FMT experiment [skip ci]

single-cell-data · Jan 8, 2025 · a8dd214 · a8dd214
1 parent 5eac48e
commit a8dd214
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Showing 9 changed files with 50 additions and 10 deletions.
diff --git a/.github/workflows/python-packaging.yml b/.github/workflows/python-packaging.yml
@@ -90,7 +90,7 @@ jobs:
         with:
           xcode-version: '15.4'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.18.1
+        uses: pypa/cibuildwheel@v2.22.0
         with:
           package-dir: tiledbsoma.tar.gz
           only: cp${{ matrix.python-version }}-${{ matrix.cibw_build }}
@@ -112,7 +112,8 @@ jobs:
           CIBW_ENVIRONMENT_LINUX : CC=/opt/rh/gcc-toolset-13/root/usr/bin/gcc CXX=/opt/rh/gcc-toolset-13/root/usr/bin/g++
           CIBW_TEST_SKIP: "*_arm64"
           CMAKE_OSX_ARCHITECTURES: ${{ matrix.cibw_archs_macos }}
-          MACOSX_DEPLOYMENT_TARGET: "13.3"
+          MACOSX_DEPLOYMENT_TARGET: "11.0"
+
       - name: Upload wheel-${{ matrix.wheel-name }}-${{ matrix.python-version }} to GitHub Actions storage
         uses: actions/upload-artifact@v4
         with:

diff --git a/apis/python/setup.py b/apis/python/setup.py
@@ -254,7 +254,8 @@ def run(self):
     CXX_FLAGS.append(f'-Wl,-rpath,{str(tiledb_dir / "lib")}')
 
 if sys.platform == "darwin":
-    CXX_FLAGS.append("-mmacosx-version-min=13.3")
+    CXX_FLAGS.append("-D_LIBCPP_DISABLE_AVAILABILITY")
+    CXX_FLAGS.append("-mmacosx-version-min=11.0")
 
 if os.name == "posix" and sys.platform != "darwin":
     LIB_DIRS.append(str(tiledbsoma_dir / "lib" / "x86_64-linux-gnu"))

diff --git a/apis/r/configure b/apis/r/configure
@@ -54,7 +54,7 @@ tools/build_libtiledbsoma.sh
 pkgincl="-I../inst/tiledb/include -I../inst/tiledbsoma/include -I../inst/tiledbsoma/include/tiledbsoma"
 pkglibs="-ltiledb -L../inst/tiledb/lib -ltiledbsoma -L../inst/tiledbsoma/lib"
 rpath="-Wl,-rpath,'\$\$ORIGIN/../tiledb/lib' -Wl,-rpath,'\$\$ORIGIN/../tiledbsoma/lib'"
-macosver=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=13.3") else cat("")'`
+macosver=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=11.0") else cat("")'`
 
 sed -e "s|@tiledb_include@|$pkgincl |" \
     -e "s|@tiledb_libs@|$pkglibs|" \

diff --git a/apis/r/src/Makevars.in b/apis/r/src/Makevars.in
@@ -1,7 +1,7 @@
 CXX_STD = CXX20
 
 ## We need the TileDB Headers, and for macOS aka Darwin need to set minimum version 13.3 for macOS
-PKG_CPPFLAGS = -I. -I../inst/include/ @tiledb_include@ @cxx20_macos@ -D SPDLOG_USE_STD_FORMAT
+PKG_CPPFLAGS = -I. -I../inst/include/ @tiledb_include@ @cxx20_macos@ -DSPDLOG_FMT_EXTERNAL_HO
 
 ## We also need the TileDB library
 PKG_LIBS = @cxx20_macos@ @tiledb_libs@ @tiledb_rpath@

diff --git a/libtiledbsoma/CMakeLists.txt b/libtiledbsoma/CMakeLists.txt
@@ -114,7 +114,7 @@ if(APPLE)
   set(CMAKE_MACOSX_RPATH ON)
 
   # Set minimum macOS version to enable certain C++20 features
-  set(CMAKE_OSX_DEPLOYMENT_TARGET 13.3)
+  # set(CMAKE_OSX_DEPLOYMENT_TARGET 13.3)
 
   # Don't allow macOS .frameworks to be used for dependencies.
   set(CMAKE_FIND_FRAMEWORK NEVER)
@@ -221,7 +221,7 @@ if(MSVC)
   )
 else()
 
-  set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra -DSPDLOG_USE_STD_FORMAT)
+  set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra -DSPDLOG_FMT_EXTERNAL_HO)
 
   if(${TILEDBSOMA_ENABLE_WERROR})
     set(TILEDBSOMA_WERROR_OPTION -Werror)

diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -50,7 +50,7 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/array_buffers.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/column_buffer.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/arrow_adapter.cc
-  ${CMAKE_CURRENT_SOURCE_DIR}/utils/logger.cc
+  # ${CMAKE_CURRENT_SOURCE_DIR}/utils/logger.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/stats.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/util.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/utils/version.cc
@@ -129,6 +129,40 @@ target_include_directories(TILEDB_SOMA_GEOMETRY_OBJECTS
   ${CMAKE_CURRENT_SOURCE_DIR}/vendor
 )
 
+# ###########################################################
+# tiledbsoma logging library target
+# ###########################################################
+
+add_library(TILEDB_SOMA_LOGGING_OBJECTS OBJECT
+  ${CMAKE_CURRENT_SOURCE_DIR}/utils/logger.cc
+)
+
+target_link_options(TILEDB_SOMA_LOGGING_OBJECTS
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
+
+target_compile_definitions(TILEDB_SOMA_LOGGING_OBJECTS
+  PRIVATE
+  -DTILEDB_NO_API_DEPRECATION_WARNINGS
+)
+
+target_compile_options(TILEDB_SOMA_LOGGING_OBJECTS
+  PRIVATE
+  ${TILEDBSOMA_COMPILE_OPTIONS}
+  ${TILEDBSOMA_WERROR_OPTION}
+  ${TILEDBSOMA_SANITIZER_OPTIONS}
+)
+
+set_property(TARGET TILEDB_SOMA_LOGGING_OBJECTS PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+target_include_directories(TILEDB_SOMA_LOGGING_OBJECTS
+  PRIVATE
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/vendor
+  $<TARGET_PROPERTY:spdlog::spdlog,INTERFACE_INCLUDE_DIRECTORIES>
+)
+
 # ###########################################################
 # tiledbsoma library target
 # ###########################################################
@@ -137,6 +171,7 @@ if(TILEDBSOMA_BUILD_STATIC)
   add_library(tiledbsoma_static STATIC
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
     $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_LOGGING_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
   )
   list(APPEND TILEDBSOMA_INSTALL_TARGETS tiledbsoma_static)
@@ -160,6 +195,7 @@ else()
   add_library(tiledbsoma SHARED
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
     $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_LOGGING_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
   )
   list(APPEND TILEDBSOMA_INSTALL_TARGETS tiledbsoma)
@@ -297,6 +333,7 @@ if(TILEDBSOMA_BUILD_CLI)
   add_executable(tiledbsoma-cli
     ${CMAKE_CURRENT_SOURCE_DIR}/cli/cli.cc
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_LOGGING_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
   )
 

diff --git a/libtiledbsoma/src/reindexer/reindexer.h b/libtiledbsoma/src/reindexer/reindexer.h
@@ -37,6 +37,7 @@
 #include <memory>
 #include <stdexcept>
 #include <vector>
+#include <format>
 
 struct kh_m64_s;
 

diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
@@ -34,8 +34,6 @@
 #include "../utils/logger.h"
 #include "../utils/util.h"
 
-#include <format>
-
 namespace tiledbsoma {
 using namespace tiledb;
 

diff --git a/libtiledbsoma/test/CMakeLists.txt b/libtiledbsoma/test/CMakeLists.txt
@@ -16,6 +16,7 @@ find_package(Catch_EP REQUIRED)
 add_executable(unit_soma
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
     $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_LOGGING_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
     common.cc
     common.h
@@ -98,6 +99,7 @@ endif()
 add_executable(unit_geometry
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
     $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_LOGGING_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
     common.cc
     common.h