git subrepo pull packages/HighFive

subrepo:
  subdir:   "packages/HighFive"
  merged:   "dfc06537f"
upstream:
  origin:   "git@github.com:BlueBrain/HighFive.git"
  branch:   "master"
  commit:   "dfc06537f"
git-subrepo:
  version:  "0.4.9"
  origin:   "git@github.com:ingydotnet/git-subrepo.git"
  commit:   "30db3b8"

packages/HighFive/.github/run_examples.sh

@@ -16,5 +16,10 @@ fi
 for f in "${examples_dir}"/*_bin
 do
   echo "-- ${f}"
+  if [[ "${f}" == *"parallel_"* ]]
+  then
+    mpiexec -np 2 "${f}"
+  else
     "${f}"
+  fi
 done

packages/HighFive/.github/workflows/ci.yml

@@ -58,6 +58,9 @@ jobs:
           - config:
               os: ubuntu-22.04
               flags: '-DHIGHFIVE_TEST_BOOST=Off -DCMAKE_CXX_STANDARD=20 -DHIGHFIVE_HAS_CONCEPTS=On'
+          - config:
+              os: ubuntu-24.04
+              flags: '-DHIGHFIVE_TEST_BOOST=Off -DCMAKE_CXX_STANDARD=20 -DHIGHFIVE_HAS_CONCEPTS=On'
 
     steps:
     - uses: actions/checkout@v3
@@ -89,6 +92,9 @@ jobs:
       run: |
         ! ctest --verbose -C $BUILD_TYPE | grep HDF5-DIAG
 
+    - name: Examples
+      working-directory: ${{github.workspace}}/build/src/examples
+      run: $GITHUB_WORKSPACE/.github/run_examples.sh
 
   # Job testing several versions of hdf5
   # ===================================================
@@ -96,7 +102,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        hdf5_version : [ hdf5-1_8_23, hdf5-1_10_11, hdf5-1_12_3, hdf5_1.14.4.1 ]
+        hdf5_version : [ hdf5-1_8_23, hdf5-1_10_11, hdf5-1_12_3, hdf5_1.14.5 ]
 
     steps:
     - uses: actions/checkout@v3
@@ -133,7 +139,6 @@ jobs:
       run: |
         ! ctest --verbose -C $BUILD_TYPE | grep HDF5-DIAG
 
-
     - name: Examples
       working-directory: ${{github.workspace}}/build/src/examples
       run: $GITHUB_WORKSPACE/.github/run_examples.sh
@@ -184,13 +189,13 @@ jobs:
   # Job running unit-test with sanitizers
   # =====================================
   Linux_Sanitizers:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
         env: [
-          {CC: clang-12, CXX: clang++-12, HIGHFIVE_SANITIZER: address},
-          {CC: clang-12, CXX: clang++-12, HIGHFIVE_SANITIZER: undefined},
-          {CC: gcc-10, CXX: g++-10, HIGHFIVE_GLIBCXX_ASSERTIONS: On},
+          {CC: clang, CXX: clang++, HIGHFIVE_SANITIZER: address},
+          {CC: clang, CXX: clang++, HIGHFIVE_SANITIZER: undefined},
+          {CC: gcc, CXX: g++, HIGHFIVE_GLIBCXX_ASSERTIONS: On},
         ]
 
     steps:
@@ -201,7 +206,7 @@ jobs:
     - name: "Install libraries"
       run: |
         sudo apt-get -qq update
-        sudo apt-get -qq install libboost-all-dev libeigen3-dev libhdf5-dev libsz2 ninja-build
+        sudo apt-get -qq install boost1.83 libeigen3-dev libhdf5-dev libsz2 ninja-build
 
     - name: Build
       env: ${{matrix.env}}
@@ -209,6 +214,7 @@ jobs:
         CMAKE_OPTIONS=(
           -GNinja
           -DHIGHFIVE_TEST_BOOST:BOOL=ON
+          -DHIGHFIVE_TEST_BOOST_SPAN:BOOL=ON
           -DHIGHFIVE_TEST_EIGEN:BOOL=ON
           -DHIGHFIVE_BUILD_DOCS:BOOL=FALSE
           -DHIGHFIVE_GLIBCXX_ASSERTIONS=${HIGHFIVE_GLIBCXX_ASSERTIONS:-OFF}
@@ -297,9 +303,6 @@ jobs:
         cxxstd: ["14", "17", "20"]
 
         include:
-          - os: "macOS-12"
-            cxxstd: "14"
-
           - os: "macOS-13"
             cxxstd: "20"
 

packages/HighFive/.github/workflows/clang_format.yml

@@ -20,18 +20,4 @@ jobs:
 
     - name: Run clang-format
       run: |
-          clang-format --version
-          for i in $(git ls-files | grep ".[ch]pp$");
-          do
-            clang-format -i "$i" > /dev/null 2>&1;
-          done
-          modified_files=$(git diff --name-only)
-          if [ -n "$modified_files" ];
-          then
-              echo "Some files are not well formatted:"
-              echo $modified_files
-              echo ""
-              echo "The diff is:"
-              git diff
-              exit 1
-          fi
+        bash bin/format.sh

packages/HighFive/.gitrepo

@@ -6,7 +6,7 @@
 [subrepo]
 	remote = git@github.com:BlueBrain/HighFive.git
 	branch = master
-	commit = 20fbd4c4d328bc18a342eeef5ffd29f17de084e0
-	parent = 35908346b20b524d4d2d9f8f6220800c27595413
+	commit = dfc06537fdb20f5e572c20bc6febd22dd5d08246
+	parent = fa321c14d4206f8183fc9029ee9bd0d216ce700b
 	method = merge
-	cmdver = 0.4.6
+	cmdver = 0.4.9

packages/HighFive/CHANGELOG.md

 # Changes
+## Version 3.0.0-beta2 - 2024-12-04
+### New Features
+    - Support `boost::span`. (#1025)
+
+### Bug Fix
+    - Fix for not-quite null-terminated, fixed-length strings. (#1056)
+    - Guard target creation in `*Config.cmake`. (#1053)
+
+## Version 3.0.0-beta1 - 2024-07-16
+This version is a major one and is breaking some usage compare to v2.
+Read the migration guide from the documentation: https://bluebrain.github.io/HighFive/md__2home_2runner_2work_2_high_five_2_high_five_2doc_2migration__guide.html
+
+The minimum version for C++ has been moved to `C++14`.
+
+### Removed
+    - Removed `read(T*, ...)`, use explicit `read_raw(T*, ...)` for `Slice` or `Attribute`. (#928)
+    - Removed `FixedLenStringArray`, use any container with strings instead. (#932)
+    - Removed `FileDriver` and `MPIOFileDriver`, use file access properties instead. (#949)
+    - Removed default constructor for `Group` and `DataSet`. (#947, #948)
+    - Broadcasting have been removed. Use `squeeze` and `reshape` feature instead. (#992)
+    - `ObjectCreateProps` and `ObjectAccessProps` those don't map well to HighFive and are unused. (#1002)
+
+### New Features
+    - Added support for `std::span`. (#987)
+    - Added `squeezeMemSpace` and `reshapeMemSpace` for `Attribute` and `Slice` to reshape the memory space. (#991)
+    - Added `ProductSet` to select a Cartesian products of (generalized) slices. (#842)
+
+### Improvements
+    - Optimized chained hyperslab selection. (#1031)
+    - Type `T[N]` or `T[N][M]` will work better. (#929)
+    - `DataspaceType` is now an enum class for `dataspace_scalar` or `dataspace_null`. (#900)
+    - `File::AccessMode` is now an enum class. (#1020)
+
 ## Version 2.9.0 - 2024-01-25
 ### New Features
     - Add named ctors for scalar and null dataspaces. (#899)

packages/HighFive/CMakeLists.txt

@@ -2,6 +2,12 @@ cmake_minimum_required(VERSION 3.13)
 cmake_policy(VERSION 3.13)
 
 project(HighFive VERSION 3.0.0)
+set(HIGHFIVE_VERSION_PRERELEASE 2)
+
+message(WARNING "=================================================================\n"
+                "HighFive development moved to:\n"
+                "  github.com/highfive-devs/highfive\n"
+                "=================================================================")
 
 # Configure HighFive
 # ------------------
@@ -58,12 +64,13 @@ option(HIGHFIVE_UNIT_TESTS "Compile unit-tests" ${HIGHFIVE_EXTRAS_DEFAULT})
 option(HIGHFIVE_EXAMPLES "Compile examples" ${HIGHFIVE_EXTRAS_DEFAULT})
 option(HIGHFIVE_BUILD_DOCS "Build documentation" ${HIGHFIVE_EXTRAS_DEFAULT})
 
-option(HIGHFIVE_TEST_SPAN "Enable std::span testing, requires C++20" ${HIGHFIVE_TEST_SPAN_DEFAULT})
-option(HIGHFIVE_TEST_BOOST "Enable Boost testing" OFF)
-option(HIGHFIVE_TEST_EIGEN "Enable Eigen testing" OFF)
-option(HIGHFIVE_TEST_OPENCV "Enable OpenCV testing" OFF)
-option(HIGHFIVE_TEST_XTENSOR "Enable xtensor testing" OFF)
-option(HIGHFIVE_TEST_HALF_FLOAT "Enable half-precision floats" OFF)
+option(HIGHFIVE_TEST_SPAN "Enable testing std::span, requires C++20" ${HIGHFIVE_TEST_SPAN_DEFAULT})
+option(HIGHFIVE_TEST_BOOST "Enable testing Boost features" OFF)
+option(HIGHFIVE_TEST_BOOST_SPAN "Additionally, enable testing `boost::span`" OFF)
+option(HIGHFIVE_TEST_EIGEN "Enable testing Eigen" OFF)
+option(HIGHFIVE_TEST_OPENCV "Enable testing OpenCV" OFF)
+option(HIGHFIVE_TEST_XTENSOR "Enable testing xtensor" OFF)
+option(HIGHFIVE_TEST_HALF_FLOAT "Enable testing half-precision floats" OFF)
 
 # TODO remove entirely.
 option(HIGHFIVE_HAS_CONCEPTS "Print readable compiler errors w/ C++20 concepts" OFF)
@@ -155,6 +162,7 @@ install(FILES
 
 if(HIGHFIVE_EXAMPLES OR HIGHFIVE_UNIT_TESTS)
   include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveWarnings.cmake)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveFlags.cmake)
   include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveOptionalDependencies.cmake)
 endif()
 

packages/HighFive/README.md

-*Note:* In preparation of `v3` of HighFive, we've started merging breaking
-changes into the main branch. More information and opportunity to comment can
-be found at:
-https://github.com/BlueBrain/HighFive/issues/864
+> [!WARNING]
+> The Blue Brain Project concluded in December 2024, so the HighFive development is ceased under the BlueBrain GitHub organization.
+>
+> The development of HighFive will continue at:
+>   https://github.com/highfive-devs/highfive
 
 # HighFive - HDF5 header-only C++ Library
 
-[![Doxygen -> gh-pages](https://github.com/BlueBrain/HighFive/workflows/gh-pages/badge.svg?branch=master)](https://BlueBrain.github.io/HighFive/actions/workflows/gh-pages.yml?query=branch%3Amaster)
-[![codecov](https://codecov.io/gh/BlueBrain/HighFive/branch/master/graph/badge.svg?token=UBKxHEn7RS)](https://codecov.io/gh/BlueBrain/HighFive)
-[![HighFive_Integration_tests](https://github.com/BlueBrain/HighFive-testing/actions/workflows/integration.yml/badge.svg)](https://github.com/BlueBrain/HighFive-testing/actions/workflows/integration.yml)
-[![Zenodo](https://zenodo.org/badge/47755262.svg)](https://zenodo.org/doi/10.5281/zenodo.10679422)
-
 Documentation: https://bluebrain.github.io/HighFive/
 
 ## Brief
@@ -23,15 +19,16 @@ It integrates nicely with other CMake projects by defining (and exporting) a Hig
 
 ### Design
 - Simple C++-ish minimalist interface
-- No other dependency than libhdf5
-- Zero overhead
-- Support C++14
+- Only hard dependency is libhdf5
+- Zero/low overhead, when possible
+- RAII for opening/closing files, groups, datasets, etc.
+- Written in C++14
 
 ### Feature support
 - create/read/write files, datasets, attributes, groups, dataspaces.
 - automatic memory management / ref counting
 - automatic conversion of `std::vector` and nested `std::vector` from/to any dataset with basic types
-- automatic conversion of `std::string` to/from variable length string dataset
+- automatic conversion of `std::string` to/from variable- or fixed-length string dataset
 - selection() / slice support
 - parallel Read/Write operations from several nodes with Parallel HDF5
 - Advanced types: Compound, Enum, Arrays of Fixed-length strings, References
@@ -41,212 +38,45 @@ It integrates nicely with other CMake projects by defining (and exporting) a Hig
 
 ### Dependencies
 - HDF5 or pHDF5, including headers
-- boost >= 1.41 (recommended)
+- boost (optional)
 - eigen3 (optional)
 - xtensor (optional)
 - half (optional)
 
-### Known flaws
-- HighFive is not thread-safe. At best it has the same limitations as the HDF5 library. However, HighFive objects modify their members without protecting these writes. Users have reported that HighFive is not thread-safe even when using the threadsafe HDF5 library, e.g., https://github.com/BlueBrain/HighFive/discussions/675.
-- Eigen support in core HighFive was broken until v3.0. See https://github.com/BlueBrain/HighFive/issues/532. H5Easy was not
-  affected.
-- The support of fixed length strings isn't ideal.
+The releases for versions 2.x.y and two prereleases of v3 can be found at:
+* https://github.com/BlueBrain/HighFive/releases
+* https://zenodo.org/doi/10.5281/zenodo.10679422
 
+The state of HighFive immediately before preparing it for archival is:
+* https://github.com/BlueBrain/HighFive/tree/v3.0.0-beta2
 
-## Examples
+All future development and new releases can be found at:
+* https://github.com/highfive-devs/highfive
 
-#### Write a std::vector<int> to 1D HDF5 dataset and read it back
+## Example
 
 ```c++
-#include <highfive/highfive.hpp>
-
 using namespace HighFive;
 
-std::string filename = "/tmp/new_file.h5";
+File file("foo.h5", File::Truncate);
 
 {
-    // We create an empty HDF55 file, by truncating an existing
-    // file if required:
-    File file(filename, File::Truncate);
-
     std::vector<int> data(50, 1);
     file.createDataSet("grp/data", data);
 }
 
 {
-    // We open the file as read-only:
-    File file(filename, File::ReadOnly);
     auto dataset = file.getDataSet("grp/data");
 
-    // Read back, with allocating:
+    // Read back, automatically allocating:
     auto data = dataset.read<std::vector<int>>();
 
-    // Because `data` has the correct size, this will
-    // not cause `data` to be reallocated:
+    // Alternatively, if `data` has the correct
+    // size, without reallocation:
     dataset.read(data);
 }
 ```
 
-**Note:** As of 2.8.0, one can use `highfive/highfive.hpp` to include
-everything HighFive. Prior to 2.8.0 one would include `highfive/H5File.hpp`.
-
-**Note:** For advanced usecases the dataset can be created without immediately
-writing to it. This is common in MPI-IO related patterns, or when growing a
-dataset over the course of a simulation.
-
-#### Write a 2 dimensional C double float array to a 2D HDF5 dataset
-
-See [create_dataset_double.cpp](https://github.com/BlueBrain/HighFive/blob/master/src/examples/create_dataset_double.cpp)
-
-#### Write and read a matrix of double float (boost::ublas) to a 2D HDF5 dataset
-
-See [boost_ublas_double.cpp](https://github.com/BlueBrain/HighFive/blob/master/src/examples/boost_ublas_double.cpp)
-
-#### Write and read a subset of a 2D double dataset
-
-See [select_partial_dataset_cpp11.cpp](https://github.com/BlueBrain/HighFive/blob/master/src/examples/select_partial_dataset_cpp11.cpp)
-
-#### Create, write and list HDF5 attributes
-
-See [create_attribute_string_integer.cpp](https://github.com/BlueBrain/HighFive/blob/master/src/examples/create_attribute_string_integer.cpp)
-
-#### And others
-
-See [src/examples/](https://github.com/BlueBrain/HighFive/blob/master/src/examples/) subdirectory for more info.
-
-
-### H5Easy
-
-For several 'standard' use cases the [highfive/H5Easy.hpp](include/highfive/H5Easy.hpp) interface is available. It allows:
-
-* Reading/writing in a single line of:
-
-    - scalars (to/from an extendible DataSet),
-    - strings,
-    - vectors (of standard types),
-    - [Eigen::Matrix](http://eigen.tuxfamily.org) (optional),
-    - [xt::xarray](https://github.com/QuantStack/xtensor) and [xt::xtensor](https://github.com/QuantStack/xtensor)
-      (optional).
-    - [cv::Mat_](https://docs.opencv.org/master/df/dfc/classcv_1_1Mat__.html)
-      (optional).
-
-* Getting in a single line:
-
-    - the size of a DataSet,
-    - the shape of a DataSet.
-
-#### Example
-
-```cpp
-#include <highfive/H5Easy.hpp>
-
-int main() {
-    H5Easy::File file("example.h5", H5Easy::File::Overwrite);
-
-    int A = ...;
-    H5Easy::dump(file, "/path/to/A", A);
-
-    A = H5Easy::load<int>(file, "/path/to/A");
-}
-```
-
-whereby the `int` type of this example can be replaced by any of the above
-types. See [easy_load_dump.cpp](src/examples/easy_load_dump.cpp) for more
-details.
-
-**Note:** Classes such as `H5Easy::File` are just short for the regular
-`HighFive` classes (in this case `HighFive::File`). They can thus be used
-interchangeably.
-
-
-## CMake integration
-There's two common paths of integrating HighFive into a CMake based project.
-The first is to "vendor" HighFive, the second is to install HighFive as a
-normal C++ library. Since HighFive makes choices about how to integrate HDF5,
-sometimes following the third Bailout Approach is needed.
-
-Regular HDF5 CMake variables can be used. Interesting variables include:
-
-* `HDF5_USE_STATIC_LIBRARIES` to link statically against the HDF5 library.
-* `HDF5_PREFER_PARALLEL` to prefer pHDF5.
-* `HDF5_IS_PARALLEL` to check if HDF5 is parallel.
-
-Please consult `tests/cmake_integration` for examples of how to write libraries
-or applications using HighFive.
-
-### Vendoring HighFive
-
-In this approach the HighFive sources are included in a subdirectory of the
-project (typically as a git submodule), for example in `third_party/HighFive`.
-
-The projects `CMakeLists.txt` add the following lines
-```cmake
-add_subdirectory(third_party/HighFive)
-target_link_libraries(foo HighFive)
-```
-
-**Note:** `add_subdirectory(third_party/HighFive)` will search and "link" HDF5
-but wont search or link any optional dependencies such as Boost.
-
-### Regular Installation of HighFive
-
-Alternatively, HighFive can be install and "found" like regular software.
-
-The project's `CMakeLists.txt` should add the following:
-```cmake
-find_package(HighFive REQUIRED)
-target_link_libraries(foo HighFive)
-```
-
-**Note:** `find_package(HighFive)` will search for HDF5. "Linking" to
-`HighFive` includes linking with HDF5. The two commands will not search for or
-"link" to optional dependencies such as Boost.
-
-### Bailout Approach
-
-To prevent HighFive from searching or "linking" to HDF5 the project's
-`CMakeLists.txt` should contain the following:
-
-```cmake
-# Prevent HighFive CMake code from searching for HDF5:
-set(HIGHFIVE_FIND_HDF5 Off)
-
-# Then "find" HighFive as usual:
-find_package(HighFive REQUIRED)
-# alternatively, when vendoring:
-# add_subdirectory(third_party/HighFive)
-
-# Finally, use the target `HighFive::Include` which
-# doesn't add a dependency on HDF5.
-target_link_libraries(foo HighFive::Include)
-
-# Proceed to find and link HDF5 as required.
-```
-
-### Optional Dependencies
-
-HighFive does not attempt to find or "link" to any optional dependencies, such
-as Boost, Eigen, etc. Any project using HighFive with any of the optional
-dependencies must include the respective header:
-```
-#include <highfive/boost.hpp>
-#include <highfive/eigen.hpp>
-```
-and add the required CMake code to find and link against the dependencies. For
-Boost the required lines might be
-```
-find_package(Boost REQUIRED)
-target_link_libraries(foo PUBLIC Boost::headers)
-```
-
-# Questions?
-
-Do you have questions on how to use HighFive? Would you like to share an interesting example or
-discuss HighFive features? Head over to the [Discussions](https://github.com/BlueBrain/HighFive/discussions)
-forum and join the community.
-
-For bugs and issues please use [Issues](https://github.com/BlueBrain/HighFive/issues).
-
 # Funding & Acknowledgment
 
 The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
@@ -255,7 +85,7 @@ HighFive releases are uploaded to Zenodo. If you wish to cite HighFive in a
 scientific publication you can use the DOIs for the
 [Zenodo records](https://zenodo.org/doi/10.5281/zenodo.10679422).
 
-Copyright © 2015-2022 Blue Brain Project/EPFL
+Copyright © 2015-2024 Blue Brain Project/EPFL
 
 
 ### License

packages/HighFive/bin/format.sh

+#!/usr/bin/env bash
+set -euo pipefail
+
+clang_format_version="19.1.3"
+
+script_dir="$(dirname "${BASH_SOURCE[0]}")"
+venv_dir="$script_dir/../.clang-format-venv"
+
+if [ ! -d "$venv_dir" ]; then
+    python3 -m venv "$venv_dir"
+    source "$venv_dir/bin/activate"
+    pip install clang-format=="$clang_format_version"
+    deactivate
+fi
+
+source "$venv_dir/bin/activate"
+
+# Check if the installed version matches the expected version
+installed_version="$(pip show clang-format | grep Version | cut -d ' ' -f 2)"
+
+if [ "$installed_version" != "$clang_format_version" ]; then
+    echo "Error: clang-format version mismatch. Expected $clang_format_version, got $installed_version"
+    echo "Please remove the virtual environment and run the script again:"
+    echo "    rm -r \"$venv_dir\" && \"$0\""
+    exit 1
+fi
+
+clang-format --version
+for i in $(git ls-files | grep ".[ch]pp$"); do
+    clang-format -i "$i" > /dev/null 2>&1
+done
+
+modified_files=$(git diff --name-only)
+if [ -n "$modified_files" ]; then
+    echo "Some files are not well formatted:"
+    echo "$modified_files"
+    echo ""
+    echo "The diff is:"
+    git --no-pager diff
+    echo ""
+    echo "To correct the formatting run:"
+    echo "  $0"
+    exit 1
+fi

packages/HighFive/cmake/HighFiveConfig.cmake

@@ -8,6 +8,7 @@ if(HIGHFIVE_FIND_HDF5)
   find_dependency(HDF5)
 endif()
 
+if(NOT TARGET HighFive)
   include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargets.cmake")
 
   if(HDF5_IS_PARALLEL)
@@ -17,3 +18,6 @@ endif()
 
   add_library(HighFive ALIAS HighFive::HighFive)
   add_library(HighFiveInclude ALIAS HighFive::Include)
+endif()
+
+

packages/HighFive/cmake/HighFiveFlags.cmake

+if(TARGET HighFiveFlags)
+    # Allow multiple `include(HighFiveWarnings)`, which would
+    # attempt to redefine `HighFiveWarnings` and fail without
+    # this check.
+    return()
+endif()
+
+add_library(HighFiveFlags INTERFACE)
+
+if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+    if(HIGHFIVE_MAX_ERRORS)
+        target_compile_options(HighFiveFlags
+            INTERFACE
+            -fmax-errors=${HIGHFIVE_MAX_ERRORS}
+        )
+    endif()
+endif()
+
+if(HIGHFIVE_GLIBCXX_ASSERTIONS)
+    target_compile_definitions(HighFiveFlags INTERFACE -D_GLIBCXX_ASSERTIONS)
+endif()
+
+if(HIGHFIVE_HAS_FRIEND_DECLARATIONS)
+    target_compile_definitions(HighFiveFlags INTERFACE -DHIGHFIVE_HAS_FRIEND_DECLARATIONS=1)
+endif()
+
+if(HIGHFIVE_SANITIZER)
+    target_compile_options(HighFiveFlags INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+    target_link_options(HighFiveFlags INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+endif()

packages/HighFive/cmake/HighFiveOptionalDependencies.cmake

@@ -7,6 +7,9 @@ if(NOT TARGET HighFiveBoostDependency)
     # -DBOOST_ALL_NO_LIB (does something on MSVC).
     target_compile_definitions(HighFiveBoostDependency INTERFACE HIGHFIVE_TEST_BOOST=1)
   endif()
+  if(HIGHFIVE_TEST_BOOST_SPAN)
+    target_compile_definitions(HighFiveBoostDependency INTERFACE HIGHFIVE_TEST_BOOST_SPAN=1)
+  endif()
 endif()
 
 if(NOT TARGET HighFiveEigenDependency)

packages/HighFive/cmake/HighFiveWarnings.cmake

@@ -6,7 +6,6 @@ if(TARGET HighFiveWarnings)
 endif()
 
 add_library(HighFiveWarnings INTERFACE)
-add_library(HighFiveFlags INTERFACE)
 
 if(CMAKE_CXX_COMPILER_ID MATCHES "Clang"
    OR CMAKE_CXX_COMPILER_ID MATCHES "GNU"
@@ -48,11 +47,3 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU")
     endif()
 endif()
 
-if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
-    if(HIGHFIVE_MAX_ERRORS)
-        target_compile_options(HighFiveFlags
-            INTERFACE
-            -fmax-errors=${HIGHFIVE_MAX_ERRORS}
-        )
-    endif()
-endif()

catch2 @ fa43b774

-Subproject commit 4e8d92bf02f7d1c8006a0e7a5ecabd8e62d98502
+Subproject commit fa43b77429ba76c462b1898d6cd2f2d7a9416b14

packages/HighFive/doc/developer_guide.md

@@ -41,22 +41,16 @@ tests.
 ### Code formatting
 The project is formatted using clang-format version 12.0.1 and CI will complain
 if a commit isn't formatted accordingly. The `.clang-format` is at the root of
-the git repository. Conveniently, `clang-format` is available via `pip`:
+the git repository. Conveniently, `clang-format` is available via `pip`.
 
+Formatting the entire code base can be done with:
 ```bash
-python -m venv venv
-source venv/bin/activate
-
-pip install clang-format==12.0.1
+    bin/format.sh
 ```
+which will install the required version of clang-format in a venv called
+`.clang-format-venv`.
 
-The changed lines can be formatted with `git-clang-format`, e.g. to format all lines changed compared to master:
-
-```bash
-git-clang-format master
-```
-(add `-f` to allow formatting unstaged changes if you trust it to not destroy
-your changes.)
+To format only the changed files `git-clang-format` can be used.
 
 ## Releasing HighFive
 Before releasing a new version perform the following:

packages/HighFive/doc/doxygen-awesome-css/doxygen-awesome.css

@@ -805,6 +805,8 @@ html.dark-mode iframe#MSearchResults {
 #nav-tree .item {
     height: var(--tree-item-height);
     line-height: var(--tree-item-height);
+    overflow: hidden;
+    text-overflow: ellipsis;
 }
 
 #nav-tree .item > a:focus {
@@ -823,6 +825,8 @@ html.dark-mode iframe#MSearchResults {
     background-image: none;
     background-color: transparent;
     position: relative;
+    color: var(--primary-color) !important;
+    font-weight: 500;
 }
 
 #nav-tree .selected::after {
@@ -1749,7 +1753,7 @@ table.fieldtable th {
     color: var(--tablehead-foreground);
 }
 
-table.fieldtable td.fieldtype, .fieldtable td.fieldname, .fieldtable td.fielddoc, .fieldtable th {
+table.fieldtable td.fieldtype, .fieldtable td.fieldname, .fieldtable td.fieldinit, .fieldtable td.fielddoc, .fieldtable th {
     border-bottom: 1px solid var(--separator-color);
     border-right: 1px solid var(--separator-color);
 }

packages/HighFive/doc/migration_guide.md

@@ -133,7 +133,7 @@ target_link_libraries(add PUBLIC boost::boost)
 # For HighFive there's two options for adding `-I ${HIGHFIVE_DIR}` and the
 # flags for HDF5.
 #
-# Option 1: HighFive is install (systemwide) as a regular library:
+# Option 1: HighFive is installed as a (system-wide) regular library:
 find_package(HighFive)
 target_link_libraries(app PUBLIC HighFive::HighFive)
 
@@ -169,7 +169,7 @@ of a "file driver". Removing the concept hopefully makes it easier to add a
 better abstraction for the handling of the property lists, when we discover
 such an abstraction.
 
-## Removal of broadcasting
+## Removal of broadcasting.
 HighFive v2 had a feature that a dataset (or attribute) of shape `[n, 1]` could
 be read into a one-dimensional array automatically.
 
@@ -233,6 +233,32 @@ multi-dimensional array isn't supported, because if we want to support array
 with runtime-defined rank, we can't deduce the correct shape, e.g. `[1]` vs.
 `[1, 1, 1]`, when read into an array.
 
-# Removal of `Object*Props`.
-To out knowledge these could not be used meaningfully. Please create an issue
+## Change to `File::Truncate` and friends.
+In `v2`, `File::{ReadOnly,Truncate,...}` was an anonymous member enum of
+`File`. Effectively it's type was the same as an `int`.
+
+To improve type-safety, we converted it into an `enum class` called
+`File::AccessMode`. In order to reduce the migration effort, we retained the
+ability to write: `File::ReadOnly`.
+
+Functions that accept a file access mode should be modernized as follows:
+```
+// old
+HighFive::File open(std::string name, int mode) {
+  return HighFive::File(name, mode);
+}
+
+// new
+HighFive::File open(std::string name, HighFive::File::AccessMode mode) {
+  return HighFive::File(name, mode);
+}
+```
+
+Note: There's a caveat, the short-hand notation `File::ReadOnly` doesn't have
+an address. Meaning one can't take it's address or const-references of it
+(results in a linker error about missing symbol `File::ReadOnly`). Use
+`File::AccessMode::ReadOnly` instead.
+
+## Removal of `Object*Props`.
+To our knowledge these could not be used meaningfully. Please create an issue
 if you relied on these.

packages/HighFive/include/highfive/H5DataSpace.hpp

@@ -19,6 +19,14 @@
 
 namespace HighFive {
 
+namespace detail {
+/// @brief Create a HighFive::DataSpace from an HID, without incrementing the id.
+///
+/// @note This is internal API and subject to change.
+/// @internal
+DataSpace make_data_space(hid_t hid);
+}  // namespace detail
+
 /// \brief Class representing the space (dimensions) of a DataSet
 ///
 /// \code{.cpp}
@@ -254,9 +262,18 @@ class DataSpace: public Object {
   protected:
     DataSpace() = default;
 
+    static DataSpace fromId(hid_t hid) {
+        DataSpace space;
+        space._hid = hid;
+
+        return space;
+    }
+
     friend class Attribute;
     friend class File;
     friend class DataSet;
+
+    friend DataSpace detail::make_data_space(hid_t hid);
 };
 
 }  // namespace HighFive

packages/HighFive/include/highfive/H5DataType.hpp

@@ -153,16 +153,18 @@ class FixedLengthStringType: public StringType {
     /// UTF8. In particular, a string with `n` UFT8 characters in general
     /// requires `4*n` bytes.
     ///
-    /// The string padding is subtle, essentially it's just a hint. A
-    /// null-terminated string is guaranteed to have one `'\0'` which marks the
-    /// semantic end of the string. The length of the buffer must be at least
-    /// `size` bytes regardless. HDF5 will read or write `size` bytes,
-    /// irrespective of the when the `\0` occurs.
-    ///
-    /// Note that when writing passing `StringPadding::NullTerminated` is a
+    /// The string padding is subtle, essentially it's just a hint. While
+    /// commonly, a null-terminated string is guaranteed to have one `'\0'`
+    /// which marks the semantic end of the string, this is not enforced by
+    /// HDF5. In fact, there are HDF5 files that contain strings that claim to
+    /// be null-terminated but aren't.  The length of the buffer must be at
+    /// least `size` bytes regardless of the padding. HDF5 will read or write
+    /// `size` bytes, irrespective of when (if at all) the `\0` occurs.
+    ///
+    /// Note that when writing, passing `StringPadding::NullTerminated` is a
     /// guarantee to the reader that it contains a `\0`. Therefore, make sure
-    /// that the string really is nullterminated. Otherwise prefer a
-    /// null-padded string which only means states that the buffer is filled up
+    /// that the string really is null-terminated. Otherwise prefer a
+    /// null-padded string. This mearly states that the buffer is filled up
     /// with 0 or more `\0`.
     FixedLengthStringType(size_t size,
                           StringPadding padding,

packages/HighFive/include/highfive/H5File.hpp

@@ -9,6 +9,7 @@
 #pragma once
 
 #include <string>
+#include <type_traits>
 
 #include "H5Object.hpp"
 #include "H5PropertyList.hpp"
@@ -17,6 +18,7 @@
 
 namespace HighFive {
 
+
 ///
 /// \brief File class
 ///
@@ -24,25 +26,35 @@ class File: public Object, public NodeTraits<File>, public AnnotateTraits<File>
   public:
     const static ObjectType type = ObjectType::File;
 
-    enum : unsigned {
+    enum class AccessMode {
+        None = 0x00u,
         /// Open flag: Read only access
-        ReadOnly = 0x00u,
+        ReadOnly = 0x01u,
         /// Open flag: Read Write access
-        ReadWrite = 0x01u,
+        ReadWrite = 0x02u,
         /// Open flag: Truncate a file if already existing
-        Truncate = 0x02u,
+        Truncate = 0x04u,
         /// Open flag: Open will fail if file already exist
-        Excl = 0x04u,
+        Excl = 0x08u,
         /// Open flag: Open in debug mode
-        Debug = 0x08u,
+        Debug = 0x10u,
         /// Open flag: Create non existing file
-        Create = 0x10u,
+        Create = 0x20u,
         /// Derived open flag: common write mode (=ReadWrite|Create|Truncate)
         Overwrite = Truncate,
         /// Derived open flag: Opens RW or exclusively creates
         OpenOrCreate = ReadWrite | Create
     };
 
+    constexpr static AccessMode ReadOnly = AccessMode::ReadOnly;
+    constexpr static AccessMode ReadWrite = AccessMode::ReadWrite;
+    constexpr static AccessMode Truncate = AccessMode::Truncate;
+    constexpr static AccessMode Excl = AccessMode::Excl;
+    constexpr static AccessMode Debug = AccessMode::Debug;
+    constexpr static AccessMode Create = AccessMode::Create;
+    constexpr static AccessMode Overwrite = AccessMode::Overwrite;
+    constexpr static AccessMode OpenOrCreate = AccessMode::OpenOrCreate;
+
     ///
     /// \brief File
     /// \param filename: filepath of the HDF5 file
@@ -51,7 +63,7 @@ class File: public Object, public NodeTraits<File>, public AnnotateTraits<File>
     ///
     /// Open or create a new HDF5 file
     explicit File(const std::string& filename,
-                  unsigned openFlags = ReadOnly,
+                  AccessMode openFlags = ReadOnly,
                   const FileAccessProps& fileAccessProps = FileAccessProps::Default());
 
     ///
@@ -63,7 +75,7 @@ class File: public Object, public NodeTraits<File>, public AnnotateTraits<File>
     ///
     /// Open or create a new HDF5 file
     File(const std::string& filename,
-         unsigned openFlags,
+         AccessMode openFlags,
          const FileCreateProps& fileCreateProps,
          const FileAccessProps& fileAccessProps = FileAccessProps::Default());
 
@@ -131,6 +143,46 @@ class File: public Object, public NodeTraits<File>, public AnnotateTraits<File>
     friend class PathTraits;
 };
 
+inline File::AccessMode operator|(File::AccessMode lhs, File::AccessMode rhs) {
+    using int_t = std::underlying_type<File::AccessMode>::type;
+    return static_cast<File::AccessMode>(static_cast<int_t>(lhs) | static_cast<int_t>(rhs));
+}
+
+inline File::AccessMode operator&(File::AccessMode lhs, File::AccessMode rhs) {
+    using int_t = std::underlying_type<File::AccessMode>::type;
+    return static_cast<File::AccessMode>(static_cast<int_t>(lhs) & static_cast<int_t>(rhs));
+}
+
+inline File::AccessMode operator^(File::AccessMode lhs, File::AccessMode rhs) {
+    using int_t = std::underlying_type<File::AccessMode>::type;
+    return static_cast<File::AccessMode>(static_cast<int_t>(lhs) ^ static_cast<int_t>(rhs));
+}
+
+inline File::AccessMode operator~(File::AccessMode mode) {
+    using int_t = std::underlying_type<File::AccessMode>::type;
+    return static_cast<File::AccessMode>(~static_cast<int_t>(mode));
+}
+
+inline const File::AccessMode& operator|=(File::AccessMode& lhs, File::AccessMode rhs) {
+    lhs = lhs | rhs;
+    return lhs;
+}
+
+inline File::AccessMode operator&=(File::AccessMode& lhs, File::AccessMode rhs) {
+    lhs = lhs & rhs;
+    return lhs;
+}
+
+inline File::AccessMode operator^=(File::AccessMode& lhs, File::AccessMode rhs) {
+    lhs = lhs ^ rhs;
+    return lhs;
+}
+
+inline bool any(File::AccessMode mode) {
+    return mode != File::AccessMode::None;
+}
+
+
 }  // namespace HighFive
 
 // H5File is the main user constructible -> bring in implementation headers