Updated version 0.0.9 from 'upstream/stretch/0.0.9'

with Debian dir 7c5269df34f7185f9a446102ee6ceadc658b36a3

CMakeLists.txt

 cmake_minimum_required(VERSION 3.0.0)
 project(h5cpp
     LANGUAGES CXX C
-    VERSION 0.0.8
+    VERSION 0.0.9
     )
 
 #=============================================================================
@@ -61,6 +61,12 @@ add_custom_target(html)
 add_subdirectory(src)
 add_subdirectory(doc)
 
+#=============================================================================
+# install the examples directory to the documentation directory
+#=============================================================================
+install(DIRECTORY examples
+        DESTINATION ${CMAKE_INSTALL_DOCDIR})
+
 #=============================================================================
 # unit tests if GTest if present
 #=============================================================================

Jenkinsfile

@@ -5,38 +5,38 @@ images = [
     'centos7-release': [
         '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',
+        'sh': '/usr/bin/scl enable rh-python35 devtoolset-6 -- /bin/bash -e',
         'cmake_flags': '-DCOV=1 -DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Release'
     ],
     'debian9-release': [
         'name': 'essdmscdm/debian9-build-node:2.0.0',
         'cmake': 'cmake',
-        'sh': 'sh',
+        'sh': 'bash -e',
         'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
     ],
     'ubuntu1804-release': [
         'name': 'essdmscdm/ubuntu18.04-build-node:1.1.0',
         'cmake': 'cmake',
-        'sh': 'sh',
+        'sh': 'bash -e',
         'cmake_flags': '-DCMAKE_BUILD_TYPE=Release'
     ],
 
     'centos7-debug': [
             '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',
+            'sh': '/usr/bin/scl enable rh-python35 devtoolset-6 -- /bin/bash -e',
             'cmake_flags': '-DWITH_MPI=1 -DCONAN_FILE=conanfile_ess_mpi.txt -DCMAKE_BUILD_TYPE=Debug'
     ],
     'debian9-debug': [
             'name': 'essdmscdm/debian9-build-node:2.0.0',
             'cmake': 'cmake',
-            'sh': 'sh',
+            'sh': 'bash -e',
             'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'
     ],
     'ubuntu1804-debug': [
             'name': 'essdmscdm/ubuntu18.04-build-node:1.1.0',
             'cmake': 'cmake',
-            'sh': 'sh',
+            'sh': 'bash -e',
             'cmake_flags': '-DCMAKE_BUILD_TYPE=Debug'
     ]
 ]
@@ -49,7 +49,7 @@ def failure_function(exception_obj, failureMessage) {
         recipientProviders: toEmails,
         subject: '${DEFAULT_SUBJECT}'
     slackSend color: 'danger',
-        message: "@afonso.mukai ${project}-${env.BRANCH_NAME}: " + failureMessage
+        message: "${project}-${env.BRANCH_NAME}: " + failureMessage
 
     throw exception_obj
 }
@@ -245,13 +245,6 @@ def get_win10_pipeline()
                 }
 
                 dir("_build") {
-                    try {
-                        bat 'C:\\Users\\dmgroup\\AppData\\Local\\Programs\\Python\\Python36\\Scripts\\conan.exe remote add desy-packages https://api.bintray.com/conan/eugenwintersberger/desy-packages'
-                        bat 'C:\\Users\\dmgroup\\AppData\\Local\\Programs\\Python\\Python36\\Scripts\\conan.exe install --build=outdated -s compiler="Visual Studio" -s compiler.version=14 ..\\conanfile_default.txt'
-                    } catch (e) {
-                        failure_function(e, 'Windows10 / getting dependencies failed')
-                    }
-
                     try {
                         bat 'cmake -DCMAKE_BUILD_TYPE=Release -G "Visual Studio 14 2015 Win64" ..'
                     } catch (e) {
@@ -260,9 +253,10 @@ def get_win10_pipeline()
 
                     try {
                         bat "cmake --build . --config Release --target unit_tests"
-                        bat "bin\\unit_tests.exe"
+                        bat """call activate_run.bat
+    	                       .\\bin\\Release\\unit_tests.exe
+    	                    """
                     } catch (e) {
-		                junit 'test/unit_tests_run.xml'
                         failure_function(e, 'Windows10 / build+test failed')
                     }
 
@@ -289,8 +283,8 @@ node('docker') {
     }
     builders['macOS-release'] = get_macos_pipeline('Release')
     builders['macOS-debug'] = get_macos_pipeline('Debug')
-//    builders['Windows10'] = get_win10_pipeline()
-    
+    builders['Windows10'] = get_win10_pipeline()
+
 
     parallel builders
     // Delete workspace when build is done

README.md

 # C++ wrapper for the HDF5 C-library
 
+[![docs](https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg)](https://ess-dmsc.github.io/h5cpp/index.html) [![DOI](https://zenodo.org/badge/99373936.svg)](https://zenodo.org/badge/latestdoi/99373936)
+
+
 *h5cpp* is a new C++ wrapper for HDF5s C-API. 
 
 ## Motivation
@@ -52,11 +55,24 @@ for the library, using it should be the same on each of these platforms.
 
 The minimum requirements for building the library are:
 
-* a C++ compiler, gcc>=4.8 should do well
+* a C++ compiler, gcc>=4.8.1 should do well
 * the boost libraries
 * the HDF5 C library (>=1.8.13 would do but >=1.10.0 is prefered)
 * cmake >= 3.0
 
+The external library dependencies can be acquired and built using [Conan](https://conan.io/). Conan can be installed with PyPI: 
+```
+pip install conan
+```
+Then run the following to configure required Conan repositories:
+```
+conan remote add ess-dmsc https://api.bintray.com/conan/ess-dmsc/conan
+conan remote add bincrafters https://api.bintray.com/conan/bincrafters/public-conan
+```
+and that's it, CMake will handle the rest!
+
+Alternatively you can manually install the dependencies to typical system locations. In this case please disable Conan by using the `-DCONAN=DISABLE` option when you run CMake. 
+
 Building the library is standard cmake & make fare, out of source. For example,
 in linux shell, you would do the following:
 
@@ -125,7 +141,7 @@ 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-0.0.8 path/to/your/source
+cmake -Dh5cpp_DIR=/home/user1/some/path/lib/cmake/h5cpp-0.0.9 path/to/your/source
 ```
 where version number may vary.
 

conanfile_ess.txt

 [requires]
-cmake_findboost_modular/1.66.0@bincrafters/stable
-boost_filesystem/1.66.0@bincrafters/stable
-boost_system/1.66.0@bincrafters/stable
+cmake_findboost_modular/1.65.1@bincrafters/stable
+boost_filesystem/1.65.1@bincrafters/stable
+boost_system/1.65.1@bincrafters/stable
 hdf5/1.10.2-dm2@ess-dmsc/stable
 gtest/3121b20-dm3@ess-dmsc/stable
 
 [generators]
 cmake
 virtualbuildenv
+virtualrunenv
 
 [options]
 boost_filesystem:shared=True

conanfile_ess_mpi.txt

 [requires]
-cmake_findboost_modular/1.66.0@bincrafters/stable
-boost_filesystem/1.66.0@bincrafters/stable
+cmake_findboost_modular/1.65.1@bincrafters/stable
+boost_filesystem/1.65.1@bincrafters/stable
 hdf5/1.10.2-dm2@ess-dmsc/stable
 gtest/3121b20-dm3@ess-dmsc/stable
 
 [generators]
 cmake
 virtualbuildenv
+virtualrunenv
 
 [options]
 boost_filesystem:shared=True
+boost_system:shared=True
 hdf5:shared=True
 hdf5:cxx=False
 hdf5:parallel=True

doc/CMakeLists.txt

@@ -22,20 +22,36 @@ add_dependencies(html api_doc)
 # Build the users guide using sphinx
 #=============================================================================
 add_subdirectory(source)
+
+
+#=============================================================================
+# C API coverage generates RST
+#=============================================================================
+if(NOT WIN32)
+	file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/capi_coverage)
+	add_custom_target(
+			capi_coverage
+			COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/capi_coverage/tally.sh
+			${CMAKE_SOURCE_DIR}/src
+			${CMAKE_CURRENT_BINARY_DIR}/source/capi
+			WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/capi_coverage
+	)
+endif(NOT WIN32)
+
 add_custom_command(OUTPUT sphinx.stamp
     COMMAND sphinx-build -bhtml source build 
     COMMAND echo "timestamp" > sphinx.stamp
-    DEPENDS ${CMAKE_SPHINX_SOURCES} doxygen.stamp
+    DEPENDS ${CMAKE_SPHINX_SOURCES} doxygen.stamp capi_coverage
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/doc
     )
 
 add_custom_target(users_guide DEPENDS sphinx.stamp api_doc)
 add_dependencies(html users_guide)
 
-
 #==============================================================================
 # need to remove some additional files after building the documentation
 #==============================================================================
 set(CLEANFILES doxygen.stamp sphinx.stamp html latex build)
 set_directory_properties(PROPERTIES
     ADDITIONAL_MAKE_CLEAN_FILES ${CLEANFILES})
+

doc/capi_coverage/functions/H5

+H5allocate_memory
+H5check_version
+H5close
+H5dont_atexit
+H5free_memory
+H5garbage_collect
+H5get_libversion
+H5is_library_threadsafe
+H5open
+H5resize_memory
+H5set_free_list_limits
+H5_VERSION_GE
+H5_VERSION_LE
\ No newline at end of file

doc/capi_coverage/functions/H5A

+H5Aclose
+H5Acreate
+H5Acreate2
+H5Acreate_by_name
+H5Adelete
+H5Adelete_by_name
+H5Adelete_by_idx
+H5Aexists
+H5Aexists_by_name
+H5Aget_create_plist
+H5Aget_info
+H5Aget_info_by_idx
+H5Aget_info_by_name
+H5Aget_name
+H5Aget_name_by_idx
+H5Aget_space
+H5Aget_storage_size
+H5Aget_type
+H5Aiterate
+H5Aiterate2
+H5Aiterate_by_name
+H5Aopen
+H5Aopen_by_idx
+H5Aopen_by_name
+H5Aread
+H5Arename
+H5Arename_by_name
+H5Awrite
\ No newline at end of file

doc/capi_coverage/functions/H5D

+H5Dclose
+H5Dcreate
+H5Dcreate2
+H5Dcreate_anon
+H5Dfill
+H5Dflush
+H5Dgather
+H5Dget_access_plist
+H5Dget_create_plist
+H5Dget_offset
+H5Dget_space
+H5Dget_space_status
+H5Dget_storage_size
+H5Dget_type
+H5Diterate
+H5Dopen
+H5Dopen2
+H5Dread
+H5Drefresh
+H5Dscatter
+H5Dset_extent
+H5Dvlen_get_buf_size
+H5Dvlen_reclaim
+H5Dwrite
\ No newline at end of file

doc/capi_coverage/functions/H5E

+H5Eauto_is_v2
+H5Eclear
+H5Eclear2
+H5Eclose_msg
+H5Eclose_stack
+H5Ecreate_msg
+H5Ecreate_stack
+H5Eget_auto
+H5Eget_auto2
+H5Eget_class_name
+H5Eget_current_stack
+H5Eget_msg
+H5Eget_num
+H5Epop
+H5Eprint
+H5Eprint2
+H5Epush
+H5Epush2
+H5Eregister_class
+H5Eset_auto
+H5Eset_auto2
+H5Eset_current_stack
+H5Eunregister_class
+H5Ewalk
+H5Ewalk2
\ No newline at end of file

doc/capi_coverage/functions/H5F

+H5Fclear_elink_file_cache
+H5Fclose
+H5Fcreate
+H5Fflush
+H5Fget_access_plist
+H5Fget_create_plist
+H5Fget_file_image
+H5Fget_filesize
+H5Fget_free_sections
+H5Fget_freespace
+H5Fget_info
+H5Fget_info2
+H5Fget_intent
+H5Fget_mdc_config
+H5Fget_mdc_hit_rate
+H5Fget_mdc_image_info
+H5Fget_mdc_logging_status
+H5Fget_mdc_size
+H5Fget_metadata_read_retry_info
+H5Fget_mpi_atomicity
+H5Fget_name
+H5Fget_obj_count
+H5Fget_obj_ids
+H5Fget_page_buffering_stats
+H5Fget_vfd_handle
+H5Fis_hdf5
+H5Fmount
+H5Fopen
+H5Freopen
+H5Freset_mdc_hit_rate_stats
+H5Freset_page_buffering_stats
+H5Fset_mdc_config
+H5Fset_mpi_atomicity
+H5Fstart_swmr_write
+H5Fstart_mdc_logging
+H5Fstop_mdc_logging
+H5Funmount
\ No newline at end of file

doc/capi_coverage/functions/H5G

+H5Gclose
+H5Gcreate
+H5Gcreate2
+H5Gcreate_anon
+H5Gflush
+H5Gget_create_plist
+H5Gget_info
+H5Gget_info_by_idx
+H5Gget_info_by_name
+H5Gopen
+H5Gopen2
+H5Grefresh
\ No newline at end of file

doc/capi_coverage/functions/H5I

+H5Iclear_type
+H5Idec_ref
+H5Idec_type_ref
+H5Idestroy_type
+H5Iget_file_id
+H5Iget_name
+H5Iget_ref
+H5Iget_type
+H5Iget_type_ref
+H5Iinc_ref
+H5Iinc_type_ref
+H5Iis_valid
+H5Inmembers
+H5Iobject_verify
+H5Iregister
+H5Iregister_type
+H5Iremove_verify
+H5Isearch
+H5Itype_exists
\ No newline at end of file

doc/capi_coverage/functions/H5L

+H5Lcopy
+H5Lcreate_external
+H5Lcreate_hard
+H5Lcreate_soft
+H5Lcreate_ud
+H5Ldelete
+H5Ldelete_by_idx
+H5Lexists
+H5Lget_info
+H5Lget_info_by_idx
+H5Lget_name_by_idx
+H5Lget_val
+H5Lget_val_by_idx
+H5Lis_registered
+H5Literate
+H5Literate_by_name
+H5Lmove
+H5Lregister
+H5Lunpack_elink_val
+H5Lunregister
+H5Lvisit
+H5Lvisit_by_name
\ No newline at end of file

doc/capi_coverage/functions/H5O

+H5O_mcdt_search_cb_t
+H5Oare_mdc_flushes_disabled
+H5Oclose
+H5Ocopy
+H5Odecr_refcount
+H5Odisable_mdc_flushes
+H5Oenable_mdc_flushes
+H5Oexists_by_name
+H5Oflush
+H5Oget_comment
+H5Oget_comment_by_name
+H5Oget_info
+H5Oget_info_by_idx
+H5Oget_info_by_name
+H5Oincr_refcount
+H5Olink
+H5Oopen
+H5Oopen_by_addr
+H5Oopen_by_idx
+H5Orefresh
+H5Ovisit
+H5Ovisit_by_name
\ No newline at end of file

doc/capi_coverage/functions/H5P

+H5Padd_merge_committed_dtype_path
+H5Pall_filters_avail
+H5Pclose
+H5Pclose_class
+H5Pcopy
+H5Pcopy_prop
+H5Pcreate
+H5Pcreate_class
+H5Pdecode
+H5Pencode
+H5Pequal
+H5Pexist
+H5Pfill_value_defined
+H5Pfree_merge_committed_dtype_paths
+H5Pget
+H5Pget_alignment
+H5Pget_all_coll_metadata_ops
+H5Pget_alloc_time
+H5Pget_append_flush
+H5Pget_attr_creation_order
+H5Pget_attr_phase_change
+H5Pget_btree_ratios
+H5Pget_buffer
+H5Pget_cache
+H5Pget_char_encoding
+H5Pget_chunk
+H5Pget_chunk_cache
+H5Pget_chunk_opts
+H5Pget_class
+H5Pget_class_name
+H5Pget_class_parent
+H5Pget_coll_metadata_write
+H5Pget_copy_object
+H5Pget_core_write_tracking
+H5Pget_create_intermediate_group
+H5Pget_data_transform
+H5Pget_driver
+H5Pget_driver_info
+H5Pget_dxpl_mpio   ||
+H5Pget_edc_check
+H5Pget_efile_prefix
+H5Pget_elink_acc_flags
+H5Pget_elink_cb
+H5Pget_elink_fapl
+H5Pget_elink_file_cache_size
+H5Pget_elink_prefix
+H5Pget_est_link_info
+H5Pget_external
+H5Pget_external_count
+H5Pget_evict_on_close
+H5Pget_family_offset
+H5Pget_fapl_core
+H5Pget_fapl_direct
+H5Pget_fapl_family
+H5Pget_fapl_mpio
+H5Pget_fapl_mpiposix
+H5Pget_fapl_multi
+H5Pget_fclose_degree
+H5Pget_file_image
+H5Pget_file_image_callbacks
+H5Pget_file_space_page_size
+H5Pget_file_space_strategy
+H5Pget_fill_time
+H5Pget_fill_value
+H5Pget_filter
+H5Pget_filter2
+H5Pget_filter_by_id
+H5Pget_filter_by_id2
+H5Pget_gc_references
+H5Pget_hyper_vector_size
+H5Pget_istore_k	   	H5Pget_layout
+H5Pget_libver_bounds
+H5Pget_link_creation_order
+H5Pget_link_phase_change
+H5Pget_local_heap_size_hint
+H5Pget_mcdt_search_cb
+H5Pget_mdc_config
+H5Pget_mdc_image_config
+H5Pget_mdc_log_options
+H5Pget_meta_block_size
+H5Pget_metadata_read_attempts
+H5Pget_mpio_actual_chunk_opt_mode
+H5Pget_mpio_actual_io_mode
+H5Pget_mpio_no_collective_cause
+H5Pget_multi_type
+H5Pget_nfilters
+H5Pget_nlinks
+H5Pget_nprops
+H5Pget_page_buffer_size
+H5Pget_obj_track_times
+H5Pget_object_flush_cb
+H5Pget_shared_mesg_index
+H5Pget_shared_mesg_nindexes
+H5Pget_shared_mesg_phase_change
+H5Pget_sieve_buf_size
+H5Pget_size
+H5Pget_sizes
+H5Pget_small_data_block_size
+H5Pget_sym_k
+H5Pget_type_conv_cb
+H5Pget_userblock
+H5Pget_version
+H5Pget_virtual_count
+H5Pget_virtual_dsetname
+H5Pget_virtual_filename
+H5Pget_virtual_printf_gap
+H5Pget_virtual_srcspace
+H5Pget_virtual_view
+H5Pget_virtual_vspace
+H5Pget_vlen_mem_manager
+H5Pinsert
+H5Pinsert2
+H5Pisa_class
+H5Piterate
+H5Pmodify_filter
+H5Pregister
+H5Pregister2
+H5Premove
+H5Premove_filter
+H5Pset
+H5Pset_alignment
+H5Pset_all_coll_metadata_ops
+H5Pset_alloc_time
+H5Pset_append_flush
+H5Pset_attr_creation_order
+H5Pset_attr_phase_change
+H5Pset_btree_ratios
+H5Pset_buffer
+H5Pset_cache
+H5Pset_char_encoding
+H5Pset_chunk
+H5Pset_chunk_cache
+H5Pset_chunk_opts
+H5Pset_coll_metadata_write
+H5Pset_copy_object
+H5Pset_core_write_tracking
+H5Pset_create_intermediate_group
+H5Pset_data_transform
+H5Pset_deflate
+H5Pset_driver
+H5Pset_dxpl_mpio
+H5Pset_dxpl_mpio_chunk_opt
+H5Pset_dxpl_mpio_chunk_opt_num
+H5Pset_dxpl_mpio_chunk_opt_ratio
+H5Pset_dxpl_mpio_collective_opt
+H5Pset_edc_check
+H5Pset_efile_prefix
+H5Pset_elink_acc_flags
+H5Pset_elink_cb
+H5Pset_elink_fapl
+H5Pset_elink_file_cache_size
+H5Pset_elink_prefix
+H5Pset_est_link_info
+H5Pset_external
+H5Pset_evict_on_close
+H5Pset_family_offset
+H5Pset_fapl_core
+H5Pset_fapl_family
+H5Pset_fapl_direct
+H5Pset_fapl_log
+H5Pset_fapl_mpio
+H5Pset_fapl_mpiposix
+H5Pset_fapl_multi
+H5Pset_fapl_sec2
+H5Pset_fapl_split
+H5Pset_fapl_stdio
+H5Pset_fapl_windows
+H5Pset_fclose_degree
+H5Pset_file_image
+H5Pset_file_image_callbacks
+H5Pset_file_space_page_size
+H5Pset_file_space_strategy
+H5Pset_fill_time
+H5Pset_fill_value
+H5Pset_filter
+H5Pset_filter_callback
+H5Pset_fletcher32
+H5Pset_gc_references
+H5Pset_hyper_vector_size
+H5Pset_istore_k
+H5Pset_layout
+H5Pset_libver_bounds
+H5Pset_link_creation_order
+H5Pset_link_phase_change
+H5Pset_local_heap_size_hint
+H5Pset_mcdt_search_cb
+H5Pset_mdc_config
+H5Pset_mdc_image_config
+H5Pset_mdc_log_options
+H5Pset_meta_block_size
+H5Pset_metadata_read_attempts
+H5Pset_multi_type
+H5Pset_nbit
+H5Pset_nlinks
+H5Pset_page_buffer_size