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Backport update to TileDB core 2.29.2
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-21
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6 files changed

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-21
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‎.github/workflows/test-cpp.yml‎

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@@ -50,7 +50,7 @@ jobs:
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run: |
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mkdir -p external
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# Please do not edit manually -- let scripts/update-tiledb-version.py update this
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wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-linux-x86_64-2.29.1-9a6284d.tar.gz
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wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-linux-x86_64-2.29.2-2cd33d3.tar.gz
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tar -C external -xzf tiledb-*.tar.gz
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ls external/lib/
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‎apis/python/HISTORY.md‎

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@@ -4,6 +4,12 @@ All notable changes to the Python TileDB-SOMA project will be documented in this
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
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## [Release 2.1.1]
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### Changed
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- \[[#4309](https://github.com/single-cell-data/TileDB-SOMA/pull/4309)\] Update [TileDB core to 2.29.2](https://github.com/TileDB-Inc/TileDB/releases/tag/2.29.2).
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## [Release 2.1.0]
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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.

‎apis/r/DESCRIPTION‎

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@@ -6,7 +6,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
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like those commonly used for single cell data analysis. It is documented at
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<https://github.com/single-cell-data>; a formal specification available is at
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<https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.
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Version: 2.1.0
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Version: 2.1.1
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Authors@R: c(
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person(given = "Paul", family = "Hoffman",
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role = c("cre", "aut"), email = "tiledb-r@tiledb.com",

‎apis/r/NEWS.md‎

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@@ -1,3 +1,9 @@
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# tiledbsoma 2.1.1
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## Changed
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- Update TileDB core version to [2.29.2](https://github.com/TileDB-Inc/TileDB/releases/tag/2.29.2). ([#4309](https://github.com/single-cell-data/TileDB-SOMA/pull/4309))
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# tiledbsoma 2.1.0
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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.

‎apis/r/tools/get_tarball.R‎

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@@ -14,16 +14,16 @@ isLinux <- Sys.info()["sysname"] == "Linux"
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if (isMac) {
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arch <- system('uname -m', intern = TRUE)
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if (arch == "x86_64") {
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-x86_64-2.29.1-9a6284d.tar.gz"
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-x86_64-2.29.2-2cd33d3.tar.gz"
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} else if (arch == "arm64") {
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-arm64-2.29.1-9a6284d.tar.gz"
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-arm64-2.29.2-2cd33d3.tar.gz"
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} else {
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stop(
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"Unsupported Mac architecture. Please have TileDB Core installed locally."
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)
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}
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} else if (isLinux) {
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-linux-x86_64-2.29.1-9a6284d.tar.gz"
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url <- "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-linux-x86_64-2.29.2-2cd33d3.tar.gz"
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} else {
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message(
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"Unsupported platform for downloading artifacts. Please have TileDB Core installed locally."

‎libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake‎

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@@ -38,8 +38,8 @@ else()
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# NB When updating the pinned URLs here, please also update in file apis/r/tools/get_tarball.R
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if(DOWNLOAD_TILEDB_PREBUILT)
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if (WIN32) # Windows
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-windows-x86_64-2.29.1-9a6284d.zip")
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SET(DOWNLOAD_SHA1 "1bde74972df26c7f9399fea8acbf498e6882b91b")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-windows-x86_64-2.29.2-2cd33d3.zip")
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SET(DOWNLOAD_SHA1 "5dbe87d66ea3840cb40aa96f7211a0e1b5c9d314")
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elseif(APPLE) # OSX
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# Status quo as of 2023-05-18:
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# o CMAKE_SYSTEM_PROCESSOR is x86_64
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if (CMAKE_OSX_ARCHITECTURES STREQUAL x86_64)
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-x86_64-2.29.1-9a6284d.tar.gz")
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SET(DOWNLOAD_SHA1 "bb177d5f57c62d601e6d0b31057da1545b97a1e1")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-x86_64-2.29.2-2cd33d3.tar.gz")
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SET(DOWNLOAD_SHA1 "ef68c7d86ae36b6126baf1ad824b4cae320a8ca1")
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elseif (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-arm64-2.29.1-9a6284d.tar.gz")
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SET(DOWNLOAD_SHA1 "fe9eb004703874a2951beb4546e78f287e1182d2")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-arm64-2.29.2-2cd33d3.tar.gz")
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SET(DOWNLOAD_SHA1 "c9cdc34f91d0d9cc6374974c7f9ede5133ff820a")
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elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(AMD64|amd64)|(^i.86$)")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-x86_64-2.29.1-9a6284d.tar.gz")
66-
SET(DOWNLOAD_SHA1 "bb177d5f57c62d601e6d0b31057da1545b97a1e1")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-x86_64-2.29.2-2cd33d3.tar.gz")
66+
SET(DOWNLOAD_SHA1 "ef68c7d86ae36b6126baf1ad824b4cae320a8ca1")
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elseif (CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "^arm")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-macos-arm64-2.29.1-9a6284d.tar.gz")
69-
SET(DOWNLOAD_SHA1 "fe9eb004703874a2951beb4546e78f287e1182d2")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-macos-arm64-2.29.2-2cd33d3.tar.gz")
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SET(DOWNLOAD_SHA1 "c9cdc34f91d0d9cc6374974c7f9ede5133ff820a")
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endif()
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7272
else() # Linux
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if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64|arm64|ARM64)")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-linux-arm64-2.29.1-9a6284d.tar.gz")
75-
SET(DOWNLOAD_SHA1 "09ea428fcf9a8fd619dd8eb3b7b3ce01f92d845e")
74+
SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-linux-arm64-2.29.2-2cd33d3.tar.gz")
75+
SET(DOWNLOAD_SHA1 "c175d860e0e4b42ae630f136724934c65c20bdd9")
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else()
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.1/tiledb-linux-x86_64-2.29.1-9a6284d.tar.gz")
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SET(DOWNLOAD_SHA1 "f50ed997436e5aa3d6a0a2ace60d028b151f2863")
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SET(DOWNLOAD_URL "https://github.com/TileDB-Inc/TileDB/releases/download/2.29.2/tiledb-linux-x86_64-2.29.2-2cd33d3.tar.gz")
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SET(DOWNLOAD_SHA1 "6c962b090c51506be9979294a21b65031a54e12e")
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endif()
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endif()
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else() # Build from source
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ExternalProject_Add(ep_tiledb
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PREFIX "externals"
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URL "https://github.com/TileDB-Inc/TileDB/archive/2.29.1.zip"
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URL_HASH SHA1=8107f7b61314adb133e20f739d4ba79c5bc2f9a1
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URL "https://github.com/TileDB-Inc/TileDB/archive/2.29.2.zip"
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URL_HASH SHA1=3b3652d40d4177522970f84f3b8f21d7eabf9962
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DOWNLOAD_NAME "tiledb.zip"
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CMAKE_ARGS
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-DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}

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