[c++/python/r] Migrate to C++20

.github/workflows/backport.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   backport:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     name: Backport
     steps:
       - name: Backport

.github/workflows/pkgdown.yaml

@@ -18,7 +18,7 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     # This is GitHub Actions magic -- there are no secrets we as package owners need to set up or manage
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/python-ci-full.yml

@@ -21,15 +21,15 @@ jobs:
       fail-fast: false
       matrix:
         # TODO: decide on Windows CI coverage
-        os: [ubuntu-latest, macos-latest]
-        # os: [ubuntu-latest, macos-latest, windows-2019]
+        os: [ubuntu-24.04, macos-latest]
+        # os: [ubuntu-24.04, macos-latest, windows-2019]
         # TODO: add 3.12
         # https://github.com/single-cell-data/TileDB-SOMA/issues/1849
         python-version: ['3.9', '3.10', '3.11', '3.12']
         include:
-          - runs-on: ubuntu-latest
-            cc: gcc-11
-            cxx: g++-11
+          - runs-on: ubuntu-24.04
+            cc: gcc-13
+            cxx: g++-13
           - runs-on: macos-latest
             cc: clang
             cxx: clang++
@@ -39,6 +39,6 @@ jobs:
       python_version: ${{ matrix.python-version }}
       cc: ${{ matrix.cc }}
       cxx: ${{ matrix.cxx }}
-      report_codecov: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' }}
-      run_lint: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' }}
+      report_codecov: ${{ matrix.os == 'ubuntu-24.04' && matrix.python-version == '3.11' }}
+      run_lint: ${{ matrix.os == 'ubuntu-24.04' && matrix.python-version == '3.11' }}
     secrets: inherit

.github/workflows/python-ci-minimal.yml

@@ -28,12 +28,12 @@ jobs:
       fail-fast: true
 
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-24.04, macos-latest]
         python-version: ['3.9', '3.12']
         include:
-          - os: ubuntu-latest
-            cc: gcc-11
-            cxx: g++-11
+          - os: ubuntu-24.04
+            cc: gcc-13
+            cxx: g++-13
           - os: macos-latest
             cc: clang
             cxx: clang++

.github/workflows/python-ci-packaging.yml

@@ -39,7 +39,7 @@ jobs:
   # Confirm shared object copying when building the Python package
   # https://github.com/single-cell-data/TileDB-SOMA/pull/1937
   docker:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     name: "SO copying (docker) TILEDB_EXISTS: ${{ matrix.TILEDB_EXISTS }} TILEDBSOMA_EXISTS: ${{ matrix.TILEDBSOMA_EXISTS }}"
     strategy:
       fail-fast: false
@@ -152,7 +152,7 @@ jobs:
   # https://github.com/single-cell-data/TileDB-SOMA/pull/1937
   # Same as job above, but running on macOS instead of in a Docker container
   macos:
-    runs-on: macos-13
+    runs-on: macos-latest
     name: "SO copying (macos) TILEDB_EXISTS: ${{ matrix.TILEDB_EXISTS }} TILEDBSOMA_EXISTS: ${{ matrix.TILEDBSOMA_EXISTS }}"
     strategy:
       fail-fast: false
@@ -168,6 +168,10 @@ jobs:
           fetch-depth: 0  # for setuptools-scm
       - name: Check if System Integrity Protection (SIP) is enabled
         run: csrutil status
+      - name: Select XCode version
+        uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '15.4'
       - name: Install pre-built libtiledb
         if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
         run: |
@@ -259,7 +263,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-24.04", "macos-latest"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -364,7 +368,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-24.04", "macos-latest"]
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/python-ci-single.yml

@@ -70,7 +70,7 @@ jobs:
       run: echo "inputs.os:" ${{ inputs.os }}
 
     - name: Linux CPU info
-      if: ${{ inputs.os == 'ubuntu-latest' }}
+      if: ${{ inputs.os == 'ubuntu-24.04' }}
       run: cat /proc/cpuinfo
 
     - name: MacOS CPU info

.github/workflows/python-packaging.yml

@@ -21,7 +21,7 @@ on:
 jobs:
   sdist:
     name: Build source distribution
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout TileDB-SOMA
         uses: actions/checkout@v4
@@ -54,7 +54,7 @@ jobs:
         cibw_build: [ manylinux_x86_64, macosx_x86_64, macosx_arm64 ]
         include:
           - cibw_build: manylinux_x86_64
-            os: ubuntu-latest
+            os: ubuntu-24.04
             wheel-name: manylinux2014
           - cibw_build: macosx_x86_64
             os: macos-latest
@@ -84,6 +84,11 @@ jobs:
           pip install setuptools
           python -c 'from distutils import util; print("distutil.util.get_platform:", util.get_platform())'
           python -c 'import platform; print("platform.platform()", platform.platform())'
+      - name: Select XCode version
+        if: startsWith(matrix.os, 'macos')
+        uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: '15.4'
       - name: Build wheels
         uses: pypa/[email protected]
         with:
@@ -127,12 +132,12 @@ jobs:
           - macos-arm64
         include:
           - wheel-name: manylinux2014
-            os: ubuntu-latest
+            os: ubuntu-24.04
             arch: x86_64
-            cc: gcc-11
-            cxx: g++-11
+            cc: gcc-13
+            cxx: g++-13
           - wheel-name: macos-x86_64
-            os: macos-13
+            os: macos-latest
             arch: x86_64
             cc: clang
             cxx: clang++
@@ -166,7 +171,7 @@ jobs:
         run: python -c 'import tiledbsoma; print(tiledbsoma.pytiledbsoma.__file__); tiledbsoma.show_package_versions()'
         # TODO: more thorough local smoke test
       - name: Smoke test in docker
-        if: ${{ matrix.os == 'ubuntu-latest' }}
+        if: ${{ matrix.os == 'ubuntu-24.04' }}
         run: |
           docker run -v $(pwd):/mnt python:${{ matrix.python.dotted-version }} bash -ec "
             apt-get -qq update && apt-get install -y python3-pip python3-wheel
@@ -178,7 +183,7 @@ jobs:
   publish-to-test-pypi:
     name: Publish package to TestPyPI
     needs: smoke-test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     if: github.event_name == 'workflow_dispatch'
     steps:
       - name: Download artifacts
@@ -202,7 +207,7 @@ jobs:
   publish-to-pypi:
     name: Publish package to PyPI
     needs: smoke-test
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     if: github.event_name == 'release'
     steps:
       - name: Download artifacts
@@ -223,7 +228,7 @@ jobs:
   # File a bug report if anything fails, but don't file tickets for manual runs
   # -- only for scheduled ones.
   create_issue_on_fail:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: [smoke-test, publish-to-test-pypi, publish-to-pypi]
     if: (failure() || cancelled()) && github.event_name != 'workflow_dispatch'
     steps:

.github/workflows/r-ci.yml

@@ -32,13 +32,13 @@ jobs:
       matrix:
         include:
           - name: linux
-            os: ubuntu-latest
+            os: ubuntu-24.04
             covr: 'no'
           - name: macos
             os: macOS-latest
             covr: 'no'
           - name: coverage
-            os: ubuntu-latest
+            os: ubuntu-24.04
             covr: 'yes'
 
     runs-on: ${{ matrix.os }}
@@ -50,7 +50,7 @@ jobs:
         run: echo "matrix.os:" ${{ matrix.os }}
 
       - name: Linux CPU info
-        if: ${{ matrix.os == 'ubuntu-latest' }}
+        if: ${{ matrix.os == 'ubuntu-24.04' }}
         run: cat /proc/cpuinfo
 
       - name: MacOS CPU info
@@ -105,7 +105,7 @@ jobs:
       #  run: sudo scripts/bld --prefix=/usr/local
 
       #- name: Call ldconfig
-      #  if: ${{ matrix.os == 'ubuntu-latest' }}
+      #  if: ${{ matrix.os == 'ubuntu-24.04' }}
       #  run: sudo ldconfig
       #
       # - name: Update Packages
@@ -136,7 +136,7 @@ jobs:
         run: cd apis/r/tests && Rscript testthat.R
 
       - name: Coverage
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.covr == 'yes' && github.event_name == 'workflow_dispatch' }}
+        if: ${{ matrix.os == 'ubuntu-24.04' && matrix.covr == 'yes' && github.event_name == 'workflow_dispatch' }}
         run: apis/r/tools/r-ci.sh coverage
 
       - name: View Logs

.github/workflows/r-python-interop-testing.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       matrix:
         include:
-          - { os: ubuntu-latest }
+          - { os: ubuntu-24.04 }
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/r-valgrind.yaml

@@ -13,7 +13,7 @@ env:
 
 jobs:
   r-valgrind:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     container:
       image: rocker/r2u:latest
     steps:

apis/python/setup.py

@@ -320,7 +320,7 @@ 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++17" if os.name != "nt" else "/std:c++17"]
+            extra_compile_args=["-std=c++20" if os.name != "nt" else "/std:c++20"]
             + CXX_FLAGS,
             language="c++",
         )

apis/r/DESCRIPTION

@@ -49,7 +49,7 @@ Imports:
     nanoarrow
 LinkingTo:
     Rcpp,
-    RcppSpdlog,
+    RcppSpdlog (>= 0.0.19),
     RcppInt64,
     nanoarrow
 Additional_repositories: https://ghrr.github.io/drat

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 @cxx17_macos@ alone for now)
+        ## substitute them in (leaving @tiledb_rpath@ and @cxx20_macos@ alone for now)
         sed -e "s|@tiledb_include@|$pkgcflags |" \
             -e "s|@tiledb_libs@|$pkglibs|" \
             -e "s|@tiledb_rpath@||" \
-            -e "s|@cxx17_macos@||" \
+            -e "s|@cxx20_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=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=11.0") else cat("")'`
+macosver=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=13.3") else cat("")'`
 
 sed -e "s|@tiledb_include@|$pkgincl |" \
     -e "s|@tiledb_libs@|$pkglibs|" \
     -e "s|@tiledb_rpath@|$rpath|" \
-    -e "s|@cxx17_macos@|$macosver|" \
+    -e "s|@cxx20_macos@|$macosver|" \
     src/Makevars.in > src/Makevars

apis/r/src/Makevars.in

@@ -1,10 +1,10 @@
-CXX_STD = CXX17
+CXX_STD = CXX20
 
 ## 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@ @cxx17_macos@
+PKG_CPPFLAGS = -I. -I../inst/include/ @tiledb_include@ @cxx20_macos@ -D SPDLOG_USE_STD_FORMAT
 
 ## We also need the TileDB library
-PKG_LIBS = @cxx17_macos@ @tiledb_libs@ @tiledb_rpath@
+PKG_LIBS = @cxx20_macos@ @tiledb_libs@ @tiledb_rpath@
 
 all: $(SHLIB)
         # On macOS aka Darwin we call install_name_tool

libtiledbsoma/CMakeLists.txt

@@ -81,8 +81,8 @@ if(CCACHE_FOUND)
   set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK ccache)
 endif()
 
-# Set C++17 as required standard for all C++ targets (C++17 minimum is required to use the TileDB C++ API).
-set(CMAKE_CXX_STANDARD 17)
+# 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_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF) # Don't use GNU extensions
 

libtiledbsoma/src/cli/cli.cc

@@ -30,6 +30,7 @@
  * 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"
@@ -77,8 +78,8 @@ void test_sdf(const std::string& uri) {
         total_num_rows += (*batch)->num_rows();
     }
 
-    LOG_INFO(fmt::format("X/data rows = {}", total_num_rows));
-    LOG_INFO(fmt::format("  batches = {}", batches));
+    LOG_INFO(std::format("X/data rows = {}", total_num_rows));
+    LOG_INFO(std::format("  batches = {}", batches));
 }
 
 namespace tdbs = tiledbsoma;
@@ -89,10 +90,10 @@ 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(fmt::format("Read of '{}' incomplete", uri));
+        tdbs::LOG_WARN(std::format("Read of '{}' incomplete", uri));
         exit(-1);
     }
-    tdbs::LOG_INFO(fmt::format(
+    tdbs::LOG_INFO(std::format(
         "Read complete with {} obs and {} cols",
         obs_data->get()->num_rows(),
         obs_data->get()->names().size()));
@@ -101,7 +102,7 @@ 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(fmt::format(
+        tdbs::LOG_INFO(std::format(
             "Accessing '{}', retrieved '{}', n_children {}",
             nm,
             schema->name,