Depend on TileDB core 2.19, TileDB-Py 0.25, TileDB-R 0.23 (#2002)

* Depend on TileDB core 2.19, TileDB-Py 0.25, TileDB-R 0.23

* updated unit-test expectation per @nguyenv and @davisp

apis/python/setup.py

@@ -294,7 +294,7 @@ def run(self):
         "scanpy>=1.9.2",
         "scipy",
         "somacore==1.0.6",
-        "tiledb~=0.24.0",
+        "tiledb~=0.25.0",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={

apis/python/tests/test_dataframe.py

@@ -145,8 +145,11 @@ def test_dataframe_with_enumeration(tmp_path):
         data["foo"] = pd.Categorical(["a", "bb", "ccc", "bb", "a"])
         data["bar"] = pd.Categorical(["cat", "dog", "cat", "cat", "cat"])
         sdf.write(pa.Table.from_pydict(data))
-        assert sdf.enumeration("foo") == enums["enmr1"]
-        assert sdf.enumeration("bar") == enums["enmr2"]
+
+    with soma.DataFrame.open(tmp_path.as_posix()) as sdf:
+        df = sdf.read().concat()
+        np.testing.assert_array_equal(df["foo"].chunk(0).dictionary, enums["enmr1"])
+        np.testing.assert_array_equal(df["bar"].chunk(0).dictionary, enums["enmr2"])
 
 
 @pytest.fixture

apis/r/DESCRIPTION

@@ -34,7 +34,7 @@ Imports:
     Matrix,
     stats,
     bit64,
-    tiledb (>= 0.22.0),
+    tiledb (>= 0.23.0),
     arrow,
     utils,
     fs,

apis/r/tools/get_tarball.R

@@ -1,8 +1,9 @@
 #!/usr/bin/env Rscript
 
 ## version pinning info
-tiledb_core_version <- "2.18.2"
-tiledb_core_sha1 <- "9ae6e1a"
+tiledb_core_version <- "2.19.0"
+# 8-nybble hash for 2.19.0 only. Please see https://github.com/TileDB-Inc/TileDB/pull/4599.
+tiledb_core_sha1 <- "fa30a88a"
 
 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/2.18.2/tiledb-windows-x86_64-2.18.2-9ae6e1a.zip")
-          SET(DOWNLOAD_SHA1 "c440403fde701e5014a7ffa046d38bb49b141e55")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-windows-x86_64-2.19.0-fa30a88a.zip")
+          SET(DOWNLOAD_SHA1 "ab8b61a35f0776e851c4eedcb1340df4d8cfb4b3")
         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/2.18.2/tiledb-macos-x86_64-2.18.2-9ae6e1a.tar.gz")
-            SET(DOWNLOAD_SHA1 "6ba986407b2d0e25fb5df19d08ed22fefeac1c2a")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-macos-x86_64-2.19.0-fa30a88a.tar.gz")
+            SET(DOWNLOAD_SHA1 "089b3aa8a92df0bd5a8f7515ed8e5b6bacb5ab47")
           elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
-            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")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-macos-arm64-2.19.0-fa30a88a.tar.gz")
+            SET(DOWNLOAD_SHA1 "83acdc7529d50dcf293dbd6bbc81263856c7c74c")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
-            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")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-macos-x86_64-2.19.0-fa30a88a.tar.gz")
+            SET(DOWNLOAD_SHA1 "089b3aa8a92df0bd5a8f7515ed8e5b6bacb5ab47")
           elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
-            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")
+            SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-macos-arm64-2.19.0-fa30a88a.tar.gz")
+            SET(DOWNLOAD_SHA1 "83acdc7529d50dcf293dbd6bbc81263856c7c74c")
           endif()
 
         else() # Linux
-          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")
+          SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.19.0/tiledb-linux-x86_64-2.19.0-fa30a88a.tar.gz")
+          SET(DOWNLOAD_SHA1 "d236688dbeff2536a8938cf8bf0d478b9f6108f6")
         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/2.18.2.zip"
-          URL_HASH SHA1=70bb2e9a7603675849830b763d1a0d17fce4bafa
+          URL "https://github.com/TileDB-Inc/TileDB/archive/2.19.0.zip"
+          URL_HASH SHA1=ade4c52490440f3d348e0f2d4677b322c83993df
           DOWNLOAD_NAME "tiledb.zip"
           CMAKE_ARGS
             -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}

scripts/update-tiledb-version.py

@@ -30,7 +30,8 @@ def get_version_hash(version):
 
     m = re.search(rf"\s(\S+)\s+refs/tags/{version}\s", output)
     if m:
-        return m.group(1)[0:7]
+        # 8-nybble hash for 2.19.0 only. Please see https://github.com/TileDB-Inc/TileDB/pull/4599.
+        return m.group(1)[0:8]
 
     print(output)
     print(f"Error: version {version} not found.")