morphio 3.4.0__tar.gz → 3.4.1__tar.gz

{morphio-3.4.0 → morphio-3.4.1}/.github/workflows/clang_format_check.yaml

@@ -7,7 +7,7 @@ env:
 jobs:
   build:
     name: clang-format-check
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     # 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-3.4.0 → morphio-3.4.1}/.github/workflows/coverage_test.yaml

@@ -2,14 +2,14 @@ name: coverage-test
 on: [pull_request, push]
 
 env:
-  CC: gcc-9
-  CXX: g++-9
+  CC: gcc-13
+  CXX: g++-13
   apt_options: -o Acquire::Retries=3
 
 jobs:
   build:
     name: coverage-test
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     # 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
@@ -29,7 +29,8 @@ jobs:
           sudo apt-get ${{env.apt_options}} install -y build-essential libhdf5-dev lcov language-pack-de
       - name: Build and run unittests
         run: |
-          locale -a 
+          locale -a
+          /usr/bin/gcov --version
           ci/coverage_test.sh
 
       - name: Upload Coverage to Coveralls

{morphio-3.4.0 → morphio-3.4.1}/.github/workflows/docstring_check.yaml

@@ -7,7 +7,7 @@ env:
 jobs:
   build:
     name: docstring-check
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     # 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
@@ -20,8 +20,8 @@ jobs:
       - name: Install packages
         run: |
           sudo apt-get ${{env.apt_options}} update -y
-          sudo apt-get ${{env.apt_options}} install -y build-essential libhdf5-dev python3-venv libclang1-12
+          sudo apt-get ${{env.apt_options}} install -y build-essential libhdf5-dev python3-venv libclang1-18
       - name: Check docstrings
         run: |
-          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-12.so
+          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-18.so
           ci/check_generated_docstrings.sh || true

{morphio-3.4.0 → morphio-3.4.1}/.github/workflows/publish-sdist-wheels.yml

@@ -6,7 +6,7 @@ env:
 
   CIBW_BUILD_VERBOSITY: 1
   CIBW_BUILD: 'cp*'
-  CIBW_SKIP: 'cp35-* cp36-* cp37-* cp38-* *-manylinux_i686 *-musllinux_* *-win32'
+  CIBW_SKIP: 'cp38-* *-manylinux_i686 *-win32 *musllinux* cp314t-*'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: pytest -s -v {project}/tests
   UNIXY_HDF5_VERSION: 1.14.3
@@ -21,8 +21,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-20.04, windows-2022, macos-13, macos-14]
+        os: [ubuntu-24.04, ubuntu-24.04-arm, windows-2022, macos-14, macos-15-intel]
 
     steps:
       - uses: actions/checkout@v4
@@ -62,9 +61,9 @@ jobs:
         run: |
           # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
           export STATIC_HDF5=True
-          export CMAKE_PREFIX_PATH=/opt/hdf5-static/install-x86_64/install/
+          export CMAKE_PREFIX_PATH=/opt/hdf5-static/install-$(uname -m)/install/
 
-          CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014 python -m cibuildwheel --output-dir dist
+          # CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014 python -m cibuildwheel --output-dir dist
           CIBW_MANYLINUX_X86_64_IMAGE=manylinux_2_28 python -m cibuildwheel --output-dir dist
 
       - name: Build wheels Mac OS
@@ -182,6 +181,9 @@ jobs:
 
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist]
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
 
     steps:
       - name: Download artifacts produced during the build_wheels and build_sdist jobs
@@ -195,9 +197,5 @@ jobs:
         run: ls -R
         working-directory: dist
 
-      - name: Publish package to PyPI
+      - name: Publish package distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}
-          packages_dir: dist/

{morphio-3.4.0 → morphio-3.4.1}/.gitmodules

@@ -1,6 +1,6 @@
 [submodule "3rdparty/HighFive"]
 	path = 3rdparty/HighFive
-	url = https://github.com/BlueBrain/HighFive.git
+	url = https://github.com/highfive-devs/highfive.git
 [submodule "3rdparty/pybind11"]
 	path = binds/python/pybind11
 	url = https://github.com/pybind/pybind11.git

{morphio-3.4.0 → morphio-3.4.1}/3rdparty/CMakeLists.txt

@@ -5,7 +5,12 @@ if (NOT EXTERNAL_HIGHFIVE)
   set(HIGHFIVE_UNIT_TESTS OFF CACHE BOOL "" FORCE)
   set(HIGHFIVE_USE_BOOST OFF CACHE BOOL "" FORCE)
   set(HIGHFIVE_USE_INSTALL_DEPS ON CACHE BOOL "" FORCE)
+
+  morphio_variable_push(CMAKE_POLICY_VERSION_MINIMUM)
+  set(CMAKE_POLICY_VERSION_MINIMUM 3.5)
   add_subdirectory(HighFive)
+  morphio_variable_pop(CMAKE_POLICY_VERSION_MINIMUM)
+
   target_include_directories(HighFive SYSTEM INTERFACE)
 endif()
 

morphio-3.4.1/3rdparty/HighFive/CMakeLists.txt

@@ -0,0 +1,191 @@
+cmake_minimum_required(VERSION 3.13)
+cmake_policy(VERSION 3.13)
+
+project(HighFive VERSION 3.2.0)
+
+# Configure HighFive
+# ------------------
+option(HIGHFIVE_VERBOSE "Set logging level to verbose." 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)
+
+option(HIGHFIVE_FIND_HDF5 "Find and link with HDF5." On)
+
+set(HIGHFIVE_CMAKE_INSTALL_DIR "lib/cmake/HighFive" CACHE STRING
+  "Directory where HighFive's CMake code will be installed. Default: lib/cmake/HighFive")
+set(HIGHFIVE_XTENSOR_HEADER_VERSION "0" CACHE STRING "XTensor header version: 1 for <xtensor/xtensor.hpp>, 2 for <xtensor/containers/xtensor.hpp>, and 0 for automatic detection.")
+
+# Configure Tests & Examples
+# --------------------------
+
+# Internal variable that controls the default value for building
+# optional things like tests, examples and docs.
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+  set(HIGHFIVE_EXTRAS_DEFAULT ON)
+else()
+  set(HIGHFIVE_EXTRAS_DEFAULT OFF)
+endif()
+
+if (CMAKE_CXX_STANDARD GREATER_EQUAL 20)
+  include(CheckIncludeFileCXX)
+  CHECK_INCLUDE_FILE_CXX(span HIGHFIVE_TEST_SPAN_DEFAULT)
+else()
+  set(HIGHFIVE_TEST_SPAN_DEFAULT Off)
+endif()
+
+option(HIGHFIVE_UNIT_TESTS "Compile unit-tests" ${HIGHFIVE_EXTRAS_DEFAULT})
+option(HIGHFIVE_EXAMPLES "Compile examples" ${HIGHFIVE_EXTRAS_DEFAULT})
+option(HIGHFIVE_BUILD_DOCS "Build documentation" ${HIGHFIVE_EXTRAS_DEFAULT})
+
+option(HIGHFIVE_TEST_SPAN "Enable testing std::span, requires C++20" ${HIGHFIVE_TEST_SPAN_DEFAULT})
+option(HIGHFIVE_TEST_BOOST "Enable testing Boost features" OFF)
+option(HIGHFIVE_TEST_BOOST_SPAN "Additionally, enable testing `boost::span`" OFF)
+option(HIGHFIVE_TEST_EIGEN "Enable testing Eigen" OFF)
+option(HIGHFIVE_TEST_OPENCV "Enable testing OpenCV" OFF)
+option(HIGHFIVE_TEST_XTENSOR "Enable testing xtensor" OFF)
+option(HIGHFIVE_TEST_HALF_FLOAT "Enable testing half-precision floats" OFF)
+
+set(HIGHFIVE_MAX_ERRORS 0 CACHE STRING "Maximum number of compiler errors.")
+option(HIGHFIVE_HAS_WERROR "Convert warnings to errors." OFF)
+option(HIGHFIVE_GLIBCXX_ASSERTIONS "Enable bounds check for STL." OFF)
+# TODO these some magic to get a drop down menu in ccmake
+set(HIGHFIVE_SANITIZER OFF CACHE STRING "Enable a group of sanitizers, requires compiler support. Supported: 'address' and 'undefined'.")
+mark_as_advanced(HIGHFIVE_SANITIZER)
+
+# Check compiler cxx_std requirements
+# -----------------------------------
+set(HIGHFIVE_CXX_STANDARD_DEFAULT 14)
+
+if(NOT DEFINED CMAKE_CXX_STANDARD)
+    set(CMAKE_CXX_STANDARD ${HIGHFIVE_CXX_STANDARD_DEFAULT})
+    set(CMAKE_CXX_STANDARD_REQUIRED ON)
+    set(CMAKE_CXX_EXTENSIONS OFF)
+endif()
+
+if(CMAKE_CXX_STANDARD EQUAL 98 OR CMAKE_CXX_STANDARD LESS ${HIGHFIVE_CXX_STANDARD_DEFAULT})
+  message(FATAL_ERROR "HighFive needs to be compiled with at least C++${HIGHFIVE_CXX_STANDARD_DEFAULT}")
+endif()
+
+add_compile_definitions(HIGHFIVE_CXX_STD=${CMAKE_CXX_STANDARD})
+
+# HighFive
+# --------
+add_library(HighFiveInclude INTERFACE)
+add_library(HighFive::Include ALIAS HighFiveInclude)
+set_target_properties(HighFiveInclude PROPERTIES EXPORT_NAME Include)
+
+target_include_directories(HighFiveInclude INTERFACE
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+  $<INSTALL_INTERFACE:include>
+)
+
+add_library(HighFive INTERFACE)
+add_library(HighFive::HighFive ALIAS HighFive)
+
+target_link_libraries(HighFive INTERFACE HighFive::Include)
+
+if(HIGHFIVE_FIND_HDF5)
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(HighFive INTERFACE HDF5::HDF5)
+endif()
+
+if(HDF5_IS_PARALLEL)
+  find_package(MPI REQUIRED)
+  target_link_libraries(HighFive
+    INTERFACE
+    $<BUILD_INTERFACE:MPI::MPI_C>
+    $<BUILD_INTERFACE:MPI::MPI_CXX>
+  )
+endif()
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/highfive/H5Version.hpp.in
+               ${CMAKE_CURRENT_SOURCE_DIR}/include/highfive/H5Version.hpp)
+
+# Install
+# -------
+include(CMakePackageConfigHelpers)
+write_basic_package_version_file(
+  ${CMAKE_CURRENT_BINARY_DIR}/cmake/HighFiveConfigVersion.cmake
+  VERSION ${PACKAGE_VERSION}
+  COMPATIBILITY AnyNewerVersion
+)
+
+configure_package_config_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveConfig.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/HighFiveConfig.cmake
+    INSTALL_DESTINATION ${HIGHFIVE_CMAKE_INSTALL_DIR}
+)
+
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
+  DESTINATION "include"
+  PATTERN "*.in" EXCLUDE)
+
+install(TARGETS HighFive HighFiveInclude EXPORT HighFiveTargets)
+install(EXPORT HighFiveTargets
+  FILE HighFiveTargets.cmake
+  NAMESPACE HighFive::
+  DESTINATION ${HIGHFIVE_CMAKE_INSTALL_DIR}
+)
+
+install(FILES
+  ${CMAKE_CURRENT_BINARY_DIR}/cmake/HighFiveConfig.cmake
+  ${CMAKE_CURRENT_BINARY_DIR}/cmake/HighFiveConfigVersion.cmake
+  DESTINATION ${HIGHFIVE_CMAKE_INSTALL_DIR}
+)
+
+# export targets into build tree
+export(
+    EXPORT HighFiveTargets
+    FILE "${CMAKE_CURRENT_BINARY_DIR}/cmake/HighFiveTargets.cmake"
+    NAMESPACE HighFive::
+)
+
+
+# Preparing local building (tests, examples)
+# ------------------------------------------
+
+if(HIGHFIVE_EXAMPLES OR HIGHFIVE_UNIT_TESTS)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveWarnings.cmake)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveFlags.cmake)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/HighFiveOptionalDependencies.cmake)
+endif()
+
+if(HIGHFIVE_EXAMPLES)
+  add_subdirectory(src/examples)
+endif()
+
+if(HIGHFIVE_UNIT_TESTS)
+  add_subdirectory(deps/catch2 EXCLUDE_FROM_ALL)
+  list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/deps/catch2/contrib)
+  enable_testing()
+  add_subdirectory(tests/unit)
+endif()
+
+if(HIGHFIVE_BUILD_DOCS)
+  add_subdirectory(doc)
+endif()

morphio-3.4.1/3rdparty/HighFive/cmake/HighFiveConfig.cmake

@@ -0,0 +1,28 @@
+include(CMakeFindDependencyMacro)
+
+if(NOT DEFINED HIGHFIVE_FIND_HDF5)
+  set(HIGHFIVE_FIND_HDF5 On)
+endif()
+
+if(HIGHFIVE_FIND_HDF5)
+  find_dependency(HDF5)
+endif()
+
+if(NOT TARGET HighFive)
+  include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargets.cmake")
+
+  if(HDF5_IS_PARALLEL)
+    find_dependency(MPI)
+    target_link_libraries(HighFive::HighFive INTERFACE MPI::MPI_C MPI::MPI_CXX)
+  endif()
+
+  add_library(HighFive ALIAS HighFive::HighFive)
+  add_library(HighFiveInclude ALIAS HighFive::Include)
+endif()
+
+if(HIGHFIVE_XTENSOR_HEADER_VERSION)
+  target_compile_definitions(HighFive::HighFive PUBLIC
+    HIGHFIVE_XTENSOR_HEADER_VERSION=${HIGHFIVE_XTENSOR_HEADER_VERSION}
+  )
+endif()
+

morphio-3.4.1/3rdparty/HighFive/cmake/HighFiveFlags.cmake

@@ -0,0 +1,30 @@
+if(TARGET HighFiveFlags)
+    # Allow multiple `include(HighFiveWarnings)`, which would
+    # attempt to redefine `HighFiveWarnings` and fail without
+    # this check.
+    return()
+endif()
+
+add_library(HighFiveFlags INTERFACE)
+
+if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+    if(HIGHFIVE_MAX_ERRORS)
+        target_compile_options(HighFiveFlags
+            INTERFACE
+            -fmax-errors=${HIGHFIVE_MAX_ERRORS}
+        )
+    endif()
+endif()
+
+if(HIGHFIVE_GLIBCXX_ASSERTIONS)
+    target_compile_definitions(HighFiveFlags INTERFACE -D_GLIBCXX_ASSERTIONS)
+endif()
+
+if(HIGHFIVE_HAS_FRIEND_DECLARATIONS)
+    target_compile_definitions(HighFiveFlags INTERFACE -DHIGHFIVE_HAS_FRIEND_DECLARATIONS=1)
+endif()
+
+if(HIGHFIVE_SANITIZER)
+    target_compile_options(HighFiveFlags INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+    target_link_options(HighFiveFlags INTERFACE -fsanitize=${HIGHFIVE_SANITIZER})
+endif()

morphio-3.4.1/3rdparty/HighFive/cmake/HighFiveOptionalDependencies.cmake

@@ -0,0 +1,64 @@
+if(NOT TARGET HighFiveBoostDependency)
+  add_library(HighFiveBoostDependency INTERFACE)
+  if(HIGHFIVE_TEST_BOOST)
+    find_package(Boost REQUIRED)
+    target_link_libraries(HighFiveBoostDependency INTERFACE Boost::headers)
+    # TODO check if we need Boost::disable_autolinking to cause:
+    # -DBOOST_ALL_NO_LIB (does something on MSVC).
+    target_compile_definitions(HighFiveBoostDependency INTERFACE HIGHFIVE_TEST_BOOST=1)
+  endif()
+  if(HIGHFIVE_TEST_BOOST_SPAN)
+    target_compile_definitions(HighFiveBoostDependency INTERFACE HIGHFIVE_TEST_BOOST_SPAN=1)
+  endif()
+endif()
+
+if(NOT TARGET HighFiveEigenDependency)
+  add_library(HighFiveEigenDependency INTERFACE)
+  if(HIGHFIVE_TEST_EIGEN)
+    find_package(Eigen3 REQUIRED NO_MODULE)
+    target_link_libraries(HighFiveEigenDependency INTERFACE Eigen3::Eigen)
+    target_compile_definitions(HighFiveEigenDependency INTERFACE HIGHFIVE_TEST_EIGEN=1)
+  endif()
+endif()
+
+if(NOT TARGET HighFiveXTensorDependency)
+  add_library(HighFiveXTensorDependency INTERFACE)
+  if(HIGHFIVE_TEST_XTENSOR)
+    find_package(xtensor REQUIRED)
+    target_link_libraries(HighFiveXTensorDependency INTERFACE xtensor)
+    target_compile_definitions(HighFiveXTensorDependency INTERFACE HIGHFIVE_TEST_XTENSOR=1)
+
+    if(HIGHFIVE_XTENSOR_HEADER_VERSION)
+      target_compile_definitions(HighFiveXTensorDependency INTERFACE
+        HIGHFIVE_XTENSOR_HEADER_VERSION=${HIGHFIVE_XTENSOR_HEADER_VERSION})
+    endif()
+  endif()
+endif()
+
+if(NOT TARGET HighFiveOpenCVDependency)
+  add_library(HighFiveOpenCVDependency INTERFACE)
+  if(HIGHFIVE_TEST_OPENCV)
+    find_package(OpenCV REQUIRED)
+    target_include_directories(HighFiveOpenCVDependency SYSTEM INTERFACE ${OpenCV_INCLUDE_DIRS})
+    target_link_libraries(HighFiveOpenCVDependency INTERFACE ${OpenCV_LIBS})
+    target_compile_definitions(HighFiveOpenCVDependency INTERFACE HIGHFIVE_TEST_OPENCV=1)
+  endif()
+endif()
+
+if(NOT TARGET HighFiveSpanDependency)
+  add_library(HighFiveSpanDependency INTERFACE)
+  if(HIGHFIVE_TEST_SPAN)
+    target_compile_definitions(HighFiveSpanDependency INTERFACE HIGHFIVE_TEST_SPAN=1)
+  endif()
+endif()
+
+if(NOT TARGET HighFiveOptionalDependencies)
+  add_library(HighFiveOptionalDependencies INTERFACE)
+  target_link_libraries(HighFiveOptionalDependencies INTERFACE
+    HighFiveBoostDependency
+    HighFiveEigenDependency
+    HighFiveXTensorDependency
+    HighFiveOpenCVDependency
+    HighFiveSpanDependency
+  )
+endif()

{morphio-3.4.0/3rdparty/HighFive/CMake → morphio-3.4.1/3rdparty/HighFive/cmake}/HighFiveWarnings.cmake

@@ -23,15 +23,20 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "Clang"
             -Wconversion
             -Wsign-conversion
     )
+endif()
 
-    if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Intel")
-        target_compile_options(HighFiveWarnings
-            INTERFACE
-                -Wpedantic
-                -Wcast-align
-                -Wdouble-promotion
-        )
-    endif()
+if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+    target_compile_options(HighFiveWarnings
+        INTERFACE
+            -Wpedantic
+            -Wcast-align
+            -Wdouble-promotion
+    )
+
+    target_compile_options(HighFiveWarnings
+        INTERFACE
+            -ftemplate-backtrace-limit=0
+    )
 
     if(HIGHFIVE_HAS_WERROR)
         target_compile_options(HighFiveWarnings
@@ -41,3 +46,4 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "Clang"
         )
     endif()
 endif()
+

{morphio-3.4.0 → morphio-3.4.1}/3rdparty/HighFive/doc/DoxygenLayout.xml

@@ -36,7 +36,7 @@
       <tab type="globals" visible="yes" title="" intro=""/>
     </tab>
     <tab type="examples" visible="yes" title="" intro=""/>  
-    <tab type="user" visible="yes" url='https://github.com/BlueBrain/HighFive' title="Github Page" intro=""/>
+    <tab type="user" visible="yes" url='https://github.com/highfive-devs/highfive' title="Github Page" intro=""/>
   </navindex>
 
   <!-- Layout definition for a class page -->