Merge branch 'master' into cornu/remove_filedriver_mpiofiledriver

BlueBrain · Feb 9, 2024 · 8cbfa98 · 8cbfa98
2 parents 1128b33 + 4914dce
commit 8cbfa98
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Showing 19 changed files with 32 additions and 99 deletions.
diff --git a/doc/migration_guide.md b/doc/migration_guide.md
@@ -61,7 +61,7 @@ When genuinely performing a "raw read", one must replace `read` with
 `read_raw`. For example:
 
 ```
-double x = malloc(2*3 * sizeof(double));
+double* x = malloc(2*3 * sizeof(double));
 dset.read_raw(x);
 ```
 is correct in `v3`.

diff --git a/include/highfive/H5Attribute.hpp b/include/highfive/H5Attribute.hpp
@@ -113,16 +113,6 @@ class Attribute: public Object, public PathTraits<Attribute> {
     template <typename T>
     void read(T& array) const;
 
-    /// \brief Read the attribute into a pre-allocated buffer.
-    /// \deprecated use `read(T&` or `read_raw`.
-    template <typename T>
-    void read(T* array, const DataType& mem_datatype) const;
-
-    /// \brief Read the attribute into a buffer.
-    /// \deprecated use `read(T&` or `read_raw`.
-    template <typename T>
-    void read(T* array) const;
-
     /// \brief Read the attribute into a pre-allocated buffer.
     /// \param array A pointer to the first byte of sufficient pre-allocated memory.
     /// \param mem_datatype The DataType of the array.

diff --git a/include/highfive/bits/H5Attribute_misc.hpp b/include/highfive/bits/H5Attribute_misc.hpp
@@ -101,11 +101,6 @@ inline void Attribute::read(T& array) const {
     }
 }
 
-template <typename T>
-inline void Attribute::read(T* array, const DataType& mem_datatype) const {
-    read_raw(array, mem_datatype);
-}
-
 template <typename T>
 inline void Attribute::read_raw(T* array, const DataType& mem_datatype) const {
     static_assert(!std::is_const<T>::value,
@@ -114,11 +109,6 @@ inline void Attribute::read_raw(T* array, const DataType& mem_datatype) const {
     detail::h5a_read(getId(), mem_datatype.getId(), static_cast<void*>(array));
 }
 
-template <typename T>
-inline void Attribute::read(T* array) const {
-    read_raw(array);
-}
-
 template <typename T>
 inline void Attribute::read_raw(T* array) const {
     using element_type = typename details::inspector<T>::base_type;

diff --git a/include/highfive/bits/H5DataType_misc.hpp b/include/highfive/bits/H5DataType_misc.hpp
@@ -520,7 +520,3 @@ inline DataType create_datatype<bool>() {
 }
 
 }  // namespace HighFive
-
-#ifdef H5_USE_HALF_FLOAT
-#include <highfive/half_float.hpp>
-#endif
diff --git a/include/highfive/bits/H5Inspector_misc.hpp b/include/highfive/bits/H5Inspector_misc.hpp
@@ -640,11 +640,3 @@ struct inspector<T[N]> {
 
 }  // namespace details
 }  // namespace HighFive
-
-#ifdef H5_USE_BOOST
-#include <highfive/boost.hpp>
-#endif
-
-#ifdef H5_USE_EIGEN
-#include <highfive/eigen.hpp>
-#endif
diff --git a/include/highfive/bits/H5Slice_traits.hpp b/include/highfive/bits/H5Slice_traits.hpp
@@ -303,36 +303,6 @@ class SliceTraits {
     template <typename T>
     void read(T& array, const DataTransferProps& xfer_props = DataTransferProps()) const;
 
-    ///
-    /// Read the entire dataset into a raw buffer
-    ///
-    /// \deprecated Use `read_raw` instead.
-    ///
-    /// No dimensionality checks will be performed, it is the user's
-    /// responsibility to ensure that the right amount of space has been
-    /// allocated.
-    /// \param array: A buffer containing enough space for the data
-    /// \param dtype: The datatype of elements of the in memory buffer.
-    /// \param xfer_props: Data Transfer properties
-    template <typename T>
-    void read(T* array,
-              const DataType& dtype,
-              const DataTransferProps& xfer_props = DataTransferProps()) const;
-
-    ///
-    /// Read the entire dataset into a raw buffer
-    ///
-    /// \deprecated Use `read_raw` instead.
-    ///
-    /// Same as `read(T*, const DataType&, const DataTransferProps&)`. However,
-    /// this overload deduces the HDF5 datatype of the element of `array` from
-    /// `T`. Note, that the file datatype is already fixed.
-    ///
-    /// \param array: A buffer containing enough space for the data
-    /// \param xfer_props: Data Transfer properties
-    template <typename T>
-    void read(T* array, const DataTransferProps& xfer_props = DataTransferProps()) const;
-
     ///
     /// Read the entire dataset into a raw buffer
     ///

diff --git a/include/highfive/bits/H5Slice_traits_misc.hpp b/include/highfive/bits/H5Slice_traits_misc.hpp
@@ -207,20 +207,6 @@ inline void SliceTraits<Derivate>::read(T& array, const DataTransferProps& xfer_
     }
 }
 
-template <typename Derivate>
-template <typename T>
-inline void SliceTraits<Derivate>::read(T* array,
-                                        const DataType& mem_datatype,
-                                        const DataTransferProps& xfer_props) const {
-    read_raw(array, mem_datatype, xfer_props);
-}
-
-template <typename Derivate>
-template <typename T>
-inline void SliceTraits<Derivate>::read(T* array, const DataTransferProps& xfer_props) const {
-    read_raw(array, xfer_props);
-}
-
 
 template <typename Derivate>
 template <typename T>

diff --git a/include/highfive/boost.hpp b/include/highfive/boost.hpp
@@ -1,12 +1,9 @@
 #pragma once
-#ifdef H5_USE_BOOST
 
 #include "bits/H5Inspector_decl.hpp"
 #include "H5Exception.hpp"
 
 #include <boost/multi_array.hpp>
-// starting Boost 1.64, serialization header must come before ublas
-#include <boost/serialization/vector.hpp>
 #include <boost/numeric/ublas/matrix.hpp>
 
 namespace HighFive {
@@ -160,5 +157,3 @@ struct inspector<boost::numeric::ublas::matrix<T>> {
 
 }  // namespace details
 }  // namespace HighFive
-
-#endif
diff --git a/include/highfive/eigen.hpp b/include/highfive/eigen.hpp
@@ -1,5 +1,4 @@
 #pragma once
-#ifdef H5_USE_EIGEN
 
 #include "bits/H5Inspector_decl.hpp"
 #include "H5Exception.hpp"
@@ -89,5 +88,3 @@ struct inspector<Eigen::Matrix<T, M, N>> {
 
 }  // namespace details
 }  // namespace HighFive
-
-#endif
diff --git a/include/highfive/half_float.hpp b/include/highfive/half_float.hpp
@@ -1,5 +1,4 @@
 #pragma once
-#ifdef H5_USE_HALF_FLOAT
 
 #include <half.hpp>
 
@@ -16,6 +15,5 @@ inline AtomicType<float16_t>::AtomicType() {
     // Floating point exponent bias
     detail::h5t_set_ebias(_hid, 15);
 }
-}  // namespace HighFive
 
-#endif
+}  // namespace HighFive
diff --git a/src/examples/boost_multi_array_2D.cpp b/src/examples/boost_multi_array_2D.cpp
@@ -8,11 +8,9 @@
  */
 #include <iostream>
 
-#undef H5_USE_BOOST
-#define H5_USE_BOOST
-
 #include <boost/multi_array.hpp>
 #include <highfive/highfive.hpp>
+#include <highfive/boost.hpp>
 
 using namespace HighFive;
 

diff --git a/src/examples/boost_multiarray_complex.cpp b/src/examples/boost_multiarray_complex.cpp
@@ -9,12 +9,9 @@
 #include <algorithm>
 #include <complex>
 
-#undef H5_USE_BOOST
-#define H5_USE_BOOST
-
 #include <highfive/highfive.hpp>
 
-#include <boost/multi_array.hpp>
+#include <highfive/boost.hpp>
 
 typedef std::complex<double> complex_t;
 

diff --git a/src/examples/boost_ublas_double.cpp b/src/examples/boost_ublas_double.cpp
@@ -8,11 +8,10 @@
  */
 #include <iostream>
 
-#undef H5_USE_BOOST
-#define H5_USE_BOOST
-
 #include <highfive/highfive.hpp>
 
+#include <highfive/boost.hpp>
+
 // In some versions of Boost (starting with 1.64), you have to include the serialization header
 // before ublas
 #include <boost/serialization/vector.hpp>

diff --git a/src/examples/create_dataset_half_float.cpp b/src/examples/create_dataset_half_float.cpp
@@ -12,6 +12,7 @@
 #include <vector>
 
 #include <highfive/highfive.hpp>
+#include <highfive/half_float.hpp>
 
 const std::string FILE_NAME("create_dataset_half_float_example.h5");
 const std::string DATASET_NAME("dset");

diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
@@ -46,6 +46,18 @@ option(HIGHFIVE_TEST_SINGLE_INCLUDES "Enable testing single includes" FALSE)
 if(HIGHFIVE_TEST_SINGLE_INCLUDES)
     file(GLOB public_headers LIST_DIRECTORIES false RELATIVE ${PROJECT_SOURCE_DIR}/include ${PROJECT_SOURCE_DIR}/include/highfive/*.hpp)
     foreach(PUBLIC_HEADER ${public_headers})
+        if(PUBLIC_HEADER STREQUAL "highfive/boost.hpp" AND NOT HIGHFIVE_USE_BOOST)
+          continue()
+        endif()
+
+        if(PUBLIC_HEADER STREQUAL "highfive/half_float.hpp" AND NOT HIGHFIVE_USE_HALF_FLOAT)
+          continue()
+        endif()
+
+        if(PUBLIC_HEADER STREQUAL "highfive/eigen.hpp" AND NOT HIGHFIVE_USE_EIGEN)
+          continue()
+        endif()
+
         get_filename_component(CLASS_NAME ${PUBLIC_HEADER} NAME_WE)
         configure_file(tests_import_public_headers.cpp "tests_${CLASS_NAME}.cpp" @ONLY)
         add_executable("tests_include_${CLASS_NAME}" "${CMAKE_CURRENT_BINARY_DIR}/tests_${CLASS_NAME}.cpp")

diff --git a/tests/unit/data_generator.hpp b/tests/unit/data_generator.hpp
@@ -8,7 +8,7 @@
 #include <array>
 
 #ifdef H5_USE_BOOST
-#include <boost/multi_array.hpp>
+#include <highfive/boost.hpp>
 #endif
 
 #include <highfive/bits/H5Inspector_misc.hpp>

diff --git a/tests/unit/tests_high_five.hpp b/tests/unit/tests_high_five.hpp
@@ -43,6 +43,8 @@ using base_test_types = std::tuple<int,
                                    fcomplex>;
 
 #ifdef H5_USE_HALF_FLOAT
+#include <highfive/half_float.hpp>
+
 using float16_t = half_float::half;
 using numerical_test_types =
     decltype(std::tuple_cat(std::declval<base_test_types>(), std::tuple<float16_t>()));

diff --git a/tests/unit/tests_high_five_base.cpp b/tests/unit/tests_high_five_base.cpp
@@ -27,6 +27,15 @@
 #include <highfive/highfive.hpp>
 #include "tests_high_five.hpp"
 
+#ifdef H5_USE_BOOST
+#include <highfive/boost.hpp>
+#endif
+
+#ifdef H5_USE_EIGEN
+#include <highfive/eigen.hpp>
+#endif
+
+
 using namespace HighFive;
 using Catch::Matchers::Equals;
 

diff --git a/tests/unit/tests_high_five_multi_dims.cpp b/tests/unit/tests_high_five_multi_dims.cpp
@@ -15,6 +15,7 @@
 
 #ifdef H5_USE_BOOST
 #include <boost/multi_array.hpp>
+#include <highfive/boost.hpp>
 #endif
 
 #include <catch2/catch_test_macros.hpp>