Re-apply 3389 for C++20 -> 17

apis/python/setup.py

@@ -325,7 +325,7 @@ def run(self):
             library_dirs=LIB_DIRS,
             libraries=["tiledbsoma"] + (["tiledb"] if os.name == "nt" else []),
             extra_link_args=CXX_FLAGS,
-            extra_compile_args=["-std=c++20" if os.name != "nt" else "/std:c++20"]
+            extra_compile_args=["-std=c++17" if os.name != "nt" else "/std:c++17"]
             + CXX_FLAGS,
             language="c++",
         )

apis/python/src/tiledbsoma/fastercsx.cc

@@ -36,7 +36,6 @@
 /* #define FASTERCSX__DEBUGGING_HOOKS 1 */
 
 #include <tiledbsoma/utils/fastercsx.h>
-#include <span>
 #include "common.h"
 
 namespace libtiledbsomacpp {
@@ -76,36 +75,36 @@ std::vector<T> to_vector_(const py::tuple& tup) {
  */
 
 template <typename T>
-std::span<T const> make_span_(py::array arr) {
+tcb::span<T const> make_span_(py::array arr) {
     assert(py::isinstance<py::array_t<T>>(arr));
-    return std::span<T const>(arr.unchecked<T, 1>().data(0), arr.size());
+    return tcb::span<T const>(arr.unchecked<T, 1>().data(0), arr.size());
 }
 
 template <typename T>
-std::span<T> make_mutable_span_(py::array arr) {
+tcb::span<T> make_mutable_span_(py::array arr) {
     assert(py::isinstance<py::array_t<T>>(arr));
-    return std::span<T>(
+    return tcb::span<T>(
         arr.mutable_unchecked<T, 1>().mutable_data(0), arr.size());
 }
 
 template <typename T, typename R>
-std::span<R const> make_casted_span_(py::array arr) {
+tcb::span<R const> make_casted_span_(py::array arr) {
     static_assert(sizeof(T) == sizeof(R));
     assert(py::isinstance<py::array_t<T>>(arr));
     std::remove_cv_t<T>* p = (std::remove_cv_t<T>*)arr
                                  .unchecked<std::remove_cv_t<T>, 1>()
                                  .data(0);
-    return std::span<R const>(reinterpret_cast<R*>(p), arr.size());
+    return tcb::span<R const>(reinterpret_cast<R*>(p), arr.size());
 }
 
 template <typename T, typename R>
-std::span<R> make_mutable_casted_span_(py::array arr) {
+tcb::span<R> make_mutable_casted_span_(py::array arr) {
     static_assert(sizeof(T) == sizeof(R));
     assert(py::isinstance<py::array_t<T>>(arr));
     std::remove_cv_t<T>* p = (std::remove_cv_t<T>*)arr
                                  .mutable_unchecked<std::remove_cv_t<T>, 1>()
                                  .data(0);
-    return std::span<R>(reinterpret_cast<R*>(p), arr.size());
+    return tcb::span<R>(reinterpret_cast<R*>(p), arr.size());
 }
 
 /*
@@ -351,8 +350,8 @@ void compress_coo(
                 typename decltype(csx_minor_index_type)::type;
             using VALUE = typename decltype(value_type)::type;
 
-            std::vector<std::span<COO_INDEX const>> Ai_views, Aj_views;
-            std::vector<std::span<remap_value_t<VALUE> const>> Ad_views;
+            std::vector<tcb::span<COO_INDEX const>> Ai_views, Aj_views;
+            std::vector<tcb::span<remap_value_t<VALUE> const>> Ad_views;
             for (size_t i = 0; i < Ai.size(); ++i) {
                 Ai_views.push_back(make_span_<COO_INDEX>(Ai[i]));
                 Aj_views.push_back(make_span_<COO_INDEX>(Aj[i]));
@@ -552,7 +551,7 @@ void count_rows(
             using CSX_MAJOR_INDEX =
                 typename decltype(csx_major_index_type)::type;
 
-            std::vector<std::span<COO_INDEX const>> Ai_views, Aj_views;
+            std::vector<tcb::span<COO_INDEX const>> Ai_views, Aj_views;
             for (size_t i = 0; i < Ai.size(); ++i) {
                 Ai_views.push_back(make_span_<COO_INDEX>(Ai[i]));
             }

apis/r/configure

@@ -18,11 +18,11 @@ if [ $? -eq 0 ]; then
         pkgcflags=`pkg-config --cflags tiledb tiledbsoma`
         pkglibs=`pkg-config --libs tiledb tiledbsoma`
 
-        ## substitute them in (leaving @tiledb_rpath@ and @cxx20_macos@ alone for now)
+        ## substitute them in (leaving @tiledb_rpath@ and @cxx17_macos@ alone for now)
         sed -e "s|@tiledb_include@|$pkgcflags |" \
             -e "s|@tiledb_libs@|$pkglibs|" \
             -e "s|@tiledb_rpath@||" \
-            -e "s|@cxx20_macos@||" \
+            -e "s|@cxx17_macos@||" \
             src/Makevars.in > src/Makevars
 
         echo "** updated src/Makevars for system library via pkg-config"
@@ -54,10 +54,10 @@ 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|" \
     -e "s|@tiledb_rpath@|$rpath|" \
-    -e "s|@cxx20_macos@|$macosver|" \
+    -e "s|@cxx17_macos@|$macosver|" \
     src/Makevars.in > src/Makevars

apis/r/inst/AUTHORS

@@ -11,6 +11,16 @@ The package also includes code written by other contributors as
 detailed below:
 
 
+-- libtiledbsoma/src/external/include/span/span.hpp ---------------------------------------------
+The span.hpp implements std::span, part of C++20, for use by C++11 or later. It
+was written by Tristan Brindle and is released at https://github.com/tcbrindle/span
+
+//          Copyright Tristan Brindle 2018.
+// Distributed under the Boost Software License, Version 1.0.
+//    (See accompanying file ../../LICENSE_1_0.txt or copy at
+//          https://www.boost.org/LICENSE_1_0.txt)
+
+
 -- libtiledbsoma/src/external/{src,include}/thread_pool/ ----------------------------------------
 The thread_pool implementation is from TileDB, Inc., and part of TileDB Embedded released at
 https://github.com/tiledb-inc/tiledb

apis/r/src/Makevars.in

@@ -1,10 +1,10 @@
-CXX_STD = CXX20
+CXX_STD = CXX17
 
 ## We need the TileDB Headers, and for macOS aka Darwin need to set minimum version 10.14 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@ @cxx17_macos@
 
 ## We also need the TileDB library
-PKG_LIBS = @cxx20_macos@ @tiledb_libs@ @tiledb_rpath@
+PKG_LIBS = @cxx17_macos@ @tiledb_libs@ @tiledb_rpath@
 
 all: $(SHLIB)
         # On macOS aka Darwin we call install_name_tool

libtiledbsoma/CMakeLists.txt

@@ -82,7 +82,7 @@ if(CCACHE_FOUND)
 endif()
 
 # Set C++20 as required standard for all C++ targets (C++17 minimum is required to use the TileDB C++ API).
-set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF) # Don't use GNU extensions
 
@@ -218,7 +218,7 @@ if(MSVC)
   )
 else()
 
-  set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra -DSPDLOG_USE_STD_FORMAT)
+  set(TILEDBSOMA_COMPILE_OPTIONS -Wall -Wextra)
 
   if(${TILEDBSOMA_ENABLE_WERROR})
     set(TILEDBSOMA_WERROR_OPTION -Werror)

libtiledbsoma/README.md

@@ -2,7 +2,7 @@
 
 ## System Dependencies
 
-* C++20 compiler
+* C++17 compiler
 * Python 3.9+
 
 Run these commands to setup a fresh Ubuntu 22.04 instance (tested on x86 and Arm):

libtiledbsoma/src/CMakeLists.txt

@@ -242,6 +242,11 @@ install(FILES
   DESTINATION "include/tiledbsoma/utils"
 )
 
+install(FILES
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/span/span.hpp
+  DESTINATION "include/tiledbsoma/soma/span"
+)
+
 install(FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow/nanoarrow.h
   ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow/nanoarrow.hpp

libtiledbsoma/src/cli/cli.cc

@@ -30,7 +30,6 @@
  * This file is currently a sandbox for C++ API experiments
  */
 
-#include <format>
 #include "soma/enums.h"
 #include "soma/soma_array.h"
 #include "utils/arrow_adapter.h"
@@ -78,8 +77,8 @@ void test_sdf(const std::string& uri) {
         total_num_rows += (*batch)->num_rows();
     }
 
-    LOG_INFO(std::format("X/data rows = {}", total_num_rows));
-    LOG_INFO(std::format("  batches = {}", batches));
+    LOG_INFO(fmt::format("X/data rows = {}", total_num_rows));
+    LOG_INFO(fmt::format("  batches = {}", batches));
 }
 
 namespace tdbs = tiledbsoma;
@@ -90,10 +89,10 @@ void test_arrow(const std::string& uri) {
     // Getting next batch:  std::optional<std::shared_ptr<ArrayBuffers>>
     auto obs_data = obs->read_next();
     if (!obs->results_complete()) {
-        tdbs::LOG_WARN(std::format("Read of '{}' incomplete", uri));
+        tdbs::LOG_WARN(fmt::format("Read of '{}' incomplete", uri));
         exit(-1);
     }
-    tdbs::LOG_INFO(std::format(
+    tdbs::LOG_INFO(fmt::format(
         "Read complete with {} obs and {} cols",
         obs_data->get()->num_rows(),
         obs_data->get()->names().size()));
@@ -102,7 +101,7 @@ void test_arrow(const std::string& uri) {
         auto buf = obs_data->get()->at(nm);
         auto pp = tdbs::ArrowAdapter::to_arrow(buf);
         ArrowSchema* schema = pp.second.get();
-        tdbs::LOG_INFO(std::format(
+        tdbs::LOG_INFO(fmt::format(
             "Accessing '{}', retrieved '{}', n_children {}",
             nm,
             schema->name,