else()
     # NB When updating the pinned URLs here, please also update in file apis/r/tools/get_tarball.R
     if(DOWNLOAD_TILEDB_PREBUILT)
         if (WIN32) # Windows
-          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-windows-x86_64-2.17.4-a1f648e.zip")
-          SET(DOWNLOAD_SHA1 "d82a090d231e5cebd10205af8b80884e934b9e9f")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-windows-x86_64-2.18.2-9ae6e1a.zip")
+          SET(DOWNLOAD_SHA1 "c440403fde701e5014a7ffa046d38bb49b141e55")
         elseif(APPLE) # OSX
 
           # Status quo as of 2023-05-18:
@@ -76,22 +76,22 @@ else()
           #   o CMAKE_SYSTEM_PROCESSOR is x86_64
 
           if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64)
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-macos-x86_64-2.17.4-a1f648e.tar.gz")
-            SET(DOWNLOAD_SHA1 "9e3807e1b63b21849a374c6d9c9f161b46a9cc5a")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-x86_64-2.18.2-9ae6e1a.tar.gz")
+            SET(DOWNLOAD_SHA1 "6ba986407b2d0e25fb5df19d08ed22fefeac1c2a")
           elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-macos-arm64-2.17.4-a1f648e.tar.gz")
-            SET(DOWNLOAD_SHA1 "e6ec0634f665943ff9879041ab122bdaa96349df")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-arm64-2.18.2-9ae6e1a.tar.gz")
+            SET(DOWNLOAD_SHA1 "4395a283db57844a944f02dab5bd0f0001eb7e30")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-macos-x86_64-2.17.4-a1f648e.tar.gz")
-            SET(DOWNLOAD_SHA1 "9e3807e1b63b21849a374c6d9c9f161b46a9cc5a")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-x86_64-2.18.2-9ae6e1a.tar.gz")
+            SET(DOWNLOAD_SHA1 "6ba986407b2d0e25fb5df19d08ed22fefeac1c2a")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-macos-arm64-2.17.4-a1f648e.tar.gz")
-            SET(DOWNLOAD_SHA1 "e6ec0634f665943ff9879041ab122bdaa96349df")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-macos-arm64-2.18.2-9ae6e1a.tar.gz")
+            SET(DOWNLOAD_SHA1 "4395a283db57844a944f02dab5bd0f0001eb7e30")
           endif()
 
         else() # Linux
-          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.4/tiledb-linux-x86_64-2.17.4-a1f648e.tar.gz")
-          SET(DOWNLOAD_SHA1 "7849cbbf19f5f9252e4be5350328754b01938aaa")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.18.2/tiledb-linux-x86_64-2.18.2-9ae6e1a.tar.gz")
+          SET(DOWNLOAD_SHA1 "6386504a58d52330f41fa688a2b259b67824e2c8")
         endif()
 
         ExternalProject_Add(ep_tiledb
@@ -113,8 +113,8 @@ else()
     else() # Build from source
         ExternalProject_Add(ep_tiledb
           PREFIX "externals"
-          URL "https://github.com/TileDB-Inc/TileDB/archive/2.17.4.zip"
-          URL_HASH SHA1=a6a848cd3d3f19ed1dd6057e3f05fb7b54740016
+          URL "https://github.com/TileDB-Inc/TileDB/archive/2.18.2.zip"
+          URL_HASH SHA1=70bb2e9a7603675849830b763d1a0d17fce4bafa
           DOWNLOAD_NAME "tiledb.zip"
           CMAKE_ARGS
             -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}