morphio 3.3.4__tar.gz → 3.3.5__tar.gz

{MorphIO-3.3.4 → MorphIO-3.3.5}/.github/workflows/clang_format_check.yaml

@@ -4,7 +4,7 @@ on: [pull_request, push]
 jobs:
   build:
     name: clang-format-check
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
 
     # Run on external PRs, but not internal PRs as they'll be run by the push
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository

{MorphIO-3.3.4 → MorphIO-3.3.5}/.github/workflows/docstring_check.yaml

@@ -4,7 +4,7 @@ on: [pull_request, push]
 jobs:
   build:
     name: docstring-check
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
 
     # Run on external PRs, but not internal PRs as they'll be run by the push
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
@@ -15,11 +15,8 @@ jobs:
         with:
           submodules: recursive
       - name: Install packages
-        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-9
+        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-12
       - name: Check docstrings
         run: |
-          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-9.so.1
-          ci/check_generated_docstrings.sh || true
-
-          export LIBCLANG_PATH=libLLVM-10.so.1
+          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-12.so
           ci/check_generated_docstrings.sh || true

{MorphIO-3.3.4 → MorphIO-3.3.5}/.github/workflows/publish-sdist-wheels.yml

@@ -4,7 +4,7 @@ on: [pull_request, push]
 env:
   CIBW_BUILD_VERBOSITY: 3
   CIBW_BUILD: 'cp*'
-  CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32 cp311-win_amd64 cp311-macosx_x86_64'
+  CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32 cp311-macosx_x86_64'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: pytest -s -v {project}/tests
 

{MorphIO-3.3.4 → MorphIO-3.3.5}/.gitmodules

@@ -13,3 +13,6 @@
 [submodule "3rdparty/Catch2"]
 	path = 3rdparty/Catch2
 	url = https://github.com/catchorg/Catch2.git
+[submodule "3rdparty/ghc_filesystem"]
+	path = 3rdparty/ghc_filesystem
+	url = https://github.com/gulrak/filesystem.git

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/CMakeLists.txt

@@ -14,3 +14,6 @@ target_include_directories(gsl-lite SYSTEM INTERFACE)
 
 add_library(lexertl INTERFACE)
 target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)
+
+add_subdirectory(ghc_filesystem)
+

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/CMake/HighFiveConfig.cmake.in

@@ -15,6 +15,8 @@ if(TARGET HighFive)
     return()
 endif()
 
+@PACKAGE_INIT@
+
 # Get HighFive targets
 include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargets.cmake")
 
@@ -55,13 +57,18 @@ endif()
 set(HIGHFIVE_USE_EIGEN "${HIGHFIVE_USE_EIGEN}" CACHE BOOL "Enable Eigen testing")
 set(HIGHFIVE_USE_XTENSOR "${HIGHFIVE_USE_XTENSOR}" CACHE BOOL "Enable xtensor testing")
 set(HIGHFIVE_PARALLEL_HDF5 @HIGHFIVE_PARALLEL_HDF5@ CACHE BOOL "Enable Parallel HDF5 support")
+option(HIGHFIVE_VERBOSE "Enable verbose logging" @HIGHFIVE_VERBOSE@)
 
 if(HIGHFIVE_USE_XTENSOR AND NOT CMAKE_VERSION VERSION_LESS 3.8)
   set_property(TARGET HighFive APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_14)
 endif()
 
-message(STATUS "HIGHFIVE @PROJECT_VERSION@: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO)")
+if(NOT HighFive_FIND_QUIETLY)
+  message(STATUS "HIGHFIVE @PROJECT_VERSION@: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO)")
+endif()
 include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargetDeps.cmake")
 foreach(dependency HighFive_libheaders libdeps)
     copy_interface_properties(HighFive ${dependency})
 endforeach()
+
+check_required_components(HighFive)

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/CMake/HighFiveTargetDeps.cmake

@@ -6,9 +6,25 @@ if(NOT TARGET libdeps)
   # Independent target to make it possible to have new dependencies each build
   add_library(libdeps INTERFACE)
 
+  if(HIGHFIVE_VERBOSE)
+    target_compile_definitions(libdeps INTERFACE -DHIGHFIVE_LOG_LEVEL=0)
+  endif()
+
+  if(HIGHFIVE_GLIBCXX_ASSERTIONS)
+    target_compile_definitions(libdeps INTERFACE -D_GLIBCXX_ASSERTIONS)
+  endif()
+
+  if(HIGHFIVE_HAS_FRIEND_DECLARATIONS)
+    target_compile_definitions(libdeps INTERFACE -DHIGHFIVE_HAS_FRIEND_DECLARATIONS=1)
+  endif()
+
+  if(HIGHFIVE_SANITIZER)
+    target_compile_options(libdeps INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+    target_link_options(libdeps INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+  endif()
+
   # HDF5
   if(NOT DEFINED HDF5_C_LIBRARIES)
-    set(HDF5_NO_FIND_PACKAGE_CONFIG_FILE TRUE)  # Consistency
     set(HDF5_PREFER_PARALLEL ${HIGHFIVE_PARALLEL_HDF5})
     find_package(HDF5 REQUIRED)
   endif()
@@ -23,13 +39,31 @@ if(NOT TARGET libdeps)
 
   # Boost
   if(HIGHFIVE_USE_BOOST)
-    set(Boost_NO_BOOST_CMAKE TRUE)  # Consistency
+    if(NOT DEFINED Boost_NO_BOOST_CMAKE)
+      # HighFive deactivated finding Boost via Boost's own CMake files
+      # in Oct 2016 (commit '25627b085'). Likely to appease one cluster.
+      # Boost's CMake support has since improved and likely this setting
+      # isn't needed anymore. It is kept for backwards compatibility.
+      # However, a rework of HighFive's CMake code should consider removing
+      # this default. Hard coding this to true has been reported to cause
+      # build failures.
+      set(Boost_NO_BOOST_CMAKE TRUE)
+    endif()
     find_package(Boost REQUIRED COMPONENTS system serialization)
     # Dont use imported targets yet, not avail before cmake 3.5
     target_include_directories(libdeps SYSTEM INTERFACE ${Boost_INCLUDE_DIR})
     target_compile_definitions(libdeps INTERFACE BOOST_ALL_NO_LIB H5_USE_BOOST)
   endif()
 
+  # Half
+  if(HIGHFIVE_USE_HALF_FLOAT)
+    find_file(FOUND_HALF half.hpp)
+    if (NOT FOUND_HALF)
+      message(FATAL_ERROR "Half-precision floating-point support requested but file half.hpp not found")
+    endif()
+    target_compile_definitions(libdeps INTERFACE H5_USE_HALF_FLOAT)
+  endif()
+
   # Eigen
   if(HIGHFIVE_USE_EIGEN)
     if (NOT EIGEN3_INCLUDE_DIRS)

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/CMake/HighFiveTargetExport.cmake

@@ -4,6 +4,7 @@ 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

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/CMake/config/CompilerFlagsHelpers.cmake

@@ -35,9 +35,7 @@ foreach(COMPILER_LANGUAGE ${SUPPORTED_COMPILER_LANGUAGE_LIST})
         OR CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID MATCHES "GNU"
         OR CMAKE_${COMPILER_LANGUAGE}_COMPILER_ID MATCHES "Intel")
 		set(CMAKE_${COMPILER_LANGUAGE}_WARNING_ALL " -Wall -Wextra")
-		string(CONCAT CMAKE_${COMPILER_LANGUAGE}_WARNING_DEBUG
-			" -Werror -Wshadow -Wnon-virtual-dtor -Wunused -Woverloaded-virtual"
-			" -Wformat=2 -Wconversion -Wsign-conversion -Wno-error=deprecated-declarations"
+		string(CONCAT CMAKE_${COMPILER_LANGUAGE}_WARNING_DEBUG " -Werror -Wshadow -Wnon-virtual-dtor -Wunused -Woverloaded-virtual -Wformat=2 -Wconversion -Wsign-conversion -Wno-error=deprecated-declarations"
 		)
 		if(NOT CMAKE_${COMPILER_LANGUAGE}_COMPILER_IS_ICC)
 			string(CONCAT CMAKE_${COMPILER_LANGUAGE}_WARNING_DEBUG

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/CMakeLists.txt

@@ -5,7 +5,7 @@ else()
   cmake_policy(VERSION 3.13)
 endif()
 
-project(HighFive VERSION 2.4.1)
+project(HighFive VERSION 2.7.1)
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/highfive/H5Version.hpp.in
                ${CMAKE_CURRENT_BINARY_DIR}/include/highfive/H5Version.hpp)
@@ -27,12 +27,45 @@ set(HIGHFIVE_UNIT_TESTS AUTO CACHE STRING "Enable unit tests (requires Catch2 to
 set_property(CACHE HIGHFIVE_UNIT_TESTS PROPERTY STRINGS AUTO ON OFF)
 
 option(HIGHFIVE_USE_BOOST "Enable Boost Support" ${USE_BOOST})
+option(HIGHFIVE_USE_HALF_FLOAT "Enable half-precision floats" ${USE_HALF_FLOAT})
 option(HIGHFIVE_USE_EIGEN "Enable Eigen testing" ${USE_EIGEN})
 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_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)
+
+# Controls if HighFive classes are friends of each other.
+#
+# There are two compiler bugs that require incompatible choices. The
+# GCC compiler bug [1] prevents us from writing:
+#
+#     template<class D>
+#     friend class NodeTraits<D>;
+#
+# While a MSVC compiler bug [2] complains that it can't access a
+# protected constructor, e.g., `HighFive::Object::Object`.
+#
+# Starting with `2.7.0` these friend declarations don't matter
+# anymore. It's mearly a means of appeasing a compiler.
+#
+# The values of `HIGHFIVE_HAS_FRIEND_DECLARATIONS` are:
+#   - that the macro is undefined.
+#   - `0` which implies not adding the friend declarations.
+#   - any non-zero integer, i.e. `1`, to add the friend declarations.
+#
+# Not defining the macro implies that it'll be set to `1` if MSVC is
+# detected (or other compilers requiring the friend declarations).
+#
+# [1]: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=52625
+# [2]: https://developercommunity.visualstudio.com/t/MSVC-compiler-improperly-implements-N489/1516410
+option(HIGHFIVE_HAS_FRIEND_DECLARATIONS "Enable additional friend declarations. Certain compiler require this On, others Off." OFF)
+mark_as_advanced(HIGHFIVE_HAS_FRIEND_DECLARATIONS)
+
+set(HIGHFIVE_SANITIZER OFF CACHE STRING "Enable a group of sanitizers, requires compiler support. Supported: 'address' and 'undefined'.")
+mark_as_advanced(HIGHFIVE_SANITIZER)
 
 # In deployments we probably don't want/cant have dynamic dependencies
 option(HIGHFIVE_USE_INSTALL_DEPS "End applications by default use detected dependencies here" OFF)
@@ -52,11 +85,12 @@ if(NOT DEFINED CMAKE_CXX_STANDARD)
     set(CMAKE_CXX_EXTENSIONS OFF)
 endif()
 
-if(HIGHFIVE_USE_XTENSOR)
+if(HIGHFIVE_USE_XTENSOR AND CMAKE_CXX_STANDARD LESS 14)
     set(CMAKE_CXX_STANDARD 14)
     set(CMAKE_CXX_STANDARD_REQUIRED ON)
 endif()
 
+add_compile_definitions(HIGHFIVE_CXX_STD=${CMAKE_CXX_STANDARD})
 
 # Search dependencies (hdf5, boost, eigen, xtensor, mpi) and build target highfive_deps
 include(${PROJECT_SOURCE_DIR}/CMake/HighFiveTargetDeps.cmake)
@@ -79,7 +113,7 @@ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include/
 
 # Disable test if Boost was expressly disabled, or if HighFive is a sub-project
 if (NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
-  if(HIGHFIVE_UNIT_TESTS)
+  if(HIGHFIVE_UNIT_TESTS AND NOT HighFive_FIND_QUIETLY)
     message(WARNING "Unit tests have been DISABLED.")
   endif()
   set(HIGHFIVE_UNIT_TESTS FALSE)

{MorphIO-3.3.4 → MorphIO-3.3.5}/3rdparty/HighFive/doc/Doxyfile

@@ -865,7 +865,9 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/../include \
-                         @CMAKE_CURRENT_SOURCE_DIR@/mainpage.md
+                         @CMAKE_CURRENT_SOURCE_DIR@/installation.md \
+                         @CMAKE_CURRENT_SOURCE_DIR@/../CHANGELOG.md \
+                         @CMAKE_CURRENT_SOURCE_DIR@/../README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1061,7 +1063,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = @CMAKE_CURRENT_SOURCE_DIR@/../README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -2176,7 +2178,7 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
@@ -2184,7 +2186,7 @@ MACRO_EXPANSION        = NO
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -2216,7 +2218,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = H5_HAVE_PARALLEL H5_USE_EIGEN H5_USE_BOOST H5_USE_OPENCV H5_USE_XTENSOR H5_USE_HALF_FLOAT H5_DEPRECATED(x):=
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The