New upstream version 0.0.8

.gitignore

@@ -2,6 +2,7 @@
 /cmake-build-*/
 *.user
 .idea/workspace.xml
+.idea/usage.statistics.xml
 
 *.swp
 /file_open.h5

.idea/misc.xml

@@ -4,6 +4,7 @@
   <component name="CidrRootsConfiguration">
     <excludeRoots>
       <file path="$PROJECT_DIR$/build" />
+      <file path="$PROJECT_DIR$/cmake-build-debug" />
     </excludeRoots>
   </component>
   <component name="JavaScriptSettings">

CMakeLists.txt

 cmake_minimum_required(VERSION 3.0.0)
 project(h5cpp
     LANGUAGES CXX C
-    VERSION 0.0.7
+    VERSION 0.0.8
     )
 
 #=============================================================================

Jenkinsfile

@@ -3,74 +3,38 @@ coverage_os = "centos7-release"
 
 images = [
     'centos7-release': [
-        'name': 'essdmscdm/centos7-build-node:1.1.0',
-        'cmake': 'CC=/usr/lib64/mpich-3.2/bin/mpicc CXX=/usr/lib64/mpich-3.2/bin/mpicxx cmake3',
-        'sh': 'sh',
-        'cmake_flags': '-DCOV=ON -DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Release'
-    ],
-    'centos7-gcc6-release': [
-        'name': 'essdmscdm/centos7-gcc6-build-node:2.2.0',
+        'name': 'essdmscdm/centos7-build-node:3.0.0',
         'cmake': 'CC=/usr/lib64/mpich-3.2/bin/mpicc CXX=/usr/lib64/mpich-3.2/bin/mpicxx cmake3',
         'sh': '/usr/bin/scl enable rh-python35 devtoolset-6 -- /bin/bash',
-        'cmake_flags': '-DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Release'
-    ],
-    'fedora25-release': [
-        'name': 'essdmscdm/fedora25-build-node:1.1.0',
-        'cmake': 'cmake',
-        'sh': 'sh',
-        'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
+        'cmake_flags': '-DCOV=1 -DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Release'
     ],
     'debian9-release': [
-        'name': 'essdmscdm/debian9-build-node:1.1.0',
-        'cmake': 'cmake',
-        'sh': 'sh',
-        'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
-    ],
-    'ubuntu1604-release': [
-        'name': 'essdmscdm/ubuntu16.04-build-node:2.4.0',
+        'name': 'essdmscdm/debian9-build-node:2.0.0',
         'cmake': 'cmake',
         'sh': 'sh',
         'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
     ],
-    'ubuntu1710-release': [
-        'name': 'essdmscdm/ubuntu17.10-build-node:2.1.1',
+    'ubuntu1804-release': [
+        'name': 'essdmscdm/ubuntu18.04-build-node:1.1.0',
         'cmake': 'cmake',
         'sh': 'sh',
         'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
     ],
 
     'centos7-debug': [
-            'name': 'essdmscdm/centos7-build-node:1.1.0',
-            'cmake': 'CC=/usr/lib64/mpich-3.2/bin/mpicc CXX=/usr/lib64/mpich-3.2/bin/mpicxx cmake3',
-            'sh': 'sh',
-            'cmake_flags': '-DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Debug'
-    ],
-    'centos7-gcc6-debug': [
-            'name': 'essdmscdm/centos7-gcc6-build-node:2.2.0',
+            'name': 'essdmscdm/centos7-build-node:3.0.0',
             'cmake': 'CC=/usr/lib64/mpich-3.2/bin/mpicc CXX=/usr/lib64/mpich-3.2/bin/mpicxx cmake3',
             'sh': '/usr/bin/scl enable rh-python35 devtoolset-6 -- /bin/bash',
             'cmake_flags': '-DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Debug'
     ],
-    'fedora25-debug': [
-            'name': 'essdmscdm/fedora25-build-node:1.1.0',
-            'cmake': 'cmake',
-            'sh': 'sh',
-            'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'
-    ],
     'debian9-debug': [
-            'name': 'essdmscdm/debian9-build-node:1.1.0',
-            'cmake': 'cmake',
-            'sh': 'sh',
-            'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'
-    ],
-    'ubuntu1604-debug': [
-            'name': 'essdmscdm/ubuntu16.04-build-node:2.4.0',
+            'name': 'essdmscdm/debian9-build-node:2.0.0',
             'cmake': 'cmake',
             'sh': 'sh',
             'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'
     ],
-    'ubuntu1710-debug': [
-            'name': 'essdmscdm/ubuntu17.10-build-node:2.1.1',
+    'ubuntu1804-debug': [
+            'name': 'essdmscdm/ubuntu18.04-build-node:1.1.0',
             'cmake': 'cmake',
             'sh': 'sh',
             'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'

README.md

@@ -125,7 +125,7 @@ cmake -DCMAKE_INSTALL_PREFIX=/home/user1/some/path ..
 ```
 and accordingly, when building the client program:
 ```bash
-cmake -Dh5cpp_DIR=/home/user1/some/path/lib/cmake/h5cpp-0.0.6 path/to/your/source
+cmake -Dh5cpp_DIR=/home/user1/some/path/lib/cmake/h5cpp-0.0.8 path/to/your/source
 ```
 where version number may vary.
 

cmake/BoostLibraryConfig.cmake

@@ -3,7 +3,7 @@ set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 
-find_package(Boost 1.41 COMPONENTS filesystem REQUIRED)
+find_package(Boost 1.41 COMPONENTS filesystem system REQUIRED)
 
 if (CMAKE_CXX_COMPILER_ID MATCHES MSVC)
   add_definitions(-DBOOST_ALL_DYN_LINK)

cmake/FindGTestFix.cmake

@@ -20,7 +20,7 @@ if(NOT GTest_FOUND)
 
       if(LSB_CODENAME MATCHES stretch)
         set(GTEST_SOURCE_DIR /usr/src/googletest/googletest)
-      elseif(LSB_CODENAME MATCHES jessie OR LSB_CODENAME MATCHES xenial)
+      elseif(LSB_CODENAME MATCHES jessie OR LSB_CODENAME MATCHES xenial OR LSB_CODENAME MATCHES bionic)
         set(GTEST_SOURCE_DIR /usr/src/gtest)
       endif()
 

conanfile_desi.txt

 [requires]
-Boost/1.62.0@lasote/stable
+cmake_findboost_modular/1.66.0@bincrafters/stable
+boost_filesystem/1.66.0@bincrafters/stable
 hdf5/1.10.1@eugenwintersberger/testing
 gtest/1.8.0@conan/stable
 zlib/1.2.8@conan/stable
@@ -9,10 +10,9 @@ bzip2/1.0.6@conan/stable
 cmake
 
 [options]
-Boost:shared=True
+boost_filesystem:shared=True
 hdf5:shared=True
 gtest:shared=True
-Boost:python=False
 zlib:shared=True
 
 [imports]

conanfile_ess.txt

 [requires]
-Boost/1.62.0@ess-dmsc/stable
+cmake_findboost_modular/1.66.0@bincrafters/stable
+boost_filesystem/1.66.0@bincrafters/stable
+boost_system/1.66.0@bincrafters/stable
 hdf5/1.10.2-dm2@ess-dmsc/stable
 gtest/3121b20-dm3@ess-dmsc/stable
 
@@ -8,7 +10,8 @@ cmake
 virtualbuildenv
 
 [options]
-Boost:shared=True
+boost_filesystem:shared=True
+boost_system:shared=True
 hdf5:shared=True
 hdf5:cxx=False
 gtest:shared=True

conanfile_ess_mpi.txt

 [requires]
-Boost/1.62.0@ess-dmsc/stable
+cmake_findboost_modular/1.66.0@bincrafters/stable
+boost_filesystem/1.66.0@bincrafters/stable
 hdf5/1.10.2-dm2@ess-dmsc/stable
 gtest/3121b20-dm3@ess-dmsc/stable
 
@@ -8,7 +9,7 @@ cmake
 virtualbuildenv
 
 [options]
-Boost:shared=True
+boost_filesystem:shared=True
 hdf5:shared=True
 hdf5:cxx=False
 hdf5:parallel=True

doc/design/source/conf.py

@@ -61,9 +61,9 @@ author = u'Eugen Wintersberger'
 # built documents.
 #
 # The short X.Y version.
-version = u'0.0.6'
+version = u'0.0.8'
 # The full version, including alpha/beta/rc tags.
-release = u'0.0.6'
+release = u'0.0.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -137,7 +137,7 @@ html_theme = 'bizstyle'
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
 #
-# html_title = u'h5++ library design v0.0.6'
+# html_title = u'h5++ library design v0.0.8'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #

doc/source/conf.py.in

@@ -141,7 +141,7 @@ html_theme = 'bizstyle'
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
 #
-# html_title = u'h5++ v0.0.6'
+# html_title = u'h5++ v0.0.8'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #

doc/source/users_guide/using.rst

@@ -7,7 +7,7 @@ Using *h5cpp* with :program:`cmake`
 
 *h5cpp* not only uses *CMake* as a build system but also provides 
 a *CMake* package which makes using the library with *CMake* quite simple. 
-The *CMake* package is installed below :file:`PREFIX/lib/cmake/h5cpp-0.0.6`
+The *CMake* package is installed below :file:`PREFIX/lib/cmake/h5cpp-0.0.8`
 where :envvar:`PREFIX` expands to the installation prefix used in the 
 inital cmake call of the installation procedure.   
 
@@ -41,7 +41,7 @@ the following :file:`CMakeLists.txt` fiel is sufficient
    cmake_minimum_required(VERSION 3.5.0)
    project(h5cpp_test 
            LANGUAGES C CXX
-           VERSION 0.0.6)
+           VERSION 0.0.8)
    set(CMAKE_CXX_STANDARD 11)
    
    find_package(h5cpp REQUIRED)
@@ -56,7 +56,7 @@ You can build the code with
 
    h5cpp_test:$ mkdir build
    h5cpp_test:$ cd build
-   h5cpp_test:$ cmake -Dh5cpp_DIR=<INSTALLPREFIX>/lib/cmake/h5cpp-0.0.6 ../
+   h5cpp_test:$ cmake -Dh5cpp_DIR=<INSTALLPREFIX>/lib/cmake/h5cpp-0.0.8 ../
    h5cpp_test:$ make
 
 The cmake variable :envvar:`h5cpp_DIR` tells :program:`cmake` where to look 

src/h5cpp/CMakeLists.txt

@@ -26,7 +26,7 @@ add_library(h5cpp SHARED
 add_doxygen_source_deps(${h5cpp_headers})
 
 target_compile_definitions(h5cpp PRIVATE DLL_BUILD)
-set(H5CPP_LINKS Boost::filesystem ${MPI_CXX_LIBRARIES})
+set(H5CPP_LINKS Boost::filesystem Boost::system ${MPI_CXX_LIBRARIES})
 
 #
 # remove the absolute path from the library name

src/h5cpp/core/path.cpp

@@ -26,7 +26,7 @@
 //
 
 #include <h5cpp/core/path.hpp>
-#include <boost/algorithm/string.hpp>
+#include <sstream>
 
 namespace hdf5 {
 
@@ -50,6 +50,34 @@ bool absolute_path_string(const std::string &str)
     return false;
 }
 
+std::string join_string(const std::list<std::string> &to_join,
+                        const std::string &separator)
+{
+  std::ostringstream ss;
+  for (const auto &string_item : to_join)
+  {
+    ss << string_item << separator;
+  }
+  std::string result = ss.str();
+  if (!result.empty())
+    result.pop_back();  // remove trailing separator
+  return result;
+}
+
+std::list<std::string> split_string(const std::string &to_split,
+                                    char delim)
+{
+  std::stringstream ss(to_split);
+  std::string item;
+  std::list<std::string> elems;
+  while (std::getline(ss, item, delim)) {
+    // Don't create empty elements when the delimiter is repeated
+    if (!item.empty())
+      elems.push_back(std::move(item));
+  }
+  return elems;
+}
+
 std::list<std::string> str_to_list(const std::string &str)
 {
   std::list<std::string> result;
@@ -66,8 +94,7 @@ std::list<std::string> str_to_list(const std::string &str)
   if(str.back()=='/') string_end--;
 
   std::string buffer(string_start,string_end);
-  boost::split(result,buffer,
-               boost::is_any_of("/"),boost::token_compress_on);
+  result = split_string(buffer, '/');
   return result;
 }
 
@@ -86,7 +113,7 @@ std::string Path::to_string() const
   if (!absolute() && link_names_.empty())
     return ".";
   return (absolute() ? "/" : "")
-      + boost::algorithm::join(link_names_, "/");
+      + join_string(link_names_, "/");
 }
 
 Path::Path():

src/h5cpp/datatype/integer.cpp

@@ -22,6 +22,7 @@
 // Authors:
 //   Eugen Wintersberger <eugen.wintersberger@desy.de>
 //   Martin Shetty <martin.shetty@esss.se>
+//   Jan Kotanski <jan.kotanski@desy.de>
 // Created on: Aug 23, 2017
 //
 
@@ -44,5 +45,22 @@ Integer::Integer(const Datatype &datatype) :
   }
 }
 
+bool Integer::is_signed() const {
+  auto s = H5Tget_sign(static_cast<hid_t>(*this));
+  if (s < 0) {
+    error::Singleton::instance().throw_with_stack("Could not retrieve datatype sign");
+    return false;
+  }
+  return bool(s);
+}
+
+void Integer::make_signed(bool sign) const {
+  if (H5Tset_sign(static_cast<hid_t>(*this), (sign ? H5T_SGN_2 : H5T_SGN_NONE)) < 0) {
+    std::stringstream ss;
+    ss << "Could not set datatype sign to " << sign;
+    error::Singleton::instance().throw_with_stack(ss.str());
+  }
+}
+
 } // namespace datatype
 } // namespace hdf5

src/h5cpp/datatype/integer.hpp

@@ -22,6 +22,7 @@
 // Authors:
 //   Eugen Wintersberger <eugen.wintersberger@desy.de>
 //   Martin Shetty <martin.shetty@esss.se>
+//   Jan Kotanski <jan.kotanski@desy.de>
 // Created on: Aug 23, 2017
 //
 #pragma once
@@ -75,6 +76,21 @@ class DLL_EXPORT Integer : public Datatype {
   //!
   Integer(const Datatype &datatype);
 
+  //!
+  //! @brief Retrieves the sign type for an integer type.
+  //!
+  //! @throws std::runtime_error in case of a failure
+  //!
+  virtual bool is_signed() const;
+
+  //!
+  //! @brief Sets the sign property for an integer type.
+  //!
+  //! @throws std::runtime_error in case of a failure
+  //!
+  virtual void make_signed(bool sign) const;
+
+
 };
 
 } // namespace datatype

src/h5cpp/node/group.cpp

@@ -231,12 +231,12 @@ bool Group::has_dataset(const Path &path, const property::LinkAccessList &lapl)
   return ret;
 }
 
-Group Group::get_group(const Path &path, const property::LinkAccessList &lapl)
+Group Group::get_group(const Path &path, const property::LinkAccessList &lapl) const
 {
   return hdf5::node::get_group(*this, path, lapl);
 }
 
-Dataset Group::get_dataset(const Path &path, const property::LinkAccessList &lapl)
+Dataset Group::get_dataset(const Path &path, const property::LinkAccessList &lapl) const
 {
   return hdf5::node::get_dataset(*this, path, lapl);
 }

src/h5cpp/node/group.hpp

@@ -362,7 +362,7 @@ class DLL_EXPORT Group : public Node
     //! \sa get_dataset
     //!
     Group get_group(const Path &path,
-                    const property::LinkAccessList &lapl = property::LinkAccessList());
+                    const property::LinkAccessList &lapl = property::LinkAccessList()) const;
 
     //!
     //! \brief get dataset
@@ -385,7 +385,7 @@ class DLL_EXPORT Group : public Node
     //! \sa get_dataset
     //!
     Dataset get_dataset(const Path &path,
-                        const property::LinkAccessList &lapl = property::LinkAccessList());
+                        const property::LinkAccessList &lapl = property::LinkAccessList()) const;
 
 
  private:

test/datatype/integer_test.cpp

@@ -39,6 +39,12 @@ class Integer : public testing::Test {
   T value_;
 };
 
+template <class T>
+class SignedInteger : public Integer<T> { };
+
+template <class T>
+class UnsignedInteger : public Integer<T> { };
+
 using testing::Types;
 
 // The list of types we want to test.
@@ -51,7 +57,24 @@ Types<
     long long, unsigned long long>
     test_types;
 
+// The list of unsigned types we want to test.
+typedef
+Types<
+    unsigned char,
+    unsigned short,
+    unsigned int,
+    unsigned long,
+    unsigned long long>
+    test_unsigned_types;
+
+// The list of signed types we want to test.
+typedef
+Types<char, signed char, short, int, long, long long>
+    test_signed_types;
+
 TYPED_TEST_CASE(Integer, test_types);
+TYPED_TEST_CASE(SignedInteger, test_signed_types);
+TYPED_TEST_CASE(UnsignedInteger, test_unsigned_types);
 
 TYPED_TEST(Integer, Exceptions) {
   datatype::Datatype dtype;
@@ -76,3 +99,23 @@ TYPED_TEST(Integer, General) {
   EXPECT_THROW((datatype::Integer(default_constructed)), std::runtime_error);
 }
 
+TYPED_TEST(SignedInteger, Signed) {
+  auto t = datatype::create<decltype(this->value_)>();
+  
+  ASSERT_EQ(t.is_signed(), true);
+  t.make_signed(true);
+  ASSERT_EQ(t.is_signed(), true);
+  t.make_signed(false);
+  ASSERT_EQ(t.is_signed(), false);
+}
+
+TYPED_TEST(UnsignedInteger, Signed) {
+  auto t = datatype::create<decltype(this->value_)>();
+  
+  ASSERT_EQ(t.is_signed(), false);
+  t.make_signed(true);
+  ASSERT_EQ(t.is_signed(), true);
+  t.make_signed(false);
+  ASSERT_EQ(t.is_signed(), false);
+}
+