Test compatibility with newer C++ standards

.github/workflows/cppstd.yml

@@ -0,0 +1,270 @@
+# Copyright (C) 2024 Roberto Rossini (roberros@uio.no)
+# SPDX-License-Identifier: MIT
+
+name: Test compatibility with newer C++ standards
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - ".github/workflows/cppstd.yml"
+      - "cmake/**"
+      - "examples/**"
+      - "src/**"
+      - "test/scripts/**"
+      - "test/units/**"
+      - "CMakeLists.txt"
+      - "conanfile.py"
+    tags:
+      - "v*.*.*"
+
+  pull_request:
+    paths:
+      - ".github/workflows/cppstd.yml"
+      - "cmake/**"
+      - "examples/**"
+      - "src/**"
+      - "test/scripts/**"
+      - "test/units/**"
+      - "CMakeLists.txt"
+      - "conanfile.py"
+
+# https://stackoverflow.com/a/72408109
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  build-deps:
+    runs-on: ubuntu-latest
+    name: Build dependencies
+    container:
+      image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19
+      options: "--user=root"
+
+    outputs:
+      cache-key: ${{ steps.generate-cache-key.outputs.conan-key }}
+
+    env:
+      CONAN_HOME: "/opt/conan/"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Fix permissions
+        run: |
+          chown -R $(id -u):$(id -g) $PWD
+
+      - name: Generate cache key
+        id: generate-cache-key
+        run: |
+          hash="${{ hashFiles('conanfile.py') }}"
+
+          echo "conan-key=conan-cppstd-$hash" | tee -a "$GITHUB_OUTPUT"
+
+      - name: Restore Conan cache
+        id: cache-conan
+        uses: actions/cache/restore@v4
+        with:
+          key: ${{ steps.generate-cache-key.outputs.conan-key }}
+          path: "${{ env.CONAN_HOME }}/p"
+          lookup-only: true
+
+      - name: Clean Conan cache (pre-build)
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          conan cache clean "*" --build
+          conan cache clean "*" --download
+          conan cache clean "*" --source
+          conan remove --confirm "*"
+
+      - name: Copy Conan settings
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          if [ ! -f "$CONAN_HOME/settings.yml" ]; then
+            cp "/root/.conan2/settings.yml" "$CONAN_HOME"
+          fi
+
+      - name: Install build dependencies (c++20)
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          conan install .                        \
+             --build=missing                     \
+             -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \
+             -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \
+             -s build_type=Debug                 \
+             -s compiler.libcxx=libstdc++11      \
+             -s compiler.cppstd=20
+
+      - name: Install build dependencies (c++23)
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          conan install .                        \
+             --build=missing                     \
+             -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \
+             -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \
+             -s build_type=Debug                 \
+             -s compiler.libcxx=libstdc++11      \
+             -s compiler.cppstd=23
+
+      - name: Clean Conan cache (post-build)
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          conan cache clean "*" --build
+          conan cache clean "*" --download
+          conan cache clean "*" --source
+
+      - name: Save Conan cache
+        uses: actions/cache/save@v4
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        with:
+          key: ${{ steps.generate-cache-key.outputs.conan-key }}
+          path: "${{ env.CONAN_HOME }}/p"
+
+  build-project:
+    runs-on: ubuntu-latest
+    name: Build project
+    needs: [build-deps]
+    container:
+      image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19
+      options: "--user=root"
+
+    env:
+      CCACHE_DIR: "/opt/ccache-cache"
+      CCACHE_COMPILERCHECK: "content"
+      CCACHE_COMPRESSLEVEL: "1"
+      CCACHE_MAXSIZE: "150M"
+      CONAN_HOME: "/opt/conan/"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        cppstd:
+          - 20
+          - 23
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Fix permissions
+        run: |
+          chown -R $(id -u):$(id -g) $PWD
+
+      - name: Generate cache key
+        id: generate-cache-key
+        run: |
+          conanfile_hash="${{ hashFiles('conanfile.py') }}"
+
+          # This can be used by to always update a cache entry (useful e.g. for ccache)
+          current_date="$(date '+%s')"
+
+          ccache_key_prefix="ccache-cppstd-${{ matrix.cppstd }}-$conanfile_hash"
+
+          echo "ccache-key=${ccache_key_prefix}-${current_date}" | tee -a "$GITHUB_OUTPUT"
+          echo "ccache-restore-key=$ccache_key_prefix" | tee -a "$GITHUB_OUTPUT"
+
+      - name: Restore Conan cache
+        id: cache-conan
+        uses: actions/cache/restore@v4
+        with:
+          key: ${{ needs.build-deps.outputs.cache-key }}
+          path: "${{ env.CONAN_HOME }}/p"
+          fail-on-cache-miss: true
+
+      - name: Copy Conan settings
+        run: |
+          if [ ! -f "$CONAN_HOME/settings.yml" ]; then
+            cp "/root/.conan2/settings.yml" "$CONAN_HOME"
+          fi
+
+      - name: Install build dependencies
+        run: |
+          conan install .                            \
+             --build=never                           \
+             -pr:b="$CONAN_DEFAULT_PROFILE_PATH"     \
+             -pr:h="$CONAN_DEFAULT_PROFILE_PATH"     \
+             -s build_type=Debug                     \
+             -s compiler.libcxx=libstdc++11          \
+             -s compiler.cppstd=${{ matrix.cppstd }} \
+             --output-folder=build
+
+      - name: Install Python headers
+        run: |
+          apt-get update
+          apt-get install -y python3.12-dev
+
+      - name: Configure project
+        run: |
+          find src test \
+            -type f \
+            -name CMakeLists.txt \
+            -exec sed -i 's/set(CMAKE_CXX_STANDARD 17)/set(CMAKE_CXX_STANDARD ${{ matrix.cppstd }})/' {} +
+
+          cmake -DCMAKE_BUILD_TYPE=Debug \
+                -DCMAKE_PREFIX_PATH="$PWD/build" \
+                -DHICTK_ENABLE_TESTING=ON \
+                -DHICTK_ENABLE_FUZZY_TESTING=ON \
+                -DHICTK_BUILD_TOOLS=OFF \
+                -DHICTK_BUILD_EXAMPLES=ON \
+                -DHICTK_DOWNLOAD_TEST_DATASET=OFF \
+                -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \
+                -S . \
+                -B build
+
+      - name: Restore Ccache folder
+        id: cache-ccache
+        uses: actions/cache/restore@v4
+        with:
+          key: ${{ steps.generate-cache-key.outputs.ccache-restore-key }}
+          path: ${{ env.CCACHE_DIR }}
+
+      - name: Reset Ccache stats
+        run: ccache --zero-stats
+
+      - name: Build project
+        run: cmake --build build -j $(nproc)
+
+      - name: Print Ccache statistics (pre-cleanup)
+        run: |
+          ccache --show-stats \
+                 --show-compression \
+                 --verbose
+
+      - name: Cleanup Ccache folder
+        run: |
+          ccache --evict-older-than=14400s # 4h
+          ccache --recompress=19 --recompress-threads="$(nproc)"
+          ccache --cleanup
+
+      - name: Print Ccache statistics (post-cleanup)
+        run: |
+          ccache --show-stats \
+                 --show-compression \
+                 --verbose
+
+      - name: Save Ccache folder
+        uses: actions/cache/save@v4
+        with:
+          key: ${{ steps.generate-cache-key.outputs.ccache-key }}
+          path: ${{ env.CCACHE_DIR }}
+        env:
+          ZSTD_CLEVEL: 1
+
+  cppstd-status-check:
+    name: Status Check (cppstd)
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    needs:
+      - build-deps
+      - build-project
+
+    steps:
+      - name: Collect job results
+        if: |
+          needs.build-deps.result != 'success' ||
+          needs.build-project.result != 'success'
+        run: exit 1

conanfile.py

@@ -85,6 +85,7 @@ def configure(self):
         self.options["boost"].without_atomic = False
         self.options["boost"].without_charconv = True
         self.options["boost"].without_chrono = True
+        self.options["boost"].without_cobalt = True
         self.options["boost"].without_container = True
         self.options["boost"].without_context = True
         self.options["boost"].without_contract = True

src/libhictk/cooler/include/hictk/cooler/impl/file_impl.hpp

@@ -293,7 +293,7 @@ inline HighFive::File File::open_file(std::string_view uri, unsigned int mode, b
     throw std::runtime_error(
         fmt::format(FMT_STRING("\"{}\" does not look like a valid Cooler file:\n"
                                "Validation report:\n{}"),
-                    uri, status));
+                    uri, fmt::to_string(status)));
   }
 
   return f;

src/libhictk/cooler/include/hictk/cooler/impl/utils_rename_chroms_impl.hpp

@@ -30,8 +30,8 @@ namespace internal {
 }
 
 template <typename NameMap>
-[[nodiscard]] inline std::vector<std::string>& rename_chromosomes(std::vector<std::string>&& names,
-                                                                  const NameMap& mappings) {
+[[nodiscard]] inline std::vector<std::string> rename_chromosomes(std::vector<std::string>&& names,
+                                                                 const NameMap& mappings) {
   for (auto& name : names) {
     auto it = mappings.find(name);
     if (it != mappings.end()) {
@@ -82,9 +82,8 @@ inline void rename_chromosomes(cooler::Dataset& chrom_dset, const NameMap& mappi
   if (mappings.empty()) {
     return;
   }
-  auto names = chrom_dset.read_all<std::vector<std::string>>();
-
-  names = internal::rename_chromosomes(std::move(names), mappings);
+  const auto names =
+      internal::rename_chromosomes(chrom_dset.read_all<std::vector<std::string>>(), mappings);
 
   // NOLINTNEXTLINE(misc-const-correctness)
   auto h5f = chrom_dset().getFile();

src/libhictk/cooler/include/hictk/cooler/singlecell_cooler.hpp

@@ -58,7 +58,7 @@ struct SingleCellAttributes {
 class SingleCellFile {
   std::unique_ptr<RootGroup> _root_grp{};
   phmap::btree_set<std::string> _cells{};
-  SingleCellAttributes _attrs{};
+  SingleCellAttributes _attrs{SingleCellAttributes::init_empty()};
   std::shared_ptr<const BinTable> _bins{};
 
   SingleCellFile(HighFive::File fp, BinTable bins, SingleCellAttributes attrs);

src/libhictk/transformers/include/hictk/transformers/impl/to_dataframe_impl.hpp

@@ -4,12 +4,19 @@
 
 #pragma once
 
+// clang-format: off
+#include "hictk/suppress_warnings.hpp"
+
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <arrow/array.h>
 #include <arrow/builder.h>
 #include <arrow/compute/api_vector.h>
 #include <arrow/datum.h>
 #include <arrow/table.h>
 #include <arrow/type.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format: on
 
 #include <algorithm>
 #include <cassert>

src/libhictk/transformers/include/hictk/transformers/to_dataframe.hpp

@@ -6,9 +6,16 @@
 
 #ifdef HICTK_WITH_ARROW
 
+// clang-format: off
+#include "hictk/suppress_warnings.hpp"
+
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <arrow/builder.h>
 #include <arrow/table.h>
 #include <arrow/type.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format: on
 
 #include <memory>
 #include <type_traits>