From fd9d458fcc13b322f4b510f2e54eabaee2a9168b Mon Sep 17 00:00:00 2001 From: John Kerl Date: Thu, 28 Sep 2023 15:51:03 -0400 Subject: [PATCH] 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 | 10 +++++++ apis/python/setup.py | 2 +- apis/r/DESCRIPTION | 2 +- apis/r/tools/get_tarball.R | 4 +-- .../cmake/Modules/FindTileDB_EP.cmake | 28 +++++++++---------- 5 files changed, 28 insertions(+), 18 deletions(-) diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml index fdb088aa93..f5652693ea 100644 --- a/.github/workflows/r-ci.yml +++ b/.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 diff --git a/apis/python/setup.py b/apis/python/setup.py index 93c58cba21..752f6114ab 100644 --- a/apis/python/setup.py +++ b/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={ diff --git a/apis/r/DESCRIPTION b/apis/r/DESCRIPTION index 58a89016da..7dd9639f7b 100644 --- a/apis/r/DESCRIPTION +++ b/apis/r/DESCRIPTION @@ -34,7 +34,7 @@ Imports: Matrix, stats, bit64, - tiledb (>= 0.21.0), + tiledb (>= 0.21.1), arrow, utils, fs, diff --git a/apis/r/tools/get_tarball.R b/apis/r/tools/get_tarball.R index 97ad341e2e..689a8b919a 100644 --- a/apis/r/tools/get_tarball.R +++ b/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) diff --git a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake b/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake index f689401ad6..9ca1dabe36 100644 --- a/libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake +++ b/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}