Issue 548 (#566)

* moved STL datatype traits to contrib/stl

Update #548

* Removed unused header files

Update #548

* attribute tests are back

Update #548

* node tests are back

update #548

* file and utility tests are back

Update #548

* datatype test is back

Update #548

* dataspace test ist back

Update #548

* moved dataspaces for STL containers to contrib

Update #548

* removed ebool code from the mainline

Update #548

* Added test build for the nexus contrib

Update #548

* Fixing ebool tests

Update #548

* add include statments

* downgrade conan version

* revert conanfile_ess.txt

* fix typo

* add CONAN_FILE for macos

* move include statement to dataset.cpp

* add back stl/string.hpp to dataset.hpp

* add newline at the end of files

* comment bzip2 from macos conanfile

* since @amues remove

* comment windows test

Co-authored-by: Jan Kotanski <[email protected]>

CMakeLists.txt

@@ -39,6 +39,12 @@ elseif(NOT ${CONAN} MATCHES "DISABLE")
   message(FATAL_ERROR "Unrecognised option for CONAN (${CONAN}), use AUTO, MANUAL or DISABLE")
 endif()
 
+#=============================================================================
+# contrib extensions
+#=============================================================================
+set(H5CPP_ENABLE_NEXUS "true" CACHE BOOL "enable support or Nexus types")
+set(H5CPP_ENABLE_STL "true" CACHE BOOL "enable STL support for H5CPP")
+
 #=============================================================================
 # General configuration
 #=============================================================================

src/h5cpp/CMakeLists.txt

@@ -6,6 +6,7 @@ install(FILES ${HEADERS}
 
 set(h5cpp_headers ${HEADERS})
 set(h5cpp_sources )
+add_subdirectory(contrib)
 add_subdirectory(core)
 add_subdirectory(attribute)
 add_subdirectory(dataspace)

src/h5cpp/attribute/attribute.cpp

@@ -28,6 +28,7 @@
 #include <h5cpp/attribute/attribute.hpp>
 #include <h5cpp/core/utilities.hpp>
 #include <h5cpp/node/link.hpp>
+#include <h5cpp/contrib/stl/string.hpp>
 
 namespace hdf5 {
 namespace attribute {

src/h5cpp/attribute/attribute.hpp

@@ -40,6 +40,7 @@
 #include <h5cpp/error/error.hpp>
 #include <initializer_list>
 #include <h5cpp/core/utilities.hpp>
+#include <h5cpp/contrib/stl/vector.hpp>
 
 namespace hdf5 {
 namespace attribute {

src/h5cpp/contrib/CMakeLists.txt

@@ -0,0 +1,13 @@
+set(CONTRIB_SOURCES)
+set(CONTRIB_HEADERS)
+
+if(H5CPP_ENABLE_STL)
+    add_subdirectory(stl)
+endif()
+
+if(H5CPP_ENABLE_NEXUS)
+    add_subdirectory(nexus)
+endif()
+
+set(h5cpp_sources ${h5cpp_sources} ${CONTRIB_SOURCES} PARENT_SCOPE)
+set(h5cpp_headers ${h5cpp_headers} ${CONTRIB_HEADERS} PARENT_SCOPE)

src/h5cpp/contrib/nexus/CMakeLists.txt

@@ -0,0 +1,8 @@
+set(SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/ebool.cpp)
+set(HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/ebool.hpp)
+
+install(FILES ${HEADERS}
+        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/h5cpp/contrib/nexus)
+
+set(CONTRIB_SOURCES ${CONTRIB_SOURCES} ${SOURCES} PARENT_SCOPE)
+set(CONTRIB_HEADERS ${CONTROB_HEADERS} ${HEADERS} PARENT_SCOPE)

src/h5cpp/datatype/ebool.cpp → src/h5cpp/contrib/nexus/ebool.cpp

@@ -26,7 +26,7 @@
 
 #include <sstream>
 #include <h5cpp/datatype/enum.hpp>
-#include <h5cpp/datatype/ebool.hpp>
+#include <h5cpp/contrib/nexus/ebool.hpp>
 #include <h5cpp/error/error.hpp>
 
 namespace hdf5

src/h5cpp/contrib/stl/CMakeLists.txt

@@ -0,0 +1,10 @@
+set(HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/array.hpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/complex.hpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/stl.hpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/string.hpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/vector.hpp)
+
+install(FILES ${HEADERS}
+        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/h5cpp/contrib/stl)
+
+set(h5cpp_headers ${h5cpp_headers} ${HEADERS} PARENT_SCOPE)

src/h5cpp/contrib/stl/array.hpp

@@ -0,0 +1,52 @@
+#pragma once
+
+#include <h5cpp/datatype/type_trait.hpp>
+#include <h5cpp/dataspace/type_trait.hpp>
+#include <h5cpp/dataspace/simple.hpp>
+#include <array>
+
+namespace hdf5 { 
+namespace datatype { 
+
+template<typename T, size_t N>
+class TypeTrait<std::array<T, N>> {
+ public:
+  using Type = std::array<T, N>;
+  using TypeClass = typename TypeTrait<T>::TypeClass;
+  static TypeClass create(const Type & = Type()) {
+    return TypeTrait<typename std::remove_const<T>::type>::create();
+  }
+  const static TypeClass & get(const Type & = Type()) {
+    const static TypeClass & cref_ = TypeTrait<typename std::remove_const<T>::type>::create();
+    return cref_;
+  }
+};
+} // end of namespace datatype
+
+namespace dataspace { 
+
+template<typename T, size_t N>
+class TypeTrait<std::array<T, N>> {
+ public:
+  using DataspaceType = Simple;
+
+  static DataspaceType create(const std::array<T, N> &) {
+    return Simple(hdf5::Dimensions{N}, hdf5::Dimensions{N});
+  }
+
+  const static DataspaceType & get(const std::array<T, N> &, DataspacePool &) {
+    const static DataspaceType & cref_ = Simple(hdf5::Dimensions{N}, hdf5::Dimensions{N});
+    return cref_;
+  }
+
+  static void *ptr(std::array<T, N> &value) {
+    return reinterpret_cast<void *>(value.data());
+  }
+
+  static const void *cptr(const std::array<T, N> &value) {
+    return reinterpret_cast<const void *>(value.data());
+  }
+};
+
+} // end of namespace dataspace
+} // end of namespace hdf5

src/h5cpp/contrib/stl/complex.hpp

@@ -0,0 +1,60 @@
+//
+// (c) Copyright 2021 DESY, ESS
+//               2021 Eugen Wintersberger <[email protected]>
+//
+// This file is part of h5cpp.
+//
+// This library is free software; you can redistribute it and/or modify it
+// under the terms of the GNU Lesser General Public License as published
+// by the Free Software Foundation; either version 2.1 of the License, or
+// (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty ofMERCHANTABILITY
+// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+// License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the
+// Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor
+// Boston, MA  02110-1301 USA
+// ===========================================================================
+//
+// Authors: Eugen Wintersberger <[email protected]>
+// Created on: Dec 23, 2021
+//
+#pragma once
+
+#include <h5cpp/datatype/type_trait.hpp>
+#include <complex>
+
+namespace hdf5 { 
+namespace datatype { 
+
+template<typename T>
+class TypeTrait<std::complex<T>>
+{
+  private:
+    using element_type = TypeTrait<T>;
+
+  public:
+    using Type = std::complex<T>;
+    using TypeClass = Compound;
+
+    static TypeClass create(const Type & = Type())
+    {
+      datatype::Compound type = datatype::Compound::create(
+        sizeof(std::complex<T>));
+
+      type.insert("real", 0, element_type::create(T()));
+      type.insert("imag", alignof(T), element_type::create(T()));
+
+      return type;
+    }
+  const static TypeClass & get(const Type & = Type()) {
+    const static TypeClass & cref_ = create();
+    return cref_;
+  }
+};
+}
+}

src/h5cpp/contrib/stl/stl.hpp

@@ -0,0 +1,32 @@
+//
+// (c) Copyright 2017 DESY,ESS
+//
+// This file is part of h5cpp.
+//
+// This library is free software; you can redistribute it and/or modify it
+// under the terms of the GNU Lesser General Public License as published
+// by the Free Software Foundation; either version 2.1 of the License, or
+// (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty ofMERCHANTABILITY
+// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+// License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the
+// Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor
+// Boston, MA  02110-1301 USA
+// ===========================================================================
+//
+// Authors: Eugen Wintersberger <[email protected]>
+//          Sebastian Koenig <[email protected]>
+//          Jan Kotanski <[email protected]>
+// Created on: Aug 28, 2017
+//
+#pragma once
+
+#include <h5cpp/contrib/stl/array.hpp>
+#include <h5cpp/contrib/stl/string.hpp>
+#include <h5cpp/contrib/stl/vector.hpp>
+#include <h5cpp/contrib/stl/complex.hpp>

src/h5cpp/contrib/stl/string.hpp

@@ -0,0 +1,52 @@
+#pragma once
+
+#include <h5cpp/datatype/type_trait.hpp>
+#include <h5cpp/datatype/string.hpp>
+#include <string>
+
+namespace hdf5 { 
+namespace datatype { 
+
+template<>
+class TypeTrait<std::string> {
+ public:
+  using Type = std::string;
+  using TypeClass = String;
+  static TypeClass create(const Type & = Type()) {
+    return datatype::String::variable();
+  }
+  const static TypeClass & get(const Type & = Type()) {
+    const static TypeClass & cref_ = create();
+    return cref_;
+  }
+};
+
+
+template<typename CharT>
+class TypeTrait<std::basic_string<CharT>> {
+ private:
+
+ public:
+  using Type = std::basic_string<CharT>;
+  using TypeClass = String;
+
+  static TypeClass create(const Type & = Type()) {
+    static_assert(std::is_same<CharT, char>::value, "Only support 8Bit characters");
+
+    String type = String::variable();
+    type.encoding(CharacterEncoding::UTF8);
+    return type;
+
+  }
+  const static TypeClass & get(const Type & = Type()) {
+    const static TypeClass & cref_ = create();
+    return cref_;
+  }
+
+};
+} // end of namespace datatype
+
+namespace dataspace { 
+
+} // end of namespace dataspace
+} // end of namespace hdf5

src/h5cpp/contrib/stl/vector.hpp

@@ -0,0 +1,50 @@
+#pragma once
+
+#include <vector>
+#include <h5cpp/datatype/type_trait.hpp>
+
+namespace hdf5 { 
+namespace datatype { 
+
+template<typename T>
+class TypeTrait<std::vector<T>> {
+ public:
+  using Type = std::vector<T>;
+  using TypeClass = typename TypeTrait<T>::TypeClass;
+  static TypeClass create(const Type & = Type()) {
+    return TypeTrait<typename std::remove_const<T>::type>::create();
+  }
+  const static TypeClass & get(const Type & = Type()) {
+    const static TypeClass & cref_ = create();
+    return cref_;
+  }
+};
+
+} // end of namespace datatype
+
+namespace dataspace {
+
+template<typename T>
+class TypeTrait<std::vector<T>> {
+ public:
+  using DataspaceType = Simple;
+
+  static Simple create(const std::vector<T> &value) {
+    return Simple(hdf5::Dimensions{value.size()}, hdf5::Dimensions{value.size()});
+  }
+
+  static const Dataspace & get(const std::vector<T> & value, DataspacePool & pool) {
+    return pool.getSimple(value.size());
+  }
+
+  static void *ptr(std::vector<T> &data) {
+    return reinterpret_cast<void *>(data.data());
+  }
+
+  static const void *cptr(const std::vector<T> &data) {
+    return reinterpret_cast<const void *>(data.data());
+  }
+};
+
+} // end of namespace dataspace
+} // end of namespace hdf5

src/h5cpp/core/types.hpp

@@ -26,10 +26,6 @@
 
 #include <h5cpp/core/hdf5_capi.hpp>
 #include <vector>
-#include <sstream>
-#include <cstring>
-#include <algorithm>
-#include <iterator>
 
 namespace hdf5 {
 

src/h5cpp/core/variable_length_string.hpp

@@ -26,8 +26,8 @@
 #pragma once
 
 #include <vector>
-#include <string>
 #include <algorithm>
+#include <cstring>
 
 namespace hdf5 {
 

src/h5cpp/dataspace/hyperslab.hpp

@@ -31,6 +31,7 @@
 #include <h5cpp/core/windows.hpp>
 #include <memory>
 #include <list>
+#include <sstream>
 
 namespace hdf5 {
 namespace dataspace {