git subrepo pull --force packages/HighFive

subrepo:
  subdir:   "packages/HighFive"
  merged:   "88fcc8989"
upstream:
  origin:   "git@github.com:BlueBrain/HighFive.git"
  branch:   "master"
  commit:   "88fcc8989"
git-subrepo:
  version:  "0.4.6"
  origin:   "git@github.com:ingydotnet/git-subrepo.git"
  commit:   "110b9eb"

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

@@ -80,7 +80,7 @@ jobs:
 
     - name: Test
       working-directory: ${{github.workspace}}/build
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE
 
 
   # Job testing several versions of hdf5
@@ -89,7 +89,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        hdf5_version : [ hdf5-1_8_23, hdf5-1_10_10, hdf5-1_12_2, hdf5-1_14_1 ]
+        hdf5_version : [ hdf5-1_8_23, hdf5-1_10_11, hdf5-1_12_2, hdf5-1_14_3 ]
 
     steps:
     - uses: actions/checkout@v3
@@ -105,7 +105,7 @@ jobs:
         wget https://github.com/HDFGroup/hdf5/archive/refs/tags/${{ matrix.hdf5_version }}.tar.gz --output-document hdf5.tar.gz
         tar xf hdf5.tar.gz
         mkdir -p hdf5-${{ matrix.hdf5_version }}/BUILD && cd hdf5-${{ matrix.hdf5_version }}/BUILD
-        cmake .. -DCMAKE_BUILD_TYPE=Release -GNinja -DCMAKE_INSTALL_PREFIX=$HOME/${{ matrix.hdf5_version }} -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DUSE_LIBAEC=ON
+        cmake .. -DCMAKE_BUILD_TYPE=Release -GNinja -DCMAKE_INSTALL_PREFIX=$HOME/${{ matrix.hdf5_version }} -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DUSE_LIBAEC=ON -DHDF5_BUILD_EXAMPLES=OFF -DBUILD_STATIC_LIBS=OFF -DBUILD_TESTING=OFF
         ninja && ninja install
 
     - name: Build
@@ -118,7 +118,7 @@ jobs:
 
     - name: Test
       working-directory: ${{github.workspace}}/build
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE
 
 
     - name: Examples
@@ -156,7 +156,7 @@ jobs:
 
     - name: Test
       working-directory: ${{github.workspace}}/build
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE
 
     - name: Examples
       working-directory: ${{github.workspace}}/build/src/examples
@@ -199,7 +199,7 @@ jobs:
 
     - name: Test
       working-directory: ${{github.workspace}}/build
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE
 
     - name: Examples
       working-directory: ${{github.workspace}}/build/src/examples
@@ -295,7 +295,7 @@ jobs:
 
     - name: Test
       working-directory: ${{github.workspace}}/build
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE
 
     - name: Examples
       working-directory: ${{github.workspace}}/build/src/examples
@@ -348,4 +348,4 @@ jobs:
     - name: Test
       working-directory: ${{github.workspace}}/build
       shell: bash -l {0}
-      run: ctest --output-on-failure -C $BUILD_TYPE
+      run: ctest -j2 --output-on-failure -C $BUILD_TYPE

packages/HighFive/.github/workflows/version_file.yml

+name: HighFive Check Version File
+
+on:
+  push:
+    branches:
+      - ci_test
+      - release/**
+  pull_request:
+    branches:
+      - master
+      - release/**
+
+jobs:
+  CheckVersion:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: true
+
+    - name: "Install libraries"
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install libhdf5-dev ninja-build
+
+    - name: Build
+      run: |
+        # Will trigger `configure_file` for H5Version.hpp.
+        cmake -DHIGHFIVE_USE_BOOST=Off -B build .
+
+    - name: Test
+      run: |
+        # Check that the file hasn't changed, i.e. was updated
+        # after changing the version number.
+        ! git status | grep include/highfive/H5Version.hpp

packages/HighFive/.gitrepo

@@ -6,7 +6,7 @@
 [subrepo]
 	remote = git@github.com:BlueBrain/HighFive.git
 	branch = master
-	commit = 7340d1fcc7c455519c113216d8415e003ed37cc6
-	parent = 95783fdd2e50f442c21e5a9e668d14d4985bf2a0
+	commit = 88fcc898970f93a63be8e25760d6b9f33589690f
+	parent = 88cd46aaec511360705df0fc7e577098877862d0
 	method = merge
 	cmdver = 0.4.6

packages/HighFive/AUTHORS.txt

@@ -2,6 +2,7 @@ Adrien Devresse
 Alexandru Săvulescu
 Ali Can Demiralp
 Angelos Plastropoulos
+@antonysigma
 Chris Byrohl
 Chris De Grendele
 @contre
@@ -12,6 +13,8 @@ Fernando L. Pereira
 @guoxy
 Haoran Ni
 Henry Schreiner
+@hn-sl
+Hunter Belanger
 @JaWSnl
 Jia Li
 John W. Peterson
@@ -49,6 +52,7 @@ Tino Wagner
 Tobias Klauser
 Tom de Geus
 Tom Vander Aa
+Torsten Reuschel
 Tristan Carel
 Wolf Vollprecht
 Y. Yang

packages/HighFive/CHANGELOG.md

 # Changes
-## Version 2.8.0 - 2023-MM-DD
+## Version 2.8.0 - 2023-11-02
+### Important Change
+    - `Eigen::Matrix` is (by default) stored with column-major index ordering. Under
+      certain conditions `Eigen::Matrix` was written and read as row-major.
+      Due to code duplication H5Easy isn't affected by this bug. Starting
+      `2.8.0` HighFive will now throw an exception whenever prior versions would
+      have read with incorrect assumptions about the index ordering. (#731)
+
 ### New Features
+    - Improve reading and writing `std::string` as fixed and variable length HDF5 strings (#744).
     - Implement creation of hard links (#765). Thanks to @Quark-X10.
     - Get the size of file and amound of tracked unused space (#764). Thanks to @Quark-X10.
+    - `class DataType` has a new ctor to open a commited `DataType` (#796). Thanks to @Quark-X10.
+    - Allow user-specified `mem_space` for hyperslabs. (#740)
+    - New properties: `AttributePhaseChange`. (#785)
+    - New options to link against HDF5 statically (#823). Thanks @HunterBelanger.
+    - Add support for `std::complex<integral_type>` valid with C++23 (#828). Thanks @unbtorsten.
+    - Add a top-level header to include all compononents (#818).
 
 ### Improvements
+    - Add concept checks to `Property` if C++20 for better errors (#811). Thanks @antonysigma.
     - Add parallel HDF5 test in CI (#760).
     - Simplify github workflow (#761).
     - Move inspectors in their own file to be able to better implements strings (#759).
 
+### Bug Fix
+    - Fix vector constructor ambiguity in H5DataType.hpp (#775). Thanks to @hn-sl.
+    - `getElementCount()` fixed. (#787)
+    - Remove leak when calling dtor of `CompoundType`. (#798)
+
 ## Version 2.7.1 - 2023-04-04
 ### Bug Fix
     - Revert removing `#include "H5FileDriver.hpp"` from `H5File.hpp` (#711).

packages/HighFive/CMake/HighFiveTargetDeps.cmake

@@ -26,6 +26,7 @@ if(NOT TARGET libdeps)
   # HDF5
   if(NOT DEFINED HDF5_C_LIBRARIES)
     set(HDF5_PREFER_PARALLEL ${HIGHFIVE_PARALLEL_HDF5})
+    set(HDF5_USE_STATIC_LIBRARIES ${HIGHFIVE_STATIC_HDF5})
     find_package(HDF5 REQUIRED)
   endif()
 

packages/HighFive/CMake/HighFiveTargetExport.cmake

@@ -4,7 +4,6 @@ add_library(libheaders INTERFACE)
 
 target_include_directories(libheaders INTERFACE
   "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
-  "$<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>"
   "$<INSTALL_INTERFACE:include>")
 
 # Combined HighFive

packages/HighFive/CMakeLists.txt

@@ -5,10 +5,10 @@ else()
   cmake_policy(VERSION 3.13)
 endif()
 
-project(HighFive VERSION 2.7.1)
+project(HighFive VERSION 2.8.0)
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/highfive/H5Version.hpp.in
-               ${CMAKE_CURRENT_BINARY_DIR}/include/highfive/H5Version.hpp)
+               ${CMAKE_CURRENT_SOURCE_DIR}/include/highfive/H5Version.hpp)
 # INCLUDES
 list(APPEND CMAKE_MODULE_PATH
   ${CMAKE_CURRENT_SOURCE_DIR}/CMake
@@ -32,6 +32,7 @@ option(HIGHFIVE_USE_OPENCV "Enable OpenCV testing" ${USE_OPENCV})
 option(HIGHFIVE_USE_XTENSOR "Enable xtensor testing" ${USE_XTENSOR})
 option(HIGHFIVE_EXAMPLES "Compile examples" ON)
 option(HIGHFIVE_PARALLEL_HDF5 "Enable Parallel HDF5 support" OFF)
+option(HIGHFIVE_STATIC_HDF5 "Staticly link to HDF5 library" OFF)
 option(HIGHFIVE_BUILD_DOCS "Enable documentation building" ON)
 option(HIGHFIVE_VERBOSE "Set logging level to verbose." OFF)
 option(HIGHFIVE_GLIBCXX_ASSERTIONS "Enable bounds check for STL." OFF)
@@ -103,11 +104,6 @@ install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
   DESTINATION "include"
   PATTERN "*.in" EXCLUDE)
 
-# Installation of configured headers
-install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include/
-  DESTINATION "include")
-
-
 # Preparing local building (tests, examples)
 # ------------------------------------------
 

packages/HighFive/README.md

@@ -53,7 +53,7 @@ It integrates nicely with other CMake projects by defining (and exporting) a Hig
 #### Write a std::vector<int> to 1D HDF5 dataset and read it back
 
 ```c++
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
 
 using namespace HighFive;
 

packages/HighFive/doc/developer_guide.md

@@ -42,7 +42,7 @@ the git repository. Conveniently, `clang-format` is available via `pip`:
 python -m venv venv
 source venv/bin/activate
 
-pip install clang-format=12.0.1
+pip install clang-format==12.0.1
 ```
 
 The changed lines can be formatted with `git-clang-format`, e.g. to format all lines changed compared to master:
@@ -57,6 +57,7 @@ your changes.)
 Before releasing a new version perform the following:
 
 * Update `CHANGELOG.md` and `AUTHORS.txt` as required.
+* Update `CMakeLists.txt` and `include/highfive/H5Version.hpp`.
 * Follow semantic versioning when deciding the next version number.
 * Check that
   [HighFive-testing](https://github.com/BlueBrain/HighFive-testing/actions) ran

packages/HighFive/doc/installation.md

@@ -202,7 +202,7 @@ install. The detailed instructions would be
 
     git clone --recursive https://github.com/BlueBrain/HighFive.git
     cd HighFive
-    git checkout v2.7.1
+    git checkout v2.8.0
 
 If it complains that Catch is missing, you forgot the `--recursive`. To fix
 this you type
@@ -218,7 +218,7 @@ Okay, on to configure, compile and install. The CMake commands are
 ### Confirming It Works
 We again need a dummy file called `dummy.cpp` with the following contents
 
-    #include <highfive/H5File.hpp>
+    #include <highfive/highfive.hpp>
 
     int main() {
       auto file = HighFive::File("foo.h5", HighFive::File::Create);

packages/HighFive/doc/poster/example3.cpp

-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
 
 
 typedef struct {

packages/HighFive/doc/poster/example6.cpp

@@ -2,9 +2,7 @@
 
 #include <mpi.h>
 
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
 
 
 int main(int argc, char** argv) {

packages/HighFive/doc/poster/example_boost.cpp

 #include <complex>
 
 #define H5_USE_BOOST 1
+#include <highfive/highfive.hpp>
 
 #include <boost/multi_array.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
 
 using complex_t = std::complex<double>;
 

packages/HighFive/doc/poster/example_boost_ublas.cpp

 #include <iostream>
 
 #define H5_USE_BOOST 1
+#include <highfive/highfive.hpp>
 
 // In some versions of Boost (starting with 1.64), you have to
 // include the serialization header before ublas
@@ -8,7 +9,6 @@
 
 #include <boost/numeric/ublas/io.hpp>
 #include <boost/numeric/ublas/matrix.hpp>
-#include <highfive/H5File.hpp>
 
 using namespace HighFive;
 

packages/HighFive/doc/poster/example_easy_highfive.cpp

 #include <xtensor/xarray.hpp>
+
 #include <highfive/H5Easy.hpp>
 
 int main() {

packages/HighFive/doc/poster/example_props.cpp

-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
 
 using namespace HighFive;
 

packages/HighFive/include/highfive/H5DataType.hpp

@@ -11,6 +11,8 @@
 #include <type_traits>
 #include <vector>
 
+#include <H5Tpublic.h>
+
 #include "H5Object.hpp"
 #include "bits/H5Utils.hpp"
 

packages/HighFive/include/highfive/H5Version.hpp

+/*
+ *  Copyright (c), 2020
+ *
+ *  Distributed under the Boost Software License, Version 1.0.
+ *    (See accompanying file LICENSE_1_0.txt or copy at
+ *          http://www.boost.org/LICENSE_1_0.txt)
+ *
+ */
+#pragma once
+
+#define HIGHFIVE_VERSION_MAJOR 2
+#define HIGHFIVE_VERSION_MINOR 8
+#define HIGHFIVE_VERSION_PATCH 0
+
+/** \brief Concatenated representation of the HighFive version.
+ *
+ *  \warning The macro `HIGHFIVE_VERSION` by itself isn't valid C/C++.
+ *
+ *  However, it can be stringified with two layers of macros, e.g.,
+ *  \code{.cpp}
+ *  #define STRINGIFY_VALUE(s) STRINGIFY_NAME(s)
+ *  #define STRINGIFY_NAME(s) #s
+ *
+ *  std::cout << STRINGIFY_VALUE(HIGHFIVE_VERSION) << "\n";
+ *  \endcode
+ */
+#define HIGHFIVE_VERSION 2.8.0
+
+/** \brief String representation of the HighFive version.
+ *
+ *  \warning This macro only exists from 2.7.1 onwards.
+ */
+#define HIGHFIVE_VERSION_STRING "2.8.0"

packages/HighFive/include/highfive/bits/H5Attribute_misc.hpp

@@ -87,8 +87,10 @@ inline void Attribute::read(T& array) const {
     read(r.getPointer(), buffer_info.data_type);
     // re-arrange results
     r.unserialize(array);
-    auto t = create_datatype<typename details::inspector<T>::base_type>();
+
+    auto t = buffer_info.data_type;
     auto c = t.getClass();
+
     if (c == DataTypeClass::VarLen || t.isVariableStr()) {
 #if H5_VERSION_GE(1, 12, 0)
         // This one have been created in 1.12.0