temporarily Merge branch 'clang-tidy-sanitizer-ubuntu-24.04' into dont-require-shape-for-constant-components

franzpoeschel · franzpoeschel · commit 05bbff0fbd3e · 2025-09-10T16:33:43.000+02:00
diff --git a/.clang-tidy b/.clang-tidy
@@ -2,5 +2,5 @@
 # FIXME: all performance-* reports
 # FIXME: all cert-* reports
 # FIXME: all bugprone-* reports
-Checks: -*,bugprone-*,-bugprone-unhandled-self-assignment,-bugprone-parent-virtual-call,-bugprone-narrowing-conversions,-bugprone-exception-escape,-bugprone-string-literal-with-embedded-nul,cppcoreguidelines-slicing,mpi-*,readability-non-const-parameter,performance-*,modernize-*,-modernize-use-trailing-return-type,-modernize-use-bool-literals,-modernize-avoid-c-arrays,-modernize-use-auto,-modernize-return-braced-init-list,-bugprone-easily-swappable-parameters
+Checks: -*,bugprone-*,-bugprone-unhandled-self-assignment,-bugprone-parent-virtual-call,-bugprone-narrowing-conversions,-bugprone-exception-escape,-bugprone-string-literal-with-embedded-nul,cppcoreguidelines-slicing,mpi-*,readability-non-const-parameter,performance-*,-performance-avoid-endl,modernize-*,-modernize-use-trailing-return-type,-modernize-use-bool-literals,-modernize-avoid-c-arrays,-modernize-use-auto,-modernize-return-braced-init-list,-bugprone-easily-swappable-parameters,-bugprone-chained-comparison
 HeaderFilterRegex: '((^(?!\/share\/openPMD\/).*)*include\/openPMD\/.+\.hpp|src\/^(?!binding).+\.cpp$)'
diff --git a/.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml b/.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/spack.yaml
@@ -14,54 +14,78 @@ spack:
   packages:
     adios2:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2 ~mgard
+
     c-blosc2:
       # snappy broken on CMake 4.0
       # fixed snappy not yet deployed to a Spack release
       variants: ~snappy
+
     cmake:
       externals:
-      - spec: cmake@3.31.5
-        prefix: /usr
+      - spec: cmake@3.31.8
+        prefix: /usr/local
       buildable: False
+
     openmpi:
       externals:
-      - spec: openmpi@4.1.2
+      - spec: openmpi@4.1.6
         prefix: /usr
       buildable: False
+
     perl:
       externals:
-      - spec: perl@5.34.0
+      - spec: perl@5.38.2
         prefix: /usr
       buildable: False
+
     python:
       externals:
-      - spec: python@3.10.12
+      - spec: python@3.12.3
         prefix: /usr
       buildable: False
+
     all:
       target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
-      compiler: [clang@14.0.0]
+        cc: [llvm]
+        cxx: [llvm]
+        fortran: [gcc]
+
+    llvm:
+      externals:
+      - spec: llvm@19.1.1
+        prefix: /usr
+        paths:
+          cc: /usr/bin/clang-19
+          cxx: /usr/bin/clang++-19
+        modules: []
+        environment: {}
+        extra_rpaths: []
+      buildable: False
+
+    gcc:
+      externals:
+      - spec: gcc@13.3.0
+        prefix: /usr
+        paths:
+          cc: /usr/bin/gcc
+          cxx: /usr/bin/g++
+          fortran: /usr/bin/gfortran
+        modules: []
+        environment: {}
+        extra_rpaths: []
+      buildable: False
 
-  compilers:
-  - compiler:
-      environment: {}
-      extra_rpaths: []
-      flags: {}
-      modules: []
-      operating_system: ubuntu22.04
-      paths:
-        cc: /usr/bin/clang-14
-        cxx: /usr/bin/clang++-14
-        f77: /usr/bin/gfortran
-        fc: /usr/bin/gfortran
-      spec: clang@14.0.0
-      target: x86_64
+    gcc-runtime:
+      buildable: false
+      externals:
+        - spec: gcc-runtime@13.3.0
+          prefix: /usr
 
   config:
     build_jobs: 2
 
   mirrors:
-    E4S: https://cache.e4s.io
+    spack-public: https://mirror.spack.io
diff --git a/.github/workflows/dependencies/install_spack b/.github/workflows/dependencies/install_spack
@@ -3,7 +3,7 @@
 
 set -eu -o pipefail
 
-spack_ver="0.22.3"
+spack_ver="${SPACK_VER:-0.22.3}"
 
 cd /opt
 if [[ -d spack && ! -f spack_${spack_ver} ]]
diff --git a/.github/workflows/tooling.yml b/.github/workflows/tooling.yml
@@ -7,20 +7,21 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  clangtidy14_nopy_ompi_h5_ad2:
+  clangtidy19_nopy_ompi_h5_ad2:
     name: clang-tidy w/o py
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: clangtidy14_nopy_ompi_h5_ad2 }
+      with: {path: /opt/spack, key: clangtidy19_nopy_ompi_h5_ad2 }
     - name: Install
       run: |
         sudo apt-get update
         sudo apt-get install clang clang-tidy gfortran libopenmpi-dev python-is-python3
-        sudo .github/workflows/dependencies/install_spack
+        SPACK_VER=1.0.1 sudo -E .github/workflows/dependencies/install_spack
+        echo "SPACK VERSION: $(spack --version)"
     - name: Build
       env: {CC: clang, CXX: clang++}
       run: |
@@ -36,32 +37,31 @@ jobs:
         cat build/clang-tidy.log
         if [[ $(wc -m <build/clang-tidy.log) -gt 1 ]]; then exit 1; fi
 
-  clangsanitizer14_py38_ompi_h5_ad2:
+  clangsanitizer19_py38_ompi_h5_ad2:
     name: Clang ASAN UBSAN
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4
     - name: Spack Cache
       uses: actions/cache@v3
-      with: {path: /opt/spack, key: clang14_nopy_ompi_h5_ad2 }
+      with: {path: /opt/spack, key: clang19_nopy_ompi_h5_ad2 }
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install clang-14 libc++-dev libc++abi-dev python3 gfortran libopenmpi-dev
-        python3 -m pip install -U pip
-        python3 -m pip install -U numpy
-        sudo .github/workflows/dependencies/install_spack
+        sudo apt-get install clang-19 libc++-dev libc++abi-dev python3 gfortran libopenmpi-dev python3-numpy
+        SPACK_VER=1.0.1 sudo -E .github/workflows/dependencies/install_spack
+        echo "SPACK VERSION: $(spack --version)"
     - name: Build
-      env: {CC: mpicc, CXX: mpic++, OMPI_CC: clang-14, OMPI_CXX: clang++-14, CXXFLAGS: -Werror, OPENPMD_HDF5_CHUNKS: none, OPENPMD_TEST_NFILES_MAX: 100}
+      env: {CC: mpicc, CXX: mpic++, OMPI_CC: clang-19, OMPI_CXX: clang++-19, CXXFLAGS: -Werror, OPENPMD_HDF5_CHUNKS: none, OPENPMD_TEST_NFILES_MAX: 100}
       run: |
         sudo ln -s "$(which cmake)" /usr/bin/cmake
         eval $(spack env activate --sh .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad2/)
         spack install
         SOURCEPATH="$(pwd)"
         share/openPMD/download_samples.sh build
         export LDFLAGS="${LDFLAGS} -fsanitize=address,undefined -shared-libsan"
-        export CXXFLAGS="${CXXFLAGS} -fsanitize=address,undefined -shared-libsan"
+        export CXXFLAGS="${CXXFLAGS} -fsanitize=address,undefined -shared-libsan -DOMPI_SKIP_MPICXX"
         cmake -S . -B build               \
           -DopenPMD_USE_MPI=ON            \
           -DopenPMD_USE_PYTHON=ON         \
@@ -73,8 +73,7 @@ jobs:
         cmake --build build --parallel 2
         export ASAN_OPTIONS=detect_stack_use_after_return=1:detect_leaks=1:check_initialization_order=true:strict_init_order=true:detect_stack_use_after_scope=1:fast_unwind_on_malloc=0
         export LSAN_OPTIONS=suppressions="$SOURCEPATH/.github/ci/sanitizer/clang/Leak.supp"
-        export LD_PRELOAD=/usr/lib/clang/14/lib/linux/libclang_rt.asan-x86_64.so
-        ASAN_OPTIONS="abort_on_error=1:halt_on_error=1:fast_unwind_on_malloc=0:$ASAN_OPTIONS" LSAN_OPTIONS="verbosity=1:log_threads=1:$LSAN_OPTIONS" ctest --test-dir build -R MPI.8a_benchmark_write_parallel
-        ASAN_OPTIONS="abort_on_error=1:halt_on_error=1:fast_unwind_on_malloc=0:$ASAN_OPTIONS" LSAN_OPTIONS="verbosity=1:log_threads=1:$LSAN_OPTIONS" ctest --test-dir build -E 3b --output-on-failure
+        export LD_PRELOAD=/usr/lib/clang/19/lib/linux/libclang_rt.asan-x86_64.so
+        ctest --test-dir build -E 3b --output-on-failure
         export OPENPMD_HDF5_CHUNKS="auto"
         ctest --test-dir build -R 3b --output-on-failure
diff --git a/examples/8b_benchmark_read_parallel.cpp b/examples/8b_benchmark_read_parallel.cpp
@@ -135,7 +135,6 @@ class Timer
     ~Timer()
     {
         MPI_Barrier(MPI_COMM_WORLD);
-        std::string tt = "~" + m_Tag;
         // MemoryProfiler (m_Rank, tt.c_str());
         m_End = std::chrono::system_clock::now();
 
diff --git a/include/openPMD/IO/JSON/JSONIOHandlerImpl.hpp b/include/openPMD/IO/JSON/JSONIOHandlerImpl.hpp
@@ -525,9 +525,7 @@ class JSONIOHandlerImpl : public AbstractIOHandlerImpl
     };
 
     template <typename T>
-    struct JsonToCpp<
-        T,
-        typename std::enable_if<std::is_floating_point<T>::value>::type>
+    struct JsonToCpp<T, typename std::enable_if_t<std::is_floating_point_v<T>>>
     {
         T operator()(nlohmann::json const &);
     };
diff --git a/include/openPMD/backend/BaseRecord.hpp b/include/openPMD/backend/BaseRecord.hpp
@@ -317,7 +317,7 @@ class BaseRecord
     template <class InputIt>
     void insert(InputIt first, InputIt last);
     void insert(std::initializer_list<value_type> ilist);
-    void swap(BaseRecord &other);
+    void swap(BaseRecord &other) noexcept;
     bool contains(key_type const &key) const;
     template <class... Args>
     auto emplace(Args &&...args) -> std::pair<iterator, bool>;
diff --git a/src/IO/AbstractIOHandlerHelper.cpp b/src/IO/AbstractIOHandlerHelper.cpp
@@ -81,7 +81,7 @@ std::unique_ptr<AbstractIOHandler> createIOHandler<json::TracingJSON>(
         return constructIOHandler<ParallelHDF5IOHandler, openPMD_HAVE_HDF5>(
             "HDF5",
             std::move(initialize_from),
-            path,
+            std::move(path),
             access,
             comm,
             std::move(options));
@@ -139,7 +139,7 @@ std::unique_ptr<AbstractIOHandler> createIOHandler<json::TracingJSON>(
         return constructIOHandler<JSONIOHandler, openPMD_HAVE_JSON>(
             "JSON",
             std::move(initialize_from),
-            path,
+            std::move(path),
             access,
             comm,
             std::move(options),
@@ -149,7 +149,7 @@ std::unique_ptr<AbstractIOHandler> createIOHandler<json::TracingJSON>(
         return constructIOHandler<JSONIOHandler, openPMD_HAVE_JSON>(
             "JSON",
             std::move(initialize_from),
-            path,
+            std::move(path),
             access,
             comm,
             std::move(options),
@@ -181,7 +181,7 @@ std::unique_ptr<AbstractIOHandler> createIOHandler<json::TracingJSON>(
         return constructIOHandler<HDF5IOHandler, openPMD_HAVE_HDF5>(
             "HDF5",
             std::move(initialize_from),
-            path,
+            std::move(path),
             access,
             std::move(options));
     case Format::ADIOS2_BP:
diff --git a/src/IO/JSON/JSONIOHandlerImpl.cpp b/src/IO/JSON/JSONIOHandlerImpl.cpp
@@ -1203,13 +1203,13 @@ void JSONIOHandlerImpl::writeAttribute(
     switch (m_attributeMode.m_mode)
     {
     case AttributeMode::Long:
-        (*jsonVal)[filePosition->id]["attributes"][parameter.name] = {
+        (*jsonVal)[filePosition->id]["attributes"][name] = {
             {"datatype", jsonDatatypeToString(parameter.dtype)},
             {"value", value}};
         break;
     case AttributeMode::Short:
         // short form
-        (*jsonVal)[filePosition->id]["attributes"][parameter.name] = value;
+        (*jsonVal)[filePosition->id]["attributes"][name] = value;
         break;
     }
     writable->written = true;
@@ -1540,7 +1540,6 @@ void JSONIOHandlerImpl::readAttribute(
     auto const &jsonContents = obtainJsonContents(writable);
     auto const &jsonLoc = jsonContents["attributes"];
     setAndGetFilePosition(writable);
-    std::string error_msg("[JSON] No such attribute '");
     if (!hasKey(jsonLoc, name))
     {
         throw error::ReadError(
@@ -2365,9 +2364,9 @@ nlohmann::json JSONIOHandlerImpl::platformSpecifics()
         Datatype::CDOUBLE,
         Datatype::CLONG_DOUBLE,
         Datatype::BOOL};
-    for (auto it = std::begin(datatypes); it != std::end(datatypes); it++)
+    for (auto &datatype : datatypes)
     {
-        res[jsonDatatypeToString(*it)] = toBytes(*it);
+        res[jsonDatatypeToString(datatype)] = toBytes(datatype);
     }
     return res;
 }
@@ -2483,10 +2482,9 @@ std::array<T, n> JSONIOHandlerImpl::JsonToCpp<std::array<T, n>>::operator()(
 }
 
 template <typename T>
-T JSONIOHandlerImpl::JsonToCpp<
-    T,
-    typename std::enable_if<std::is_floating_point<T>::value>::type>::
-operator()(nlohmann::json const &j)
+T JSONIOHandlerImpl::
+    JsonToCpp<T, std::enable_if_t<std::is_floating_point_v<T>>>::operator()(
+        nlohmann::json const &j)
 {
     try
     {
diff --git a/src/RecordComponent.cpp b/src/RecordComponent.cpp
@@ -251,6 +251,12 @@ RecordComponent &RecordComponent::resetDataset(Dataset d)
     rc.m_isEmpty = false;
     if (written())
     {
+        if (!rc.m_dataset.has_value())
+        {
+            throw error::Internal(
+                "Internal control flow error: Written record component must "
+                "have defined datatype and extent.");
+        }
         rc.m_dataset.value().extend(std::move(d.extent));
     }
     else
diff --git a/src/Series.cpp b/src/Series.cpp
@@ -1116,6 +1116,12 @@ void Series::initSeries(
     series.m_filenamePrefix = input->filenamePrefix;
     series.m_filenamePostfix = input->filenamePostfix;
     series.m_filenamePadding = input->filenamePadding;
+    if (!input->filenameExtension)
+    {
+        throw error::Internal(
+            "Control flow error: filename extension has not been resolved.");
+    }
+    // NOLINTNEXTLINE(bugprone-unchecked-optional-access)
     series.m_filenameExtension = input->filenameExtension.value();
 
     if (series.m_iterationEncoding == IterationEncoding::fileBased &&
@@ -1728,7 +1734,8 @@ void Series::readFileBased(
         {
             if (forwardFirstError.has_value())
             {
-                auto &firstError = forwardFirstError.value();
+                // NOLINTNEXTLINE(bugprone-unchecked-optional-access)
+                auto &firstError = *forwardFirstError;
                 firstError.description.append(
                     "\n[Note] Not a single iteration can be successfully "
                     "parsed (see above errors). Returning the first observed "
@@ -3438,7 +3445,7 @@ auto Series::currentSnapshot() -> std::optional<std::vector<IterationIndex_t>>
         auto res = attribute.getOptional<vec_t>();
         if (res.has_value())
         {
-            return res.value();
+            return res;
         }
         else
         {
@@ -3461,6 +3468,7 @@ AbstractIOHandler *Series::runDeferredInitialization()
     auto &series = get();
     if (series.m_deferred_initialization.has_value())
     {
+        // NOLINTNEXTLINE(bugprone-unchecked-optional-access)
         auto functor = std::move(*m_series->m_deferred_initialization);
         m_series->m_deferred_initialization = std::nullopt;
         return functor(*this);
diff --git a/src/auxiliary/Memory.cpp b/src/auxiliary/Memory.cpp
@@ -40,7 +40,8 @@ allocatePtr(Datatype dtype, uint64_t numPoints)
     {
         using DT = Datatype;
     case DT::VEC_STRING:
-        data = new char *[numPoints];
+        // NOLINTNEXTLINE(bugprone-multi-level-implicit-pointer-conversion)
+        data = static_cast<void *>(new char *[numPoints]);
         del = [](void *p) { delete[] static_cast<char **>(p); };
         break;
     case DT::VEC_LONG_DOUBLE:
diff --git a/src/backend/Attribute.cpp b/src/backend/Attribute.cpp
@@ -73,6 +73,8 @@ auto Attribute::get_impl() const -> std::variant<U, std::runtime_error>
     switch (index)
     {
         OPENPMD_FOREACH_DATATYPE(OPENPMD_ENUMERATE_TYPES)
+    default:
+        return {std::runtime_error("Unreachable!")};
     }
 #undef OPENPMD_ENUMERATE_TYPES
 
diff --git a/src/backend/BaseRecord.cpp b/src/backend/BaseRecord.cpp
@@ -744,7 +744,7 @@ auto BaseRecord<T_elem>::insert(std::initializer_list<value_type> ilist) -> void
 }
 
 template <typename T_elem>
-auto BaseRecord<T_elem>::swap(BaseRecord &other) -> void
+auto BaseRecord<T_elem>::swap(BaseRecord &other) noexcept -> void
 {
     detail::verifyNonscalar(this);
     detail::verifyNonscalar(&other);
diff --git a/src/backend/Writable.cpp b/src/backend/Writable.cpp
diff --git a/src/binding/python/RecordComponent.cpp b/src/binding/python/RecordComponent.cpp
diff --git a/src/cli/convert-toml-json.cpp b/src/cli/convert-toml-json.cpp
diff --git a/src/snapshots/ContainerImpls.cpp b/src/snapshots/ContainerImpls.cpp
diff --git a/src/snapshots/StatefulIterator.cpp b/src/snapshots/StatefulIterator.cpp

Original file line number	Diff line number	Diff line change
`@@ -135,7 +135,6 @@ class Timer`
`135`	`135`	`~Timer()`
`136`	`136`	`{`
`137`	`137`	`MPI_Barrier(MPI_COMM_WORLD);`
`138`		`- std::string tt = "~" + m_Tag;`
`139`	`138`	`// MemoryProfiler (m_Rank, tt.c_str());`
`140`	`139`	`m_End = std::chrono::system_clock::now();`
`141`	`140`
Original file line number	Diff line number	Diff line change
`@@ -1203,13 +1203,13 @@ void JSONIOHandlerImpl::writeAttribute(`
`1203`	`1203`	`switch (m_attributeMode.m_mode)`
`1204`	`1204`	`{`
`1205`	`1205`	`case AttributeMode::Long:`
`1206`		`- (*jsonVal)[filePosition->id]["attributes"][parameter.name] = {`
	`1206`	`+ (*jsonVal)[filePosition->id]["attributes"][name] = {`
`1207`	`1207`	`{"datatype", jsonDatatypeToString(parameter.dtype)},`
`1208`	`1208`	`{"value", value}};`
`1209`	`1209`	`break;`
`1210`	`1210`	`case AttributeMode::Short:`
`1211`	`1211`	`// short form`
`1212`		`- (*jsonVal)[filePosition->id]["attributes"][parameter.name] = value;`
	`1212`	`+ (*jsonVal)[filePosition->id]["attributes"][name] = value;`
`1213`	`1213`	`break;`
`1214`	`1214`	`}`
`1215`	`1215`	`writable->written = true;`
`@@ -1540,7 +1540,6 @@ void JSONIOHandlerImpl::readAttribute(`
`1540`	`1540`	`auto const &jsonContents = obtainJsonContents(writable);`
`1541`	`1541`	`auto const &jsonLoc = jsonContents["attributes"];`
`1542`	`1542`	`setAndGetFilePosition(writable);`
`1543`		`- std::string error_msg("[JSON] No such attribute '");`
`1544`	`1543`	`if (!hasKey(jsonLoc, name))`
`1545`	`1544`	`{`
`1546`	`1545`	`throw error::ReadError(`
`@@ -2365,9 +2364,9 @@ nlohmann::json JSONIOHandlerImpl::platformSpecifics()`
`2365`	`2364`	`Datatype::CDOUBLE,`
`2366`	`2365`	`Datatype::CLONG_DOUBLE,`
`2367`	`2366`	`Datatype::BOOL};`
`2368`		`- for (auto it = std::begin(datatypes); it != std::end(datatypes); it++)`
	`2367`	`+ for (auto &datatype : datatypes)`
`2369`	`2368`	`{`
`2370`		`- res[jsonDatatypeToString(it)] = toBytes(it);`
	`2369`	`+ res[jsonDatatypeToString(datatype)] = toBytes(datatype);`
`2371`	`2370`	`}`
`2372`	`2371`	`return res;`
`2373`	`2372`	`}`
`@@ -2483,10 +2482,9 @@ std::array<T, n> JSONIOHandlerImpl::JsonToCpp<std::array<T, n>>::operator()(`
`2483`	`2482`	`}`
`2484`	`2483`
`2485`	`2484`	`template <typename T>`
`2486`		`-T JSONIOHandlerImpl::JsonToCpp<`
`2487`		`- T,`
`2488`		`- typename std::enable_if<std::is_floating_point<T>::value>::type>::`
`2489`		`-operator()(nlohmann::json const &j)`
	`2485`	`+T JSONIOHandlerImpl::`
	`2486`	`+ JsonToCpp<T, std::enable_if_t<std::is_floating_point_v<T>>>::operator()(`
	`2487`	`+ nlohmann::json const &j)`
`2490`	`2488`	`{`
`2491`	`2489`	`try`
`2492`	`2490`	`{`
Original file line number	Diff line number	Diff line change
`@@ -251,6 +251,12 @@ RecordComponent &RecordComponent::resetDataset(Dataset d)`
`251`	`251`	`rc.m_isEmpty = false;`
`252`	`252`	`if (written())`
`253`	`253`	`{`
	`254`	`+ if (!rc.m_dataset.has_value())`
	`255`	`+ {`
	`256`	`+ throw error::Internal(`
	`257`	`+ "Internal control flow error: Written record component must "`
	`258`	`+ "have defined datatype and extent.");`
	`259`	`+ }`
`254`	`260`	`rc.m_dataset.value().extend(std::move(d.extent));`
`255`	`261`	`}`
`256`	`262`	`else`