diff --git a/packages/HighFive/.github/workflows/ci.yml b/packages/HighFive/.github/workflows/ci.yml
index de0810d06dba11528658ba249599f5f9fd4098d1..e7f5fca10b9bf26ceb00276ec3dc749e11b0b94c 100644
--- a/packages/HighFive/.github/workflows/ci.yml
+++ b/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
diff --git a/packages/HighFive/.github/workflows/version_file.yml b/packages/HighFive/.github/workflows/version_file.yml
new file mode 100644
index 0000000000000000000000000000000000000000..816137e955fe920c432cf985cbd3a43fa2e924ff
--- /dev/null
+++ b/packages/HighFive/.github/workflows/version_file.yml
@@ -0,0 +1,36 @@
+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
diff --git a/packages/HighFive/.gitrepo b/packages/HighFive/.gitrepo
index 8a0046eea29d1f2b4fac6534ac21ac2f845e2dea..14b8f5fba715beda2d02da0beb4c2e267ac16373 100644
--- a/packages/HighFive/.gitrepo
+++ b/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
diff --git a/packages/HighFive/AUTHORS.txt b/packages/HighFive/AUTHORS.txt
index 0a3cdf580fa008d4fb622a6fdcd5128955cb58ee..78f573a9a6abfe5db14e7ea8921b89e80bb78d21 100644
--- a/packages/HighFive/AUTHORS.txt
+++ b/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
diff --git a/packages/HighFive/CHANGELOG.md b/packages/HighFive/CHANGELOG.md
index eeeb628c95f46f9680f4a79d9609b1257e89e4cd..9a8cd86139f80bc1523e6f0e33fc049316a0f830 100644
--- a/packages/HighFive/CHANGELOG.md
+++ b/packages/HighFive/CHANGELOG.md
@@ -1,14 +1,34 @@
# 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).
diff --git a/packages/HighFive/CMake/HighFiveTargetDeps.cmake b/packages/HighFive/CMake/HighFiveTargetDeps.cmake
index da28423bce60dad614c0cf9fb83673dff9af63ce..919b53544ea198e040d86d5620bb05f05ab5a7f2 100644
--- a/packages/HighFive/CMake/HighFiveTargetDeps.cmake
+++ b/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 ${HIGHFIVE_STATIC_HDF5})
find_package(HDF5 REQUIRED)
endif()
diff --git a/packages/HighFive/CMake/HighFiveTargetExport.cmake b/packages/HighFive/CMake/HighFiveTargetExport.cmake
index 011f7f4832973f3816abc5293b4d1b2a5465e969..9906f39513c385e9dba2dca5194453fe9b2eec16 100644
--- a/packages/HighFive/CMake/HighFiveTargetExport.cmake
+++ b/packages/HighFive/CMake/HighFiveTargetExport.cmake
@@ -4,7 +4,6 @@ add_library(libheaders INTERFACE)
target_include_directories(libheaders INTERFACE
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
- "$<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>"
"$<INSTALL_INTERFACE:include>")
# Combined HighFive
diff --git a/packages/HighFive/CMakeLists.txt b/packages/HighFive/CMakeLists.txt
index a9deba11342bb3bcd1263ccc4ff861885f867bf3..af274d9e25ea0ba40cfbd0407531db449be95f67 100644
--- a/packages/HighFive/CMakeLists.txt
+++ b/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)
# ------------------------------------------
diff --git a/packages/HighFive/README.md b/packages/HighFive/README.md
index 2ef1de8d547294e619de2158c7e109d5767f0f8f..3ea0680157cdc72040a39c68c2f4ebe2d1569ca1 100644
--- a/packages/HighFive/README.md
+++ b/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;
diff --git a/packages/HighFive/doc/developer_guide.md b/packages/HighFive/doc/developer_guide.md
index 9b33cdcf9c6702bae0c049d0fe4764eec5c71902..3017289b5172bbb443829da0daf6bcaa04413e54 100644
--- a/packages/HighFive/doc/developer_guide.md
+++ b/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
diff --git a/packages/HighFive/doc/installation.md b/packages/HighFive/doc/installation.md
index 36676c2c7fee35263c46337cc6366f6f2572e6b1..41521bba5e57212e7a7cd08b9423c5fcea655ddd 100644
--- a/packages/HighFive/doc/installation.md
+++ b/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);
diff --git a/packages/HighFive/doc/poster/example3.cpp b/packages/HighFive/doc/poster/example3.cpp
index 64f2ed6be7630c7d47b20cafed007383fae8c622..e18fbbf83e4fb015647a70d91857f18902eb0c39 100644
--- a/packages/HighFive/doc/poster/example3.cpp
+++ b/packages/HighFive/doc/poster/example3.cpp
@@ -1,4 +1,4 @@
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
typedef struct {
diff --git a/packages/HighFive/doc/poster/example6.cpp b/packages/HighFive/doc/poster/example6.cpp
index 8f7419f23fd1a7054491b14bc27db6d31c2976c6..41a050570598d4fb1a2dec0aa040eee6d72763d5 100644
--- a/packages/HighFive/doc/poster/example6.cpp
+++ b/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) {
diff --git a/packages/HighFive/doc/poster/example_boost.cpp b/packages/HighFive/doc/poster/example_boost.cpp
index aceaa20681b31b14d46a94bac2a0a0391e7ebde0..56b78d074e3b136c193dc4781b9812e9074db88c 100644
--- a/packages/HighFive/doc/poster/example_boost.cpp
+++ b/packages/HighFive/doc/poster/example_boost.cpp
@@ -1,11 +1,9 @@
#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>;
diff --git a/packages/HighFive/doc/poster/example_boost_ublas.cpp b/packages/HighFive/doc/poster/example_boost_ublas.cpp
index 3a2b4c73a583060aec3441ccdaa890daecd03fee..986a671de57f59d2f0da98c2d1e76efa529bef83 100644
--- a/packages/HighFive/doc/poster/example_boost_ublas.cpp
+++ b/packages/HighFive/doc/poster/example_boost_ublas.cpp
@@ -1,6 +1,7 @@
#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;
diff --git a/packages/HighFive/doc/poster/example_easy_highfive.cpp b/packages/HighFive/doc/poster/example_easy_highfive.cpp
index 07d37a22c5f3584aa34fbf544c4394679c5522da..700056cae978ecc043c60d558927f282ad14b127 100644
--- a/packages/HighFive/doc/poster/example_easy_highfive.cpp
+++ b/packages/HighFive/doc/poster/example_easy_highfive.cpp
@@ -1,4 +1,5 @@
#include <xtensor/xarray.hpp>
+
#include <highfive/H5Easy.hpp>
int main() {
diff --git a/packages/HighFive/doc/poster/example_props.cpp b/packages/HighFive/doc/poster/example_props.cpp
index e46fe119ceebdee3f6a2cfa8f0c7a9ecf2edd981..0e5b14bde7ce990798d02035fd3c780bd25e0058 100644
--- a/packages/HighFive/doc/poster/example_props.cpp
+++ b/packages/HighFive/doc/poster/example_props.cpp
@@ -1,4 +1,4 @@
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/include/highfive/H5DataType.hpp b/packages/HighFive/include/highfive/H5DataType.hpp
index 8403618e2596cac6a9605d7a7c176d4f07d0e2c2..886107961b87e32911702f3aaf3496acc8ce8c26 100644
--- a/packages/HighFive/include/highfive/H5DataType.hpp
+++ b/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"
diff --git a/packages/HighFive/include/highfive/H5Version.hpp b/packages/HighFive/include/highfive/H5Version.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..dc238432cb01d651769c663276ea15a94008f3e9
--- /dev/null
+++ b/packages/HighFive/include/highfive/H5Version.hpp
@@ -0,0 +1,33 @@
+/*
+ * 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"
diff --git a/packages/HighFive/include/highfive/bits/H5Attribute_misc.hpp b/packages/HighFive/include/highfive/bits/H5Attribute_misc.hpp
index 5c52f7bbb1ce507228b1c54b953b1f8e843f3b9a..6516788297819c9f6e318bd588df3ac668ac63fd 100644
--- a/packages/HighFive/include/highfive/bits/H5Attribute_misc.hpp
+++ b/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
diff --git a/packages/HighFive/include/highfive/bits/H5Converter_misc.hpp b/packages/HighFive/include/highfive/bits/H5Converter_misc.hpp
index 8f4411118a7a40f33ae41118b458f2e27709ff58..00749d1b6d6157bc745a86005a7a80d6b195fbb3 100644
--- a/packages/HighFive/include/highfive/bits/H5Converter_misc.hpp
+++ b/packages/HighFive/include/highfive/bits/H5Converter_misc.hpp
@@ -16,11 +16,23 @@
namespace HighFive {
namespace details {
+template <class T>
+struct is_std_string {
+ static constexpr bool value =
+ std::is_same<typename inspector<T>::base_type, std::string>::value;
+};
+
template <class T, class V = void>
-struct enable_shallow_copy: public std::enable_if<inspector<T>::is_trivially_copyable, V> {};
+struct enable_shallow_copy
+ : public std::enable_if<!is_std_string<T>::value && inspector<T>::is_trivially_copyable, V> {};
template <class T, class V = void>
-struct enable_deep_copy: public std::enable_if<!inspector<T>::is_trivially_copyable, V> {};
+struct enable_deep_copy
+ : public std::enable_if<!is_std_string<T>::value && !inspector<T>::is_trivially_copyable, V> {};
+
+template <class T, class V = void>
+struct enable_string_copy: public std::enable_if<is_std_string<T>::value, V> {};
+
template <typename T, bool IsReadOnly>
struct ShallowCopyBuffer {
@@ -85,6 +97,243 @@ struct DeepCopyBuffer {
std::vector<size_t> dims;
};
+enum class BufferMode { Read, Write };
+
+
+///
+/// \brief String length in bytes excluding the `\0`.
+///
+inline size_t char_buffer_size(char const* const str, size_t max_string_length) {
+ for (size_t i = 0; i <= max_string_length; ++i) {
+ if (str[i] == '\0') {
+ return i;
+ }
+ }
+
+ return max_string_length;
+}
+
+
+///
+/// \brief A buffer for reading/writing strings.
+///
+/// A string in HDF5 can be represented as a fixed or variable length string.
+/// The important difference for this buffer is that `H5D{read,write}` expects
+/// different input depending on whether the strings are fixed or variable length.
+/// For fixed length strings, it expects an array of chars, i.e. one string
+/// packed after the other contiguously. While for variable length strings it
+/// expects a list of pointers to the beginning of each string. Variable length
+/// string must be null-terminated; because that's how their length is
+/// determined.
+///
+/// This buffer hides the difference between fixed and variable length strings
+/// by having internal data structures available for both cases at compile time.
+/// The choice which internal buffer to use is made at runtime.
+///
+/// Consider an HDF5 dataset with N fixed-length strings, each of which is M
+/// characters long. Then the in-memory strings are copied into an internal
+/// buffer of size N*M. If null- or space-padded the buffer should be filled
+/// with the appropriate character. This is important if the in-memory strings
+/// are less than M characters long.
+///
+/// An HDF5 dataset with N variable-length strings (all null-terminated) uses
+/// the internal list of pointers to the beginning of each string. Those
+/// pointers can either point to the in-memory strings themselves, if those
+/// strings are known to be null-terminated. Otherwise the in-memory strings are
+/// copied to an internal buffer of null-terminated strings; and the pointer
+/// points to the start of the string in the internal buffer.
+///
+/// This class is responsible for arranging the strings properly before passing
+/// the buffers to HDF5. To keep this class generic, it provides a generic
+/// read/write interface to the internal strings, i.e. a pointer with a size.
+/// For reading from the buffer the proxy is called `StringConstView`. This
+/// proxy object is to be used by the `inspector` to copy from the buffer into
+/// the final destination, e.g. an `std::string`. Similarly, there's a proxy
+/// object for serializing into the buffer, i.e. the `StringView`. Again the
+/// `inspector` is responsible for obtaining the pointer, size and padding of
+/// the string.
+///
+/// Nomenclature:
+/// - size of a string is the number of bytes required to store the string,
+/// including the null character for null-terminated strings.
+///
+/// - length of a string is the number of bytes without the null character.
+///
+/// Note: both 'length' and 'size' are counted in number of bytes, not number
+/// of symbols or characters. Even for UTF8 strings.
+template <typename T, BufferMode buffer_mode>
+struct StringBuffer {
+ using type = unqualified_t<T>;
+ using hdf5_type = typename inspector<type>::hdf5_type;
+
+ class StringView {
+ public:
+ StringView(StringBuffer<T, buffer_mode>& _buffer, size_t _i)
+ : buffer(_buffer)
+ , i(_i) {}
+
+ ///
+ /// \brief Assign the in-memory string to the buffer.
+ ///
+ /// This method copies the in-memory string to the appropriate
+ /// internal buffer as needed.
+ ///
+ /// The `length` is the length of the string in bytes.
+ void assign(char const* data, size_t length, StringPadding padding) {
+ if (buffer.isVariableLengthString()) {
+ if (padding == StringPadding::NullTerminated) {
+ buffer.variable_length_pointers[i] = data;
+ } else {
+ buffer.variable_length_buffer[i] = std::string(data, length);
+ buffer.variable_length_pointers[i] = buffer.variable_length_buffer[i].data();
+ }
+ } else if (buffer.isFixedLengthString()) {
+ // If the buffer is fixed-length and null-terminated, then
+ // `buffer.string_length` doesn't include the null-character.
+ if (length > buffer.string_length) {
+ throw std::invalid_argument("String length too big.");
+ }
+
+ memcpy(&buffer.fixed_length_buffer[i * buffer.string_size], data, length);
+ }
+ }
+
+ private:
+ StringBuffer<T, buffer_mode>& buffer;
+ size_t i;
+ };
+
+
+ class StringConstView {
+ public:
+ StringConstView(const StringBuffer<T, buffer_mode>& _buffer, size_t _i)
+ : buffer(_buffer)
+ , i(_i) {}
+
+ /// \brief Pointer to the first byte of the string.
+ ///
+ /// The valid indices for this pointer are: 0, ..., length() - 1.
+ char const* data() const {
+ if (buffer.isVariableLengthString()) {
+ return buffer.variable_length_pointers[i];
+ } else {
+ return &buffer.fixed_length_buffer[i * buffer.string_size];
+ }
+ }
+
+ /// \brief Length of the string in bytes.
+ ///
+ /// Note that for null-terminated strings the "length" doesn't include
+ /// the null character. Hence, if storing this string as a
+ /// null-terminated string, the destination buffer needs to be at least
+ /// `length() + 1` bytes long.
+ size_t length() const {
+ if (buffer.isNullTerminated()) {
+ return char_buffer_size(data(), buffer.string_length);
+ } else {
+ return buffer.string_length;
+ }
+ }
+
+ private:
+ const StringBuffer<T, buffer_mode>& buffer;
+ size_t i;
+ };
+
+
+ class Iterator {
+ public:
+ Iterator(StringBuffer<T, buffer_mode>& _buffer, size_t _pos)
+ : buffer(_buffer)
+ , pos(_pos) {}
+
+ Iterator operator+(size_t n_strings) const {
+ return Iterator(buffer, pos + n_strings);
+ }
+
+ void operator+=(size_t n_strings) {
+ pos += n_strings;
+ }
+
+ StringView operator*() {
+ return StringView(buffer, pos);
+ }
+
+ StringConstView operator*() const {
+ return StringConstView(buffer, pos);
+ }
+
+ private:
+ StringBuffer<T, buffer_mode>& buffer;
+ size_t pos;
+ };
+
+ StringBuffer(std::vector<size_t> _dims, const DataType& _file_datatype)
+ : file_datatype(_file_datatype.asStringType())
+ , padding(file_datatype.getPadding())
+ , string_size(file_datatype.isVariableStr() ? size_t(-1) : file_datatype.getSize())
+ , string_length(string_size - size_t(isNullTerminated()))
+ , dims(_dims) {
+ if (string_size == 0 && isNullTerminated()) {
+ throw DataTypeException(
+ "Fixed-length, null-terminated need at least one byte to store the "
+ "null-character.");
+ }
+
+ auto n_strings = compute_total_size(dims);
+ if (isVariableLengthString()) {
+ variable_length_buffer.resize(n_strings);
+ variable_length_pointers.resize(n_strings);
+ } else {
+ char pad = padding == StringPadding::SpacePadded ? ' ' : '\0';
+ fixed_length_buffer.assign(n_strings * string_size, pad);
+ }
+ }
+
+ bool isVariableLengthString() const {
+ return file_datatype.isVariableStr();
+ }
+
+ bool isFixedLengthString() const {
+ return file_datatype.isFixedLenStr();
+ }
+
+ bool isNullTerminated() const {
+ return file_datatype.getPadding() == StringPadding::NullTerminated;
+ }
+
+
+ void* getPointer() {
+ if (file_datatype.isVariableStr()) {
+ return variable_length_pointers.data();
+ } else {
+ return fixed_length_buffer.data();
+ }
+ }
+
+ Iterator begin() {
+ return Iterator(*this, 0ul);
+ }
+
+ void unserialize(T& val) {
+ inspector<type>::unserialize(begin(), dims, val);
+ }
+
+ private:
+ StringType file_datatype;
+ StringPadding padding;
+ size_t string_size; // Size of buffer required to store the string.
+ // Meaningful for fixed length strings only.
+ size_t string_length; // Semantic length of string.
+ std::vector<size_t> dims;
+
+ std::vector<char> fixed_length_buffer;
+ std::vector<std::string> variable_length_buffer;
+ std::vector<
+ typename std::conditional<buffer_mode == BufferMode::Write, const char, char>::type*>
+ variable_length_pointers;
+};
+
template <typename T, typename Enable = void>
struct Writer;
@@ -107,6 +356,14 @@ struct Writer<T, typename enable_deep_copy<T>::type>: public DeepCopyBuffer<T> {
}
};
+template <typename T>
+struct Writer<T, typename enable_string_copy<T>::type>: public StringBuffer<T, BufferMode::Write> {
+ explicit Writer(const T& val, const DataType& _file_datatype)
+ : StringBuffer<T, BufferMode::Write>(inspector<T>::getDimensions(val), _file_datatype) {
+ inspector<T>::serialize(val, this->begin());
+ }
+};
+
template <typename T, typename Enable = void>
struct Reader;
@@ -133,6 +390,15 @@ struct Reader<T, typename enable_deep_copy<T>::type>: public DeepCopyBuffer<T> {
};
+template <typename T>
+struct Reader<T, typename enable_string_copy<T>::type>: public StringBuffer<T, BufferMode::Write> {
+ public:
+ explicit Reader(const std::vector<size_t>& _dims,
+ const T& /* val */,
+ const DataType& _file_datatype)
+ : StringBuffer<T, BufferMode::Write>(_dims, _file_datatype) {}
+};
+
struct data_converter {
template <typename T>
static Writer<T> serialize(const typename inspector<T>::type& val,
diff --git a/packages/HighFive/include/highfive/bits/H5DataType_misc.hpp b/packages/HighFive/include/highfive/bits/H5DataType_misc.hpp
index 934d5f5e5f64e40f1b13bb433f9a8b11ec416753..8535d617ab443405dbdd88353f52cf4850f8e7d1 100644
--- a/packages/HighFive/include/highfive/bits/H5DataType_misc.hpp
+++ b/packages/HighFive/include/highfive/bits/H5DataType_misc.hpp
@@ -22,7 +22,7 @@
#include <half.hpp>
#endif
-#include "H5Converter_misc.hpp"
+#include "H5Inspector_misc.hpp"
namespace HighFive {
@@ -300,8 +300,8 @@ class AtomicType<std::complex<T>>: public DataType {
: DataType(
CompoundType({{"r", create_datatype<T>(), 0}, {"i", create_datatype<T>(), sizeof(T)}},
sizeof(std::complex<T>))) {
- static_assert(std::is_floating_point<T>::value,
- "std::complex accepts only floating point numbers.");
+ static_assert(std::is_arithmetic<T>::value,
+ "std::complex accepts only floating point and integral numbers.");
}
};
diff --git a/packages/HighFive/include/highfive/bits/H5Inspector_misc.hpp b/packages/HighFive/include/highfive/bits/H5Inspector_misc.hpp
index c25bcfbd566649a33ea372ca4f202bf6ea29fe7c..05ed6bc3ec0250b18e0ce4311ff710e703a6fca9 100644
--- a/packages/HighFive/include/highfive/bits/H5Inspector_misc.hpp
+++ b/packages/HighFive/include/highfive/bits/H5Inspector_misc.hpp
@@ -12,6 +12,9 @@
#include <type_traits>
#include <cstring>
#include <cassert>
+#include <vector>
+#include <array>
+#include <string>
#include <numeric>
#include "../H5Reference.hpp"
@@ -28,7 +31,9 @@
#include <Eigen/Eigen>
#endif
+
namespace HighFive {
+
namespace details {
inline bool checkDimensions(const std::vector<size_t>& dims, size_t n_dim_requested) {
@@ -260,14 +265,15 @@ struct inspector<std::string>: type_helper<std::string> {
throw DataSpaceException("A std::string cannot be written directly.");
}
- static void serialize(const type& val, hdf5_type* m) {
- *m = val.c_str();
+ template <class It>
+ static void serialize(const type& val, It m) {
+ (*m).assign(val.data(), val.size(), StringPadding::NullTerminated);
}
- static void unserialize(const hdf5_type* vec,
- const std::vector<size_t>& /* dims */,
- type& val) {
- val = vec[0];
+ template <class It>
+ static void unserialize(const It& vec, const std::vector<size_t>& /* dims */, type& val) {
+ const auto& view = *vec;
+ val.assign(view.data(), view.length());
}
};
@@ -488,6 +494,7 @@ struct inspector<std::array<T, N>> {
static constexpr size_t ndim = 1;
static constexpr size_t recursive_ndim = ndim + inspector<value_type>::recursive_ndim;
static constexpr bool is_trivially_copyable = std::is_trivially_copyable<value_type>::value &&
+ sizeof(type) == N * sizeof(T) &&
inspector<value_type>::is_trivially_copyable;
static std::vector<size_t> getDimensions(const type& val) {
diff --git a/packages/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp b/packages/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp
index 9da473b05e9fa63730f8e6c1e486658d7ab51ae7..c8e73617400fa9cec3b727d84fb49f1ac8e74c11 100644
--- a/packages/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp
+++ b/packages/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp
@@ -19,9 +19,13 @@ template <typename T>
using unqualified_t = typename std::remove_const<typename std::remove_reference<T>::type>::type;
// Find the type of an eventual char array, otherwise void
-template <typename>
+template <typename T>
struct type_char_array {
- using type = void;
+ using type = typename std::conditional<
+ std::is_same<typename inspector<T>::base_type, std::string>::value,
+ std::string,
+ void>::type;
+ static constexpr bool is_char_array = false;
};
template <typename T>
@@ -29,6 +33,7 @@ struct type_char_array<T*> {
using type = typename std::conditional<std::is_same<unqualified_t<T>, char>::value,
char*,
typename type_char_array<T>::type>::type;
+ static constexpr bool is_char_array = true;
};
template <typename T, std::size_t N>
@@ -36,6 +41,7 @@ struct type_char_array<T[N]> {
using type = typename std::conditional<std::is_same<unqualified_t<T>, char>::value,
char[N],
typename type_char_array<T>::type>::type;
+ static constexpr bool is_char_array = true;
};
template <typename T>
@@ -43,7 +49,7 @@ struct BufferInfo {
using type_no_const = typename std::remove_const<T>::type;
using elem_type = typename details::inspector<type_no_const>::base_type;
using char_array_t = typename details::type_char_array<type_no_const>::type;
- static constexpr bool is_char_array = !std::is_same<char_array_t, void>::value;
+ static constexpr bool is_char_array = details::type_char_array<type_no_const>::is_char_array;
enum Operation { read, write };
const Operation op;
@@ -85,6 +91,16 @@ struct string_type_checker<void> {
}
};
+template <>
+struct string_type_checker<std::string> {
+ inline static DataType getDataType(const DataType&, const DataType& file_datatype) {
+ // The StringBuffer ensures that the data is transformed such that it
+ // matches the datatype of the dataset, i.e. `file_datatype` and
+ // `mem_datatype` are the same.
+ return file_datatype;
+ }
+};
+
template <std::size_t FixedLen>
struct string_type_checker<char[FixedLen]> {
inline static DataType getDataType(const DataType& element_type, const DataType& dtype) {
@@ -98,8 +114,9 @@ struct string_type_checker<char[FixedLen]> {
template <>
struct string_type_checker<char*> {
inline static DataType getDataType(const DataType&, const DataType& dtype) {
- if (dtype.isFixedLenStr())
+ if (dtype.isFixedLenStr()) {
throw DataSetException("Can't output variable-length to fixed-length strings");
+ }
DataType return_type = AtomicType<std::string>();
enforce_ascii_hack(return_type, dtype);
return return_type;
@@ -116,11 +133,6 @@ BufferInfo<T>::BufferInfo(const DataType& dtype, F getName, Operation _op)
((is_fixed_len_string && is_char_array) ? 1 : 0))
, data_type(
string_type_checker<char_array_t>::getDataType(create_datatype<elem_type>(), dtype)) {
- if (is_fixed_len_string && std::is_same<elem_type, std::string>::value) {
- throw DataSetException(
- "Can't output std::string as fixed-length. "
- "Use raw arrays or FixedLenStringArray");
- }
// We warn. In case they are really not convertible an exception will rise on read/write
if (dtype.getClass() != data_type.getClass()) {
HIGHFIVE_LOG_WARN(getName() + "\": data and hdf5 dataset have different types: " +
diff --git a/packages/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp b/packages/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp
index a5dc9ee378e5d494b1e46bc62804322836dae937..7b07c9abf9406b214e068aadd7c5a34011eb3d60 100644
--- a/packages/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp
+++ b/packages/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp
@@ -199,7 +199,8 @@ inline void SliceTraits<Derivate>::read(T& array, const DataTransferProps& xfer_
read(r.getPointer(), buffer_info.data_type, xfer_props);
// 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)
diff --git a/packages/HighFive/include/highfive/bits/string_padding.hpp b/packages/HighFive/include/highfive/bits/string_padding.hpp
index 984549e240a9f402752ebf86aecb60d13aa1e3e1..e6e6908ddc5e320019bff48fb5cf494c76bb96b0 100644
--- a/packages/HighFive/include/highfive/bits/string_padding.hpp
+++ b/packages/HighFive/include/highfive/bits/string_padding.hpp
@@ -1,5 +1,7 @@
#pragma once
+#include <H5Tpublic.h>
+
namespace HighFive {
enum class StringPadding : std::underlying_type<H5T_str_t>::type {
diff --git a/packages/HighFive/include/highfive/highfive.hpp b/packages/HighFive/include/highfive/highfive.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..f5e20cae9131ae7e6440f6fa7f16bc8b3430b336
--- /dev/null
+++ b/packages/HighFive/include/highfive/highfive.hpp
@@ -0,0 +1,14 @@
+#pragma once
+
+#include <highfive/H5Attribute.hpp>
+#include <highfive/H5DataSet.hpp>
+#include <highfive/H5DataSpace.hpp>
+#include <highfive/H5DataType.hpp>
+#include <highfive/H5File.hpp>
+#include <highfive/H5FileDriver.hpp>
+#include <highfive/H5Group.hpp>
+#include <highfive/H5PropertyList.hpp>
+#include <highfive/H5Reference.hpp>
+#include <highfive/H5Selection.hpp>
+#include <highfive/H5Utility.hpp>
+#include <highfive/H5Version.hpp>
diff --git a/packages/HighFive/src/benchmarks/highfive_bench.cpp b/packages/HighFive/src/benchmarks/highfive_bench.cpp
index e4e04dee8e7a970eafd2010a8fcf13132359b511..bcc7be93ce742701d03e8daa6f21286f838efe9e 100644
--- a/packages/HighFive/src/benchmarks/highfive_bench.cpp
+++ b/packages/HighFive/src/benchmarks/highfive_bench.cpp
@@ -1,4 +1,4 @@
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
#include <vector>
const std::vector<std::vector<int>> data(1000000, {1, 2, 3, 4, 5, 6, 7, 8, 9, 10});
diff --git a/packages/HighFive/src/examples/boost_multi_array_2D.cpp b/packages/HighFive/src/examples/boost_multi_array_2D.cpp
index 582049efdde323ba89eaf207a490cce51a4adc37..4bec1ec12991391a58549e8fb044294523f4a74b 100644
--- a/packages/HighFive/src/examples/boost_multi_array_2D.cpp
+++ b/packages/HighFive/src/examples/boost_multi_array_2D.cpp
@@ -12,7 +12,7 @@
#define H5_USE_BOOST
#include <boost/multi_array.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/boost_multiarray_complex.cpp b/packages/HighFive/src/examples/boost_multiarray_complex.cpp
index 1b66b3ddf3cfe106fd7191bf13613781cbd59b4b..37481db625b5b21d7d13c0ae7da4223c9d7eb327 100644
--- a/packages/HighFive/src/examples/boost_multiarray_complex.cpp
+++ b/packages/HighFive/src/examples/boost_multiarray_complex.cpp
@@ -12,10 +12,9 @@
#undef H5_USE_BOOST
#define H5_USE_BOOST
+#include <highfive/highfive.hpp>
+
#include <boost/multi_array.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
typedef std::complex<double> complex_t;
diff --git a/packages/HighFive/src/examples/boost_ublas_double.cpp b/packages/HighFive/src/examples/boost_ublas_double.cpp
index ca3307ecfc53281b6672fabe38fd385ff86d2a6c..b025475b9584b2f27c6dbfcd51e3ee402898031a 100644
--- a/packages/HighFive/src/examples/boost_ublas_double.cpp
+++ b/packages/HighFive/src/examples/boost_ublas_double.cpp
@@ -11,13 +11,14 @@
#undef H5_USE_BOOST
#define H5_USE_BOOST
+#include <highfive/highfive.hpp>
+
// In some versions of Boost (starting with 1.64), you have to include the serialization header
// before ublas
#include <boost/serialization/vector.hpp>
#include <boost/numeric/ublas/io.hpp>
#include <boost/numeric/ublas/matrix.hpp>
-#include <highfive/H5File.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/compound_types.cpp b/packages/HighFive/src/examples/compound_types.cpp
index d456859a432e7b35a34c8203c2d47c96ed962943..158bc6dc6de6e53314470d1db57bc392bdb765aa 100644
--- a/packages/HighFive/src/examples/compound_types.cpp
+++ b/packages/HighFive/src/examples/compound_types.cpp
@@ -10,7 +10,7 @@
// Compound datatype test :: May 2021
// //////////////////////////////////
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
typedef struct {
diff --git a/packages/HighFive/src/examples/create_attribute_string_integer.cpp b/packages/HighFive/src/examples/create_attribute_string_integer.cpp
index a716c827a4b3b14ecacb4e9225930eaa2a1a55ef..f658457adfe0e0a51534a7e4512ca982c13fae11 100644
--- a/packages/HighFive/src/examples/create_attribute_string_integer.cpp
+++ b/packages/HighFive/src/examples/create_attribute_string_integer.cpp
@@ -10,10 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5Attribute.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/create_dataset_double.cpp b/packages/HighFive/src/examples/create_dataset_double.cpp
index e5b96fcf6bf042372eb33ec0ec767db17fbf41d4..d15fbdc54f196195880347cd56f2e7e6783e453d 100644
--- a/packages/HighFive/src/examples/create_dataset_double.cpp
+++ b/packages/HighFive/src/examples/create_dataset_double.cpp
@@ -10,9 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
// Create a dataset name "dset" of double 4x6
int main(void) {
diff --git a/packages/HighFive/src/examples/create_dataset_half_float.cpp b/packages/HighFive/src/examples/create_dataset_half_float.cpp
index 204e45374bc1d2134a21d0ed22b659ecacf74cd8..2b720cd187036c98392ed7fd2e9518934ae948ce 100644
--- a/packages/HighFive/src/examples/create_dataset_half_float.cpp
+++ b/packages/HighFive/src/examples/create_dataset_half_float.cpp
@@ -13,9 +13,7 @@
#include <string>
#include <vector>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
const std::string FILE_NAME("create_dataset_half_float_example.h5");
const std::string DATASET_NAME("dset");
diff --git a/packages/HighFive/src/examples/create_datatype.cpp b/packages/HighFive/src/examples/create_datatype.cpp
index d1e342bb4a5d911391b9f1d845e51bdde77dced8..0b1a0fb52044c915f185c52d5145f1738d279834 100644
--- a/packages/HighFive/src/examples/create_datatype.cpp
+++ b/packages/HighFive/src/examples/create_datatype.cpp
@@ -1,7 +1,6 @@
#include <iostream>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataType.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/create_extensible_dataset.cpp b/packages/HighFive/src/examples/create_extensible_dataset.cpp
index 53a6b2b43ae0d846714101819a597649de35fcc2..17153cd5740bda666808a2d7f45f7fa19c262235 100644
--- a/packages/HighFive/src/examples/create_extensible_dataset.cpp
+++ b/packages/HighFive/src/examples/create_extensible_dataset.cpp
@@ -10,9 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
const std::string FILE_NAME("create_extensible_dataset_example.h5");
const std::string DATASET_NAME("dset");
diff --git a/packages/HighFive/src/examples/create_large_attribute.cpp b/packages/HighFive/src/examples/create_large_attribute.cpp
index 004386e6eb6dc83a269a5af614a32150ee69e118..022d11d87bcfdd8e9ab9c6719ea37a500e837176 100644
--- a/packages/HighFive/src/examples/create_large_attribute.cpp
+++ b/packages/HighFive/src/examples/create_large_attribute.cpp
@@ -1,9 +1,8 @@
-#include <H5Fpublic.h>
-#include <highfive/H5File.hpp>
-#include <highfive/H5Group.hpp>
#include <numeric>
#include <vector>
+#include <highfive/highfive.hpp>
+
int main() {
std::vector<double> large_attr(16000, 0.0);
diff --git a/packages/HighFive/src/examples/create_page_allocated_files.cpp b/packages/HighFive/src/examples/create_page_allocated_files.cpp
index 73f15c5fb2cd92c34da5629fd3dc1d1484e9b340..0b4d29dffb3c1a21ca90114b122ef020fd394ae2 100644
--- a/packages/HighFive/src/examples/create_page_allocated_files.cpp
+++ b/packages/HighFive/src/examples/create_page_allocated_files.cpp
@@ -12,7 +12,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
// This example requires HDF5 version 1.10.1 or newer.
#if H5_VERSION_GE(1, 10, 1)
diff --git a/packages/HighFive/src/examples/hl_hdf5_inmemory_files.cpp b/packages/HighFive/src/examples/hl_hdf5_inmemory_files.cpp
index 58bdbbec1c0909fd0465c227e4c86a930a46d2f5..088fd71cc8db6a165cecdde1307212b4f828e18d 100644
--- a/packages/HighFive/src/examples/hl_hdf5_inmemory_files.cpp
+++ b/packages/HighFive/src/examples/hl_hdf5_inmemory_files.cpp
@@ -9,8 +9,8 @@
#include <iostream>
#include <vector>
+#include <highfive/highfive.hpp>
-#include <highfive/H5File.hpp>
#include <hdf5_hl.h>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/parallel_hdf5_collective_io.cpp b/packages/HighFive/src/examples/parallel_hdf5_collective_io.cpp
index c7d7f9920d08e9fd310f6b8558c794548d96d00e..7261b7cf1d8b8a92623ef166bea72156250d9b7b 100644
--- a/packages/HighFive/src/examples/parallel_hdf5_collective_io.cpp
+++ b/packages/HighFive/src/examples/parallel_hdf5_collective_io.cpp
@@ -13,10 +13,7 @@
#include <mpi.h>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5PropertyList.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("parallel_collective_example.h5");
const std::string dataset_name("dset");
diff --git a/packages/HighFive/src/examples/parallel_hdf5_independent_io.cpp b/packages/HighFive/src/examples/parallel_hdf5_independent_io.cpp
index f56d87f05c5dd7cfbc80def6dbfd7c3867fc6e09..b43012890c209a05dfd0700333f608a6dd247211 100644
--- a/packages/HighFive/src/examples/parallel_hdf5_independent_io.cpp
+++ b/packages/HighFive/src/examples/parallel_hdf5_independent_io.cpp
@@ -13,10 +13,7 @@
#include <mpi.h>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5PropertyList.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("parallel_independent_example.h5");
diff --git a/packages/HighFive/src/examples/read_write_dataset_string.cpp b/packages/HighFive/src/examples/read_write_dataset_string.cpp
index c5cf658a2d6bf8d41a2c34633383e4ea5062b61e..2a4c3c491105c8585ec3838fe609279e71b52ba9 100644
--- a/packages/HighFive/src/examples/read_write_dataset_string.cpp
+++ b/packages/HighFive/src/examples/read_write_dataset_string.cpp
@@ -10,9 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/read_write_fixedlen_string.cpp b/packages/HighFive/src/examples/read_write_fixedlen_string.cpp
index 123e9443ff9a28c2b9c3a540e86723c9a29ea73f..60589637ea97e6c526ab8b8c6754026c7191331d 100644
--- a/packages/HighFive/src/examples/read_write_fixedlen_string.cpp
+++ b/packages/HighFive/src/examples/read_write_fixedlen_string.cpp
@@ -9,9 +9,7 @@
#include <iostream>
#include <string>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/read_write_raw_ptr.cpp b/packages/HighFive/src/examples/read_write_raw_ptr.cpp
index 5a95b03f53c10351e870d485b6d1e0e81aa683bd..b6cd9eda59e74e842a988f777ca5c95ffb26b702 100644
--- a/packages/HighFive/src/examples/read_write_raw_ptr.cpp
+++ b/packages/HighFive/src/examples/read_write_raw_ptr.cpp
@@ -11,9 +11,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("read_write_raw_ptr.h5");
const std::string dataset_name("array");
diff --git a/packages/HighFive/src/examples/read_write_single_scalar.cpp b/packages/HighFive/src/examples/read_write_single_scalar.cpp
index b32d9b3b51c4791db0b116637379c82604c65121..4b4c6887c96e47bffba798dff3cebfd2ce3cbccd 100644
--- a/packages/HighFive/src/examples/read_write_single_scalar.cpp
+++ b/packages/HighFive/src/examples/read_write_single_scalar.cpp
@@ -10,9 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("read_write_scalar.h5");
const std::string dataset_name("single_scalar");
diff --git a/packages/HighFive/src/examples/read_write_std_strings.cpp b/packages/HighFive/src/examples/read_write_std_strings.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7699e0c0c4177da12ccc6d0372c9e42f10691246
--- /dev/null
+++ b/packages/HighFive/src/examples/read_write_std_strings.cpp
@@ -0,0 +1,114 @@
+/*
+ * Copyright (c), 2023, Blue Brain Project, EPFL
+ *
+ * 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)
+ *
+ */
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include <highfive/H5File.hpp>
+#include <highfive/H5DataSet.hpp>
+#include <highfive/H5DataSpace.hpp>
+
+using namespace HighFive;
+
+// This example shows how to write (containers of) `std::string`
+// to dataset either as fixed or variable length HDF5 strings.
+// The feature is available from 2.8.0 onwards.
+int main(void) {
+ auto file = File("read_write_std_string.h5", File::Truncate);
+
+ // A string of length 3 in a buffer of size 4 bytes. We'll use "length" for
+ // the semantic length of the string, i.e. excluding the '\0' character and
+ // "size" to refer to the length of the buffer in which the string is stored.
+ // For null-terminated strings, the `size == length + 1`.
+ std::string ascii_string = "foo";
+ auto scalar_dataspace = DataSpace(DataSpace::dataspace_scalar);
+
+ // Just write the string:
+ file.createDataSet("single_automatic", ascii_string);
+
+ // The above results in writing the string as an HDF5 variable length UTF8
+ // string. In HDF5 a variable length string doesn't specify the length of
+ // the string. Variable length strings are always null-terminated.
+ auto variable_stringtype = VariableLengthStringType();
+ file.createDataSet("single_variable", scalar_dataspace, variable_stringtype)
+ .write(ascii_string);
+
+ // HDF5 also has the concept of fixed length string. In fixed length strings
+ // the size of the string, in bytes, is part of the datatype. The HDF5 API
+ // for fixed and variable length strings is distinct. Hence, when writing
+ // string that need to be read by other programs, it can matter if the string
+ // is stored as fixed or variable length.
+ //
+ // Important: The HDF5 string size is the size of the buffer required to
+ // store the string.
+ //
+ // We know that ascii_string requires 4 bytes to store, but want to store
+ // it in fixed length strings of length 8. Additionally, we promise that
+ // the strings are null-terminated. The character set defaults to ASCII.
+ auto fixed_stringtype = FixedLengthStringType(8, StringPadding::NullTerminated);
+ file.createDataSet("single_fixed_nullterm", scalar_dataspace, fixed_stringtype)
+ .write(ascii_string);
+
+ // When reading into an `std::string` it doesn't matter if the HDF5 datatype
+ // is fixed or variable length. HighFive will internally read into a buffer
+ // and then write to the final destination.
+ auto from_variable = file.getDataSet("single_variable").read<std::string>();
+ auto from_fixed = file.getDataSet("single_fixed_nullterm").read<std::string>();
+
+ // Note that because the fixed length string is null-terminated,
+ // `from_fixed.size() == ascii_string.size()` despite it being stored as a string of
+ // length 8.
+ std::cout << "from_variable = '" << from_variable << "' size = " << from_variable.size()
+ << "\n";
+ std::cout << "from_fixed = '" << from_fixed << "' size = " << from_fixed.size() << "\n";
+
+ // Fixed-length string don't have to be null-terminated. Their length could
+ // be defined simply by the known size of the buffer required to store the
+ // string. To deal with the situation where the string is shorter than the
+ // buffer, one defines a padding character. This must be either the null or
+ // space character. We'll show null-padded, space-padded works the same way.
+ auto fixed_nullpad = FixedLengthStringType(8, StringPadding::NullPadded);
+ file.createDataSet("single_fixed_nullpad", scalar_dataspace, fixed_nullpad).write(ascii_string);
+
+ // Note that because we only know that the string is padded with nulls, but we
+ // don't know if those nulls were part of the string to begin with. The full
+ // size of the buffer is read into the `std::string`. The length of the
+ // `std::string` is the size of the string type.
+ auto from_nullpad = file.getDataSet("single_fixed_nullpad").read<std::string>();
+ std::cout << "from_nullpad = '" << from_nullpad << "' size = " << from_nullpad.size() << "\n";
+
+ // Let's look at UTF8 strings. In HDF5 the size of a string is the size in
+ // bytes of the buffer required to store the string. A UTF8 symbol/character
+ // requires 1 to 4 bytes.
+ //
+ // The 'a' is 1 byte, the 'α' 2 bytes, therefore a total of 3 bytes (same
+ // as `utf8_string.size()`). Which including the null character fits into
+ // 8 bytes. However, 8 bytes would, in general not be enough to store 2
+ // UTF8 characters and the null character. Which would require 9 bytes.
+ std::string utf8_string = "aα";
+ auto fixed_utf8_type =
+ FixedLengthStringType(8, StringPadding::NullTerminated, CharacterSet::Utf8);
+ file.createDataSet("single_fixed_utf8", scalar_dataspace, fixed_utf8_type).write(utf8_string);
+
+ auto from_utf8 = file.getDataSet("single_fixed_utf8").read<std::string>();
+ std::cout << "from_utf8 = '" << from_utf8 << "' size = " << from_utf8.size() << "\n";
+
+ // Finally, containers of `std::string`s work analogously:
+ auto ascii_strings = std::vector<std::string>{"123", "456"};
+ file.createDataSet("multi_fixed_nullterm", DataSpace::From(ascii_strings), fixed_stringtype)
+ .write(ascii_strings);
+
+ auto ascii_strings_from_fixed =
+ file.getDataSet("multi_fixed_nullterm").read<std::vector<std::string>>();
+
+ // In order to see details of how each is stored in the HDF5 file use:
+ // h5dump read_write_std_string.h5
+
+ return 0;
+}
diff --git a/packages/HighFive/src/examples/read_write_vector_dataset.cpp b/packages/HighFive/src/examples/read_write_vector_dataset.cpp
index 605a231a534f96c48e45d94e16ccafa9fc8016ef..9718c1c2bc6d3cb915f6c504dc8d94aabfcccdf9 100644
--- a/packages/HighFive/src/examples/read_write_vector_dataset.cpp
+++ b/packages/HighFive/src/examples/read_write_vector_dataset.cpp
@@ -10,9 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/read_write_vector_dataset_references.cpp b/packages/HighFive/src/examples/read_write_vector_dataset_references.cpp
index 2d9a8ac89703ee6ba137e4e3d5b48b0b5eb619e1..ca08467682184a6c5244dc63707f097012b05c8b 100644
--- a/packages/HighFive/src/examples/read_write_vector_dataset_references.cpp
+++ b/packages/HighFive/src/examples/read_write_vector_dataset_references.cpp
@@ -10,10 +10,7 @@
#include <string>
#include <vector>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5Reference.hpp>
+#include <highfive/highfive.hpp>
// create a dataset 1D from a vector of int
void write_dataset() {
diff --git a/packages/HighFive/src/examples/readme_snippet.cpp b/packages/HighFive/src/examples/readme_snippet.cpp
index 5ba18243a88f57a1c3cade7bea229699b135234f..160dabce569c7d30dd75d7aee74686f1f339d1c1 100644
--- a/packages/HighFive/src/examples/readme_snippet.cpp
+++ b/packages/HighFive/src/examples/readme_snippet.cpp
@@ -1,4 +1,4 @@
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/renaming_objects.cpp b/packages/HighFive/src/examples/renaming_objects.cpp
index 0f2a93ac70fcdb63b0ef3f7dd57934e26652053b..f0759e52a2374c9e72f63289e0fe2e0cded9c1bc 100644
--- a/packages/HighFive/src/examples/renaming_objects.cpp
+++ b/packages/HighFive/src/examples/renaming_objects.cpp
@@ -1,8 +1,4 @@
-#include <highfive/H5File.hpp>
-#include <highfive/H5Group.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5Attribute.hpp>
+#include <highfive/highfive.hpp>
using namespace HighFive;
diff --git a/packages/HighFive/src/examples/select_by_id_dataset_cpp11.cpp b/packages/HighFive/src/examples/select_by_id_dataset_cpp11.cpp
index 2e0b6f149e824257b575f9193d7a9ea5cfaadc0c..973c57435fc26ff8a2f8e1c6232ed2c837691cb6 100644
--- a/packages/HighFive/src/examples/select_by_id_dataset_cpp11.cpp
+++ b/packages/HighFive/src/examples/select_by_id_dataset_cpp11.cpp
@@ -11,9 +11,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("select_partial_string.h5");
const std::string dataset_name("message");
diff --git a/packages/HighFive/src/examples/select_partial_dataset_cpp11.cpp b/packages/HighFive/src/examples/select_partial_dataset_cpp11.cpp
index a21f67ed1c29d6d75a77edfebe21b866c9be2903..1e480c1603f460891d6b64b77f9e4d39500cab1c 100644
--- a/packages/HighFive/src/examples/select_partial_dataset_cpp11.cpp
+++ b/packages/HighFive/src/examples/select_partial_dataset_cpp11.cpp
@@ -11,9 +11,7 @@
#include <string>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
+#include <highfive/highfive.hpp>
const std::string file_name("select_partial_example.h5");
const std::string dataset_name("dset");
diff --git a/packages/HighFive/tests/test_dependent_library/include/simpleton.hpp b/packages/HighFive/tests/test_dependent_library/include/simpleton.hpp
index 279187a713e9bbe7b26b13eda7ac5966bf3d134c..b98a09fda04045dbcb72444feff720cbb9db84c4 100644
--- a/packages/HighFive/tests/test_dependent_library/include/simpleton.hpp
+++ b/packages/HighFive/tests/test_dependent_library/include/simpleton.hpp
@@ -3,21 +3,7 @@
// Include all headers here to catch any missing `inline` statements, since
// they will be included by two different compilation units.
-#include <highfive/H5Attribute.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5DataType.hpp>
-#include <highfive/H5Easy.hpp>
-#include <highfive/H5Exception.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5FileDriver.hpp>
-#include <highfive/H5Group.hpp>
-#include <highfive/H5Object.hpp>
-#include <highfive/H5PropertyList.hpp>
-#include <highfive/H5Reference.hpp>
-#include <highfive/H5Selection.hpp>
-#include <highfive/H5Utility.hpp>
-#include <highfive/H5Version.hpp>
+#include <highfive/highfive.hpp>
// Boost should always be found in this setup
#include <boost/numeric/ublas/matrix.hpp>
diff --git a/packages/HighFive/tests/unit/test_all_types.cpp b/packages/HighFive/tests/unit/test_all_types.cpp
index ed265e670424c01e6431cf57a131ec8b7f299539..d74579af6b23176cd99bd9436d690e623fdc5f9b 100644
--- a/packages/HighFive/tests/unit/test_all_types.cpp
+++ b/packages/HighFive/tests/unit/test_all_types.cpp
@@ -8,21 +8,15 @@
*/
#include <string>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5Group.hpp>
-#include <highfive/H5Reference.hpp>
-#include <highfive/H5Utility.hpp>
-
#include <catch2/catch_template_test_macros.hpp>
+#include <highfive/highfive.hpp>
#include "tests_high_five.hpp"
using namespace HighFive;
TEMPLATE_TEST_CASE("Scalar in DataSet", "[Types]", bool, std::string) {
- const std::string FILE_NAME("Test_type.h5");
+ const std::string FILE_NAME("rw_dataset_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
TestType t1{};
@@ -52,7 +46,7 @@ TEMPLATE_TEST_CASE("Scalar in DataSet", "[Types]", bool, std::string) {
}
TEMPLATE_PRODUCT_TEST_CASE("Scalar in std::vector", "[Types]", std::vector, (bool, std::string)) {
- const std::string FILE_NAME("Test_vector.h5");
+ const std::string FILE_NAME("rw_dataset_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
TestType t1(5);
@@ -84,7 +78,7 @@ TEMPLATE_PRODUCT_TEST_CASE("Scalar in std::vector<std::vector>",
"[Types]",
std::vector,
(bool, std::string)) {
- const std::string FILE_NAME("Test_vector_vector.h5");
+ const std::string FILE_NAME("rw_dataset_vector_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
std::vector<TestType> t1(5);
for (auto&& e: t1) {
@@ -118,7 +112,7 @@ TEMPLATE_PRODUCT_TEST_CASE("Scalar in std::vector<std::vector>",
}
TEMPLATE_TEST_CASE("Scalar in std::array", "[Types]", bool, std::string) {
- const std::string FILE_NAME("Test_array.h5");
+ const std::string FILE_NAME("rw_dataset_array_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
std::array<TestType, 5> t1{};
@@ -149,7 +143,7 @@ TEMPLATE_TEST_CASE("Scalar in std::array", "[Types]", bool, std::string) {
}
TEMPLATE_TEST_CASE("Scalar in std::vector<std::array>", "[Types]", bool, std::string) {
- const std::string FILE_NAME("Test_vector_array.h5");
+ const std::string FILE_NAME("rw_dataset_vector_array_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
std::vector<std::array<TestType, 6>> t1(5);
@@ -182,7 +176,7 @@ TEMPLATE_TEST_CASE("Scalar in std::vector<std::array>", "[Types]", bool, std::st
#if HIGHFIVE_CXX_STD >= 17
TEMPLATE_PRODUCT_TEST_CASE("Scalar in std::vector<std::byte>", "[Types]", std::vector, std::byte) {
- const std::string FILE_NAME("Test_vector_byte.h5");
+ const std::string FILE_NAME("rw_dataset_vector_" + typeNameHelper<TestType>() + ".h5");
const std::string DATASET_NAME("dset");
TestType t1(5, std::byte(0xCD));
diff --git a/packages/HighFive/tests/unit/tests_high_five.hpp b/packages/HighFive/tests/unit/tests_high_five.hpp
index 2d23c0879c0828dcd9e2ed8f0e282c6d34869171..0ebd58c44890e65ddbf4ee149d6c13c6662a15e3 100644
--- a/packages/HighFive/tests/unit/tests_high_five.hpp
+++ b/packages/HighFive/tests/unit/tests_high_five.hpp
@@ -12,6 +12,9 @@
#include <string>
#include <vector>
#include <tuple>
+#include <sstream>
+#include <functional>
+#include <iomanip>
// We don't need windows specific functionality. However, to better detect defects caused by macros,
// we include this header.
@@ -162,16 +165,22 @@ struct ContentGenerate<std::string> {
template <typename T>
inline std::string typeNameHelper() {
std::string name = typeid(T).name();
-#if defined(WIN32)
- // Replace illegal windows file path characters
std::replace(std::begin(name), std::end(name), ' ', '_');
std::replace(std::begin(name), std::end(name), '<', '_');
std::replace(std::begin(name), std::end(name), '>', '_');
std::replace(std::begin(name), std::end(name), ':', '_');
-#endif
- return name;
+
+ if (name.size() > 64) {
+ std::stringstream hash;
+ hash << std::hex << std::hash<std::string>{}(name);
+
+ return hash.str();
+ } else {
+ return name;
+ }
}
+
template <typename ElemT, typename DataT>
inline HighFive::DataSet readWriteDataset(const DataT& ndvec,
DataT& result,
@@ -193,4 +202,4 @@ inline HighFive::DataSet readWriteDataset(const DataT& ndvec,
dataset.read(result);
return dataset;
-}
\ No newline at end of file
+}
diff --git a/packages/HighFive/tests/unit/tests_high_five_base.cpp b/packages/HighFive/tests/unit/tests_high_five_base.cpp
index bba8ded889b600101b0b2a6143cd4931aabd9612..899170d9328683b2832e592871ff7fac917ea58e 100644
--- a/packages/HighFive/tests/unit/tests_high_five_base.cpp
+++ b/packages/HighFive/tests/unit/tests_high_five_base.cpp
@@ -18,18 +18,11 @@
#include <typeinfo>
#include <vector>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5File.hpp>
-#include <highfive/H5Group.hpp>
-#include <highfive/H5Reference.hpp>
-#include <highfive/H5Utility.hpp>
-#include <highfive/H5Version.hpp>
-
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_template_test_macros.hpp>
#include <catch2/matchers/catch_matchers_vector.hpp>
+#include <highfive/highfive.hpp>
#include "tests_high_five.hpp"
using namespace HighFive;
@@ -317,13 +310,21 @@ TEST_CASE("Test allocation time") {
CHECK(alloc_size == data.size() * sizeof(decltype(data)::value_type));
}
+/*
+ * Test to ensure legacy support: DataSet used to have a default constructor.
+ * However, it is not useful to have a DataSet object that does not actually
+ * refer to a dataset in a file. Hence, the the default constructor was
+ * deprecated.
+ * This test is to ensure that the constructor is not accidentally removed and
+ * thereby break users' code.
+ */
TEST_CASE("Test default constructors") {
- const std::string file_name("h5_group_test.h5");
+ const std::string file_name("h5_default_ctors.h5");
const std::string dataset_name("dset");
File file(file_name, File::Truncate);
auto ds = file.createDataSet(dataset_name, std::vector<int>{1, 2, 3, 4, 5});
- DataSet d2; // deprecated as it constructs unsafe objects
+ DataSet d2; // expect deprecation warning, as it constructs unsafe object
// d2.getFile(); // runtime error
CHECK(!d2.isValid());
d2 = ds; // copy
@@ -2439,7 +2440,7 @@ TEST_CASE("HighFiveHardLinks Group") {
}
TEST_CASE("HighFiveRename") {
- File file("move.h5", File::ReadWrite | File::Create | File::Truncate);
+ File file("h5_rename.h5", File::ReadWrite | File::Create | File::Truncate);
int number = 100;
@@ -2464,7 +2465,7 @@ TEST_CASE("HighFiveRename") {
}
TEST_CASE("HighFiveRenameRelative") {
- File file("move.h5", File::ReadWrite | File::Create | File::Truncate);
+ File file("h5_rename_relative.h5", File::ReadWrite | File::Create | File::Truncate);
Group group = file.createGroup("group");
int number = 100;
@@ -2928,6 +2929,229 @@ TEST_CASE("HighFiveReadType") {
CHECK(t4 == t3);
}
+class ForwardToAttribute {
+ public:
+ ForwardToAttribute(const HighFive::File& file)
+ : _file(file) {}
+
+ template <class T>
+ HighFive::Attribute create(const std::string& name, const T& value) {
+ return _file.createAttribute(name, value);
+ }
+
+ HighFive::Attribute create(const std::string& name,
+ const HighFive::DataSpace filespace,
+ const HighFive::DataType& datatype) {
+ return _file.createAttribute(name, filespace, datatype);
+ }
+
+ HighFive::Attribute get(const std::string& name) {
+ return _file.getAttribute(name);
+ }
+
+ private:
+ HighFive::File _file;
+};
+
+class ForwardToDataSet {
+ public:
+ ForwardToDataSet(const HighFive::File& file)
+ : _file(file) {}
+
+ template <class T>
+ HighFive::DataSet create(const std::string& name, const T& value) {
+ return _file.createDataSet(name, value);
+ }
+
+ HighFive::DataSet create(const std::string& name,
+ const HighFive::DataSpace filespace,
+ const HighFive::DataType& datatype) {
+ return _file.createDataSet(name, filespace, datatype);
+ }
+
+ HighFive::DataSet get(const std::string& name) {
+ return _file.getDataSet(name);
+ }
+
+ private:
+ HighFive::File _file;
+};
+
+template <class Proxy>
+void check_single_string(Proxy proxy, size_t string_length) {
+ auto value = std::string(string_length, 'o');
+ auto dataspace = DataSpace::From(value);
+
+ auto n_chars = value.size() + 1;
+ auto n_chars_overlength = n_chars + 10;
+ auto fixed_length = FixedLengthStringType(n_chars, StringPadding::NullTerminated);
+ auto overlength_nullterm = FixedLengthStringType(n_chars_overlength,
+ StringPadding::NullTerminated);
+ auto overlength_nullpad = FixedLengthStringType(n_chars_overlength, StringPadding::NullPadded);
+ auto overlength_spacepad = FixedLengthStringType(n_chars_overlength,
+ StringPadding::SpacePadded);
+ auto variable_length = VariableLengthStringType();
+
+ SECTION("automatic") {
+ proxy.create("auto", value);
+ REQUIRE(proxy.get("auto").template read<std::string>() == value);
+ }
+
+ SECTION("fixed length") {
+ proxy.create("fixed", dataspace, fixed_length).write(value);
+ REQUIRE(proxy.get("fixed").template read<std::string>() == value);
+ }
+
+ SECTION("overlength null-terminated") {
+ proxy.create("overlength_nullterm", dataspace, overlength_nullterm).write(value);
+ REQUIRE(proxy.get("overlength_nullterm").template read<std::string>() == value);
+ }
+
+ SECTION("overlength null-padded") {
+ proxy.create("overlength_nullpad", dataspace, overlength_nullpad).write(value);
+ auto expected = std::string(n_chars_overlength, '\0');
+ expected.replace(0, value.size(), value.data());
+ REQUIRE(proxy.get("overlength_nullpad").template read<std::string>() == expected);
+ }
+
+ SECTION("overlength space-padded") {
+ proxy.create("overlength_spacepad", dataspace, overlength_spacepad).write(value);
+ auto expected = std::string(n_chars_overlength, ' ');
+ expected.replace(0, value.size(), value.data());
+ REQUIRE(proxy.get("overlength_spacepad").template read<std::string>() == expected);
+ }
+
+ SECTION("variable length") {
+ proxy.create("variable", dataspace, variable_length).write(value);
+ REQUIRE(proxy.get("variable").template read<std::string>() == value);
+ }
+}
+
+template <class Proxy>
+void check_multiple_string(Proxy proxy, size_t string_length) {
+ using value_t = std::vector<std::string>;
+ auto value = value_t{std::string(string_length, 'o'), std::string(string_length, 'x')};
+
+ auto dataspace = DataSpace::From(value);
+
+ auto string_overlength = string_length + 10;
+ auto onpoint_nullpad = FixedLengthStringType(string_length, StringPadding::NullPadded);
+ auto onpoint_spacepad = FixedLengthStringType(string_length, StringPadding::SpacePadded);
+
+ auto overlength_nullterm = FixedLengthStringType(string_overlength,
+ StringPadding::NullTerminated);
+ auto overlength_nullpad = FixedLengthStringType(string_overlength, StringPadding::NullPadded);
+ auto overlength_spacepad = FixedLengthStringType(string_overlength, StringPadding::SpacePadded);
+ auto variable_length = VariableLengthStringType();
+
+ auto check = [](const value_t actual, const value_t& expected) {
+ REQUIRE(actual.size() == expected.size());
+ for (size_t i = 0; i < actual.size(); ++i) {
+ REQUIRE(actual[i] == expected[i]);
+ }
+ };
+
+ SECTION("automatic") {
+ proxy.create("auto", value);
+ check(proxy.get("auto").template read<value_t>(), value);
+ }
+
+ SECTION("variable length") {
+ proxy.create("variable", dataspace, variable_length).write(value);
+ check(proxy.get("variable").template read<value_t>(), value);
+ }
+
+ auto make_padded_reference = [&](char pad, size_t n) {
+ auto expected = std::vector<std::string>(value.size(), std::string(n, pad));
+ for (size_t i = 0; i < value.size(); ++i) {
+ expected[i].replace(0, value[i].size(), value[i].data());
+ }
+
+ return expected;
+ };
+
+ auto check_fixed_length = [&](const std::string& label, size_t length) {
+ SECTION(label + " null-terminated") {
+ auto datatype = FixedLengthStringType(length + 1, StringPadding::NullTerminated);
+ proxy.create(label + "_nullterm", dataspace, datatype).write(value);
+ check(proxy.get(label + "_nullterm").template read<value_t>(), value);
+ }
+
+ SECTION(label + " null-padded") {
+ auto datatype = FixedLengthStringType(length, StringPadding::NullPadded);
+ proxy.create(label + "_nullpad", dataspace, datatype).write(value);
+ auto expected = make_padded_reference('\0', length);
+ check(proxy.get(label + "_nullpad").template read<value_t>(), expected);
+ }
+
+ SECTION(label + " space-padded") {
+ auto datatype = FixedLengthStringType(length, StringPadding::SpacePadded);
+ proxy.create(label + "_spacepad", dataspace, datatype).write(value);
+ auto expected = make_padded_reference(' ', length);
+ check(proxy.get(label + "_spacepad").template read<value_t>(), expected);
+ }
+ };
+
+ check_fixed_length("onpoint", string_length);
+ check_fixed_length("overlength", string_length + 5);
+
+
+ SECTION("underlength null-terminated") {
+ auto datatype = FixedLengthStringType(string_length, StringPadding::NullTerminated);
+ REQUIRE_THROWS(proxy.create("underlength_nullterm", dataspace, datatype).write(value));
+ }
+
+ SECTION("underlength nullpad") {
+ auto datatype = FixedLengthStringType(string_length - 1, StringPadding::NullPadded);
+ REQUIRE_THROWS(proxy.create("underlength_nullpad", dataspace, datatype).write(value));
+ }
+
+ SECTION("underlength spacepad") {
+ auto datatype = FixedLengthStringType(string_length - 1, StringPadding::NullTerminated);
+ REQUIRE_THROWS(proxy.create("underlength_spacepad", dataspace, datatype).write(value));
+ }
+}
+
+TEST_CASE("HighFiveSTDString (dataset, single, short)") {
+ File file("std_string_dataset_single_short.h5", File::Truncate);
+ check_single_string(ForwardToDataSet(file), 3);
+}
+
+TEST_CASE("HighFiveSTDString (attribute, single, short)") {
+ File file("std_string_attribute_single_short.h5", File::Truncate);
+ check_single_string(ForwardToAttribute(file), 3);
+}
+
+TEST_CASE("HighFiveSTDString (dataset, single, long)") {
+ File file("std_string_dataset_single_long.h5", File::Truncate);
+ check_single_string(ForwardToDataSet(file), 256);
+}
+
+TEST_CASE("HighFiveSTDString (attribute, single, long)") {
+ File file("std_string_attribute_single_long.h5", File::Truncate);
+ check_single_string(ForwardToAttribute(file), 256);
+}
+
+TEST_CASE("HighFiveSTDString (dataset, multiple, short)") {
+ File file("std_string_dataset_multiple_short.h5", File::Truncate);
+ check_multiple_string(ForwardToDataSet(file), 3);
+}
+
+TEST_CASE("HighFiveSTDString (attribute, multiple, short)") {
+ File file("std_string_attribute_multiple_short.h5", File::Truncate);
+ check_multiple_string(ForwardToAttribute(file), 3);
+}
+
+TEST_CASE("HighFiveSTDString (dataset, multiple, long)") {
+ File file("std_string_dataset_multiple_short.h5", File::Truncate);
+ check_multiple_string(ForwardToDataSet(file), 256);
+}
+
+TEST_CASE("HighFiveSTDString (attribute, multiple, long)") {
+ File file("std_string_attribute_multiple_short.h5", File::Truncate);
+ check_multiple_string(ForwardToAttribute(file), 256);
+}
+
TEST_CASE("HighFiveFixedString") {
const std::string file_name("array_atomic_types.h5");
const std::string group_1("group1");
@@ -2962,6 +3186,7 @@ TEST_CASE("HighFiveFixedString") {
file.createDataSet<char[10]>("ds4", DataSpace(2)).write(strings_fixed);
}
+
{ // Cant convert flex-length to fixed-length
const char* buffer[] = {"abcd", "1234"};
SilenceHDF5 silencer;
diff --git a/packages/HighFive/tests/unit/tests_high_five_easy.cpp b/packages/HighFive/tests/unit/tests_high_five_easy.cpp
index 64a7706740fe441990884284d81d0ed4700c6efd..e003c323401a9460332883abd618fef10a9a169d 100644
--- a/packages/HighFive/tests/unit/tests_high_five_easy.cpp
+++ b/packages/HighFive/tests/unit/tests_high_five_easy.cpp
@@ -56,40 +56,66 @@ TEST_CASE("H5Easy_Compression") {
}
TEST_CASE("H5Easy_scalar") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_scalar.h5", H5Easy::File::Overwrite);
double a = 1.2345;
int b = 12345;
std::string c = "12345";
+ std::complex<double> d = std::complex<double>(1.2345, -5.4321);
+ std::complex<int32_t> e = std::complex<int32_t>(12345, -54321);
H5Easy::dump(file, "/path/to/a", a);
H5Easy::dump(file, "/path/to/b", b);
H5Easy::dump(file, "/path/to/c", c);
H5Easy::dump(file, "/path/to/c", c, H5Easy::DumpMode::Overwrite);
+ H5Easy::dump(file, "/path/to/d", d);
+ H5Easy::dump(file, "/path/to/e", e);
double a_r = H5Easy::load<double>(file, "/path/to/a");
int b_r = H5Easy::load<int>(file, "/path/to/b");
std::string c_r = H5Easy::load<std::string>(file, "/path/to/c");
+ std::complex<double> d_r = H5Easy::load<std::complex<double>>(file, "/path/to/d");
+ std::complex<int32_t> e_r = H5Easy::load<std::complex<int32_t>>(file, "/path/to/e");
CHECK(a == a_r);
CHECK(b == b_r);
CHECK(c == c_r);
+ CHECK(d == d_r);
+ CHECK(e == e_r);
}
TEST_CASE("H5Easy_vector1d") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_vector1d.h5", H5Easy::File::Overwrite);
std::vector<size_t> a = {1, 2, 3, 4, 5};
+ std::vector<std::complex<double>> b = {std::complex<double>(1, .1),
+ std::complex<double>(2, -.4),
+ std::complex<double>(3, .9),
+ std::complex<double>(4, -.16),
+ std::complex<double>(5, .25)};
+ std::vector<std::complex<int32_t>> c = {std::complex<int32_t>(1, -5),
+ std::complex<int32_t>(2, -4),
+ std::complex<int32_t>(3, -3),
+ std::complex<int32_t>(4, -2),
+ std::complex<int32_t>(5, -1)};
H5Easy::dump(file, "/path/to/a", a);
+ H5Easy::dump(file, "/path/to/b", b);
+ H5Easy::dump(file, "/path/to/c", c);
std::vector<size_t> a_r = H5Easy::load<std::vector<size_t>>(file, "/path/to/a");
+ std::vector<std::complex<double>> b_r =
+ H5Easy::load<std::vector<std::complex<double>>>(file, "/path/to/b");
+ std::vector<std::complex<int32_t>> c_r =
+ H5Easy::load<std::vector<std::complex<int32_t>>>(file, "/path/to/c");
CHECK(a == a_r);
+ CHECK(b == b_r);
+ CHECK(c == c_r);
}
TEST_CASE("H5Easy_vector2d") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_vector2d.h5", H5Easy::File::Overwrite);
std::vector<std::vector<size_t>> a({{0, 1}, {2, 3}, {4, 5}});
@@ -101,7 +127,7 @@ TEST_CASE("H5Easy_vector2d") {
}
TEST_CASE("H5Easy_vector2d_compression") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_vector2d_compression.h5", H5Easy::File::Overwrite);
std::vector<std::vector<size_t>> a({{0, 1}, {2, 3}, {4, 5}});
@@ -118,7 +144,7 @@ TEST_CASE("H5Easy_vector2d_compression") {
}
TEST_CASE("H5Easy_vector3d") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_vector3d.h5", H5Easy::File::Overwrite);
using type = std::vector<std::vector<std::vector<size_t>>>;
@@ -132,7 +158,7 @@ TEST_CASE("H5Easy_vector3d") {
}
TEST_CASE("H5Easy_Attribute_scalar") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_attribute_scalar.h5", H5Easy::File::Overwrite);
double a = 1.2345;
int b = 12345;
@@ -155,7 +181,7 @@ TEST_CASE("H5Easy_Attribute_scalar") {
#ifdef H5_USE_XTENSOR
TEST_CASE("H5Easy_extend1d") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_extend1d.h5", H5Easy::File::Overwrite);
for (size_t i = 0; i < 10; ++i) {
H5Easy::dump(file, "/path/to/A", i, {i});
@@ -172,7 +198,7 @@ TEST_CASE("H5Easy_extend1d") {
}
TEST_CASE("H5Easy_extend2d") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_extend2d.h5", H5Easy::File::Overwrite);
for (size_t i = 0; i < 10; ++i) {
for (size_t j = 0; j < 5; ++j) {
@@ -193,7 +219,7 @@ TEST_CASE("H5Easy_extend2d") {
}
TEST_CASE("H5Easy_xtensor") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_xtensor.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
@@ -209,7 +235,7 @@ TEST_CASE("H5Easy_xtensor") {
}
TEST_CASE("H5Easy_xarray") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_xarray.h5", H5Easy::File::Overwrite);
xt::xarray<double> A = 100. * xt::random::randn<double>({20, 5});
xt::xarray<int> B = A;
@@ -225,7 +251,7 @@ TEST_CASE("H5Easy_xarray") {
}
TEST_CASE("H5Easy_view") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_view.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
auto a = xt::view(A, xt::range(0, 10), xt::range(0, 10));
@@ -238,7 +264,7 @@ TEST_CASE("H5Easy_view") {
}
TEST_CASE("H5Easy_xtensor_compress") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_xtensor_compress.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
@@ -260,7 +286,7 @@ TEST_CASE("H5Easy_xtensor_compress") {
}
TEST_CASE("H5Easy_Attribute_xtensor") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_attribute_xtensor.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
@@ -280,7 +306,7 @@ TEST_CASE("H5Easy_Attribute_xtensor") {
#ifdef H5_USE_EIGEN
TEST_CASE("H5Easy_Eigen_MatrixX") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_MatrixX.h5", H5Easy::File::Overwrite);
Eigen::MatrixXd A = 100. * Eigen::MatrixXd::Random(20, 5);
Eigen::MatrixXi B = A.cast<int>();
@@ -296,7 +322,7 @@ TEST_CASE("H5Easy_Eigen_MatrixX") {
}
TEST_CASE("H5Easy_Eigen_ArrayXX") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_ArrayXX.h5", H5Easy::File::Overwrite);
Eigen::ArrayXXf A = 100. * Eigen::ArrayXXf::Random(20, 5);
Eigen::ArrayXXi B = A.cast<int>();
@@ -312,7 +338,7 @@ TEST_CASE("H5Easy_Eigen_ArrayXX") {
}
TEST_CASE("H5Easy_Eigen_ArrayX") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_ArrayX.h5", H5Easy::File::Overwrite);
Eigen::ArrayXf A = Eigen::ArrayXf::Random(50);
Eigen::ArrayXi B = A.cast<int>();
@@ -329,7 +355,7 @@ TEST_CASE("H5Easy_Eigen_ArrayX") {
TEST_CASE("H5Easy_Eigen_VectorX") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_VectorX.h5", H5Easy::File::Overwrite);
Eigen::VectorXd A = 100. * Eigen::VectorXd::Random(20);
Eigen::VectorXi B = A.cast<int>();
@@ -348,7 +374,7 @@ TEST_CASE("H5Easy_Eigen_MatrixXRowMajor") {
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXd;
typedef Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXi;
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("H5Easy_Eigen_MatrixXRowMajor.h5", H5Easy::File::Overwrite);
MatrixXd A = 100. * MatrixXd::Random(20, 5);
MatrixXi B = A.cast<int>();
@@ -367,7 +393,7 @@ TEST_CASE("H5Easy_Eigen_VectorXRowMajor") {
typedef Eigen::Matrix<double, 1, Eigen::Dynamic, Eigen::RowMajor> VectorXd;
typedef Eigen::Matrix<int, 1, Eigen::Dynamic, Eigen::RowMajor> VectorXi;
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_VectorXRowMajor.h5", H5Easy::File::Overwrite);
VectorXd A = 100. * VectorXd::Random(20);
VectorXi B = A.cast<int>();
@@ -383,7 +409,7 @@ TEST_CASE("H5Easy_Eigen_VectorXRowMajor") {
}
TEST_CASE("H5Easy_Eigen_Map") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_eigen_Map.h5", H5Easy::File::Overwrite);
std::vector<int> A = {1, 2, 3, 4, 5, 6, 7, 8, 9};
Eigen::Map<Eigen::VectorXi> mapped_vector(A.data(), static_cast<int>(A.size()));
@@ -396,7 +422,7 @@ TEST_CASE("H5Easy_Eigen_Map") {
}
TEST_CASE("H5Easy_Attribute_Eigen_MatrixX") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_attribute_eigen_MatrixX.h5", H5Easy::File::Overwrite);
Eigen::MatrixXd A = 100. * Eigen::MatrixXd::Random(20, 5);
Eigen::MatrixXi B = A.cast<int>();
@@ -415,7 +441,7 @@ TEST_CASE("H5Easy_Attribute_Eigen_MatrixX") {
#ifdef H5_USE_OPENCV
TEST_CASE("H5Easy_OpenCV_Mat_") {
- H5Easy::File file("test.h5", H5Easy::File::Overwrite);
+ H5Easy::File file("h5easy_opencv_Mat_.h5", H5Easy::File::Overwrite);
using T = typename cv::Mat_<double>;
@@ -436,6 +462,7 @@ TEST_CASE("H5Easy_OpenCV_Mat_") {
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "attr", A);
+
T A_r = H5Easy::load<T>(file, "/path/to/A");
T B_r = H5Easy::loadAttribute<T>(file, "/path/to/A", "attr");
diff --git a/packages/HighFive/tests/unit/tests_high_five_multi_dims.cpp b/packages/HighFive/tests/unit/tests_high_five_multi_dims.cpp
index 4a4b8231cef368fc977825c116b916ff43ecc6e3..442f1c9cc5d92ceb3a4ef4729d03a724ab900e8c 100644
--- a/packages/HighFive/tests/unit/tests_high_five_multi_dims.cpp
+++ b/packages/HighFive/tests/unit/tests_high_five_multi_dims.cpp
@@ -10,8 +10,7 @@
#include <string>
#include <iostream>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5File.hpp>
+#include <highfive/highfive.hpp>
#ifdef H5_USE_BOOST
diff --git a/packages/HighFive/tests/unit/tests_high_five_parallel.cpp b/packages/HighFive/tests/unit/tests_high_five_parallel.cpp
index b5518f48c661628b38ee1c284e4529d0fac83b95..8b096205e8528df17c6ff03cb68c592c81e0c9bd 100644
--- a/packages/HighFive/tests/unit/tests_high_five_parallel.cpp
+++ b/packages/HighFive/tests/unit/tests_high_five_parallel.cpp
@@ -13,15 +13,11 @@
#include <typeinfo>
#include <vector>
-#include <highfive/H5File.hpp>
-#include <highfive/H5DataSet.hpp>
-#include <highfive/H5DataSpace.hpp>
-#include <highfive/H5Group.hpp>
-
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_template_test_macros.hpp>
#include <catch2/catch_session.hpp>
+#include <highfive/highfive.hpp>
#include "tests_high_five.hpp"
using namespace HighFive;