Depend on core 2.17.1, TileDB-Py 0.23.1, TileDB-R 0.21.1 (#1731)

* Depend on core 2.17.1, TileDB-Py 0.23.1, TileDB-R 0.21.1

* code-review feedback

.github/workflows/r-ci.yml

@@ -40,6 +40,16 @@ jobs:
 
       - name: Install BioConductor package SingleCellExperiment
         run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment
+
+      # Given propagation delay for binaries at https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/
+      - name: Install r-universe build of tiledb-r (macOS)
+        if: ${{ matrix.os == 'macOS-latest' }}
+        run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))"
+
+      # Given propagation delay for binaries at https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/
+      - name: Install r-universe build of tiledb-r (linux)
+        if: ${{ matrix.os != 'macOS-latest' }}
+        run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))"  
 
       - name: Dependencies
         run: cd apis/r && tools/r-ci.sh install_all

apis/python/setup.py

@@ -283,7 +283,7 @@ def run(self):
         "scanpy>=1.9.2",
         "scipy",
         "somacore==1.0.4",
-        "tiledb~=0.23.0",
+        "tiledb~=0.23.1",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={

apis/r/DESCRIPTION

@@ -34,7 +34,7 @@ Imports:
     Matrix,
     stats,
     bit64,
-    tiledb (>= 0.21.0),
+    tiledb (>= 0.21.1),
     arrow,
     utils,
     fs,

apis/r/tools/get_tarball.R

@@ -1,8 +1,8 @@
 #!/usr/bin/env Rscript
 
 ## version pinning info
-tiledb_core_version <- "2.17.0"
-tiledb_core_sha1 <- "93c173d"
+tiledb_core_version <- "2.17.1"
+tiledb_core_sha1 <- "7c8c73b"
 
 if ( ! dir.exists("inst/") ) {
     stop("No 'inst/' directory. Exiting.", call. = FALSE)

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/2.17.0/tiledb-windows-x86_64-2.17.0-93c173d.zip")
-          SET(DOWNLOAD_SHA1 "d43589b22de95d45b40de9918d105a6174ec352e")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-windows-x86_64-2.17.1-7c8c73b.zip")
+          SET(DOWNLOAD_SHA1 "c3757a9205299a4184bd4de7621ff9f5118f14ca")
         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/2.17.0/tiledb-macos-x86_64-2.17.0-93c173d.tar.gz")
-            SET(DOWNLOAD_SHA1 "9a232015cbf09c5bd37375537cef80a382e1ffa4")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-macos-x86_64-2.17.1-7c8c73b.tar.gz")
+            SET(DOWNLOAD_SHA1 "998c099297c0441af40729634642bd358c962da6")
           elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-arm64-2.17.0-93c173d.tar.gz")
-            SET(DOWNLOAD_SHA1 "b861b90b462963db44fe0217087fac3510fd6293")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-macos-arm64-2.17.1-7c8c73b.tar.gz")
+            SET(DOWNLOAD_SHA1 "23b2c8a18b7ad4198516f7975b51ce47e7dee56d")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-x86_64-2.17.0-93c173d.tar.gz")
-            SET(DOWNLOAD_SHA1 "9a232015cbf09c5bd37375537cef80a382e1ffa4")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-macos-x86_64-2.17.1-7c8c73b.tar.gz")
+            SET(DOWNLOAD_SHA1 "998c099297c0441af40729634642bd358c962da6")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
-            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-macos-arm64-2.17.0-93c173d.tar.gz")
-            SET(DOWNLOAD_SHA1 "b861b90b462963db44fe0217087fac3510fd6293")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-macos-arm64-2.17.1-7c8c73b.tar.gz")
+            SET(DOWNLOAD_SHA1 "23b2c8a18b7ad4198516f7975b51ce47e7dee56d")
           endif()
 
         else() # Linux
-          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.0/tiledb-linux-x86_64-2.17.0-93c173d.tar.gz")
-          SET(DOWNLOAD_SHA1 "5c04c07a73d3fe48a9ba8f3ad8af5e1912a39ce8")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.17.1/tiledb-linux-x86_64-2.17.1-7c8c73b.tar.gz")
+          SET(DOWNLOAD_SHA1 "c01bf6898ef5bd108d49b378aa30aadfc3131b75")
         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/2.17.0.zip"
-          URL_HASH SHA1=bbf5b34fec1c729f048f48bf1a0f03abb447d7de
+          URL "https://github.com/TileDB-Inc/TileDB/archive/2.17.1.zip"
+          URL_HASH SHA1=fd5bac0daf95eaff5a3ec53bfc930f3a32dd0ce0
           DOWNLOAD_NAME "tiledb.zip"
           CMAKE_ARGS
             -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}