morphio 3.4.0__tar.gz → 3.4.2__tar.gz

{morphio-3.4.0 → morphio-3.4.2}/.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-3.4.2}/.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-3.4.2}/.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-3.4.2}/.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
@@ -77,6 +76,9 @@ jobs:
             mkdir -p $PWD/src-cache
             ln -s $PWD/src-cache /Users/runner/work/src-cache
             bash ci/hdf5-build.sh /Users/runner/work/src-cache
+          # brew may pull in something that uses libunwind that's built using the llvm version,
+          # not the system one; tell delocate to ignore this
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} --exclude libunwind.1.0.dylib -v {wheel}"
         run: |
           # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
           export STATIC_HDF5=True
@@ -182,6 +184,9 @@ 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 +200,5 @@ 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-3.4.2}/.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-3.4.2}/3rdparty/CMakeLists.txt

@@ -5,12 +5,17 @@ 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()
 
 add_subdirectory(GSL_LITE)
-target_include_directories(gsl-lite SYSTEM INTERFACE)
+target_include_directories(gsl-lite-v1 SYSTEM INTERFACE)
 
 add_library(lexertl INTERFACE)
 target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)

morphio-3.4.2/3rdparty/GSL_LITE/CMakeLists.txt

@@ -0,0 +1,67 @@
+# Copyright 2015-2019 by Martin Moene
+# Copyright 2019-2025 by Moritz Beutel
+#
+# https://github.com/gsl-lite/gsl-lite
+#
+# gsl-lite is originally based on Microsoft GSL, which is an implementation of the C++ Core Guidelines Support Library:
+# https://github.com/microsoft/GSL
+#
+# This code is licensed under the MIT License (MIT).
+
+
+cmake_minimum_required( VERSION 3.16 FATAL_ERROR )
+
+project(
+    gsl-lite
+    VERSION 1.0.1
+    DESCRIPTION "defensive programming utilities for C++98, C++11 up"
+    HOMEPAGE_URL "https://github.com/gsl-lite/gsl-lite"
+    LANGUAGES CXX
+)
+message( STATUS "Project '${PROJECT_NAME}', version: '${${PROJECT_NAME}_VERSION}'" )
+
+# Define build options.
+# Do not build tests or examples by default.
+option( GSL_LITE_OPT_BUILD_TESTS                 "Build and perform gsl-lite tests"                 OFF )
+option( GSL_LITE_OPT_BUILD_CUDA_TESTS            "Build and perform gsl-lite CUDA tests"            OFF )
+option( GSL_LITE_OPT_BUILD_EXAMPLES              "Build gsl-lite examples"                          OFF )
+option( GSL_LITE_OPT_BUILD_STATIC_ANALYSIS_DEMOS "Build and perform gsl-lite static analysis demos" OFF )
+
+# Include target definitions.
+add_subdirectory( src )
+
+# If requested, build and perform tests, build examples.
+if ( GSL_LITE_OPT_BUILD_TESTS )
+    set( ENABLE_TESTING ON )
+    include( CTest )
+    add_subdirectory( test )
+endif()
+if ( GSL_LITE_OPT_BUILD_CUDA_TESTS )
+    set( ENABLE_TESTING ON )
+    include( CTest )
+    add_subdirectory( test/cuda )
+endif()
+
+if ( GSL_LITE_OPT_BUILD_EXAMPLES )
+    add_subdirectory( example )
+endif()
+
+# Install.
+include( cmake/InstallBasicPackageFiles.cmake )
+install_basic_package_files( gsl-lite
+    COMPATIBILITY SameMajorVersion
+    ARCH_INDEPENDENT
+    INCLUDE_CONTENT
+"
+# Define legacy aliases for imported targets.
+if( NOT TARGET gsl::gsl-lite )
+    add_library( gsl::gsl-lite ALIAS gsl-lite::gsl-lite )
+endif()
+if( NOT TARGET gsl::gsl-lite-v0 )
+    add_library( gsl::gsl-lite-v0 ALIAS gsl-lite::gsl-lite-v0 )
+endif()
+if( NOT TARGET gsl::gsl-lite-v1 )
+    add_library( gsl::gsl-lite-v1 ALIAS gsl-lite::gsl-lite-v1 )
+endif()
+"
+)

morphio-3.4.2/3rdparty/GSL_LITE/cmake/CommonPresets.json

@@ -0,0 +1,245 @@
+{
+    // Collection of generally useful CMake configuration presets.
+    // Version 0.1.0β
+    // The contents of this file are in the public domain.
+    // (Moritz Beutel, 2025)
+    "version": 7,
+    "configurePresets": [
+        {
+            "name": "use Vcpkg",
+            "hidden": true,
+            "toolchainFile": "$env{VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake"
+        },
+
+        {
+            "name": "compiler presets",
+            "hidden": true,
+            "environment": {
+                "_CFLAGS": "$penv{CFLAGS} $env{_PRESET_CFLAGS} $env{_USE_PRESET_ASAN} $env{_USE_PRESET_UBSAN} $env{_USE_PRESET_TSAN} $env{_USE_PRESET_STDLIB}",
+                "_CXXFLAGS": "$penv{CXXFLAGS} $env{_PRESET_CXXFLAGS} $env{_USE_PRESET_ASAN} $env{_USE_PRESET_UBSAN} $env{_USE_PRESET_TSAN} $env{_USE_PRESET_STDLIB} $env{_USE_PRESET_DEBUGCHECKS}",
+                "_CUDAFLAGS": "$penv{CUDAFLAGS} $env{_PRESET_CUDAFLAGS} $env{_CUDA_USE_PRESET_STDLIB} $env{_USE_PRESET_DEBUGCHECKS}",
+                "CFLAGS": "$env{_CFLAGS}",
+                "CXXFLAGS": "$env{_CXXFLAGS}",
+                "CUDAFLAGS": "$env{_CUDAFLAGS}",
+                "MY_COMPILE_OPTIONS": "$env{_USE_PRESET_WARN};$env{_USE_PRESET_WARNERR}"
+            }
+        },
+
+        {
+            // "CI" covers AppVeyor, GitHub Actions, GitLab CI, Travis CI, and possibly others.
+            "name": "CI",
+            "hidden": true,
+            "condition": {
+                "type": "notEquals",
+                "lhs": "$env{CI}$env{CIRCLECI}$env{TF_BUILD}",
+                "rhs": ""
+            }
+        },
+
+        {
+            // For MSVC, enable UTF-8 source file encoding, the highest warning level, and some additional warnings:
+            // W44062: enumerator 'identifier' in a switch of enum 'enumeration' is not handled
+            // W44242: 'identifier': conversion from 'type1' to 'type2', possible loss of data
+            // W44254: 'operator': conversion from 'type1' to 'type2', possible loss of data
+            // W44265: 'class': class has virtual functions, but destructor is not virtual
+            "name": "MSVC presets",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_PRESET_CFLAGS": "/utf-8",
+                "_PRESET_CXXFLAGS": "/utf-8",
+                "_PRESET_CUDAFLAGS": "-Xcompiler=/utf-8",
+                "_PRESET_WARN": "$<$<COMPILE_LANGUAGE:C,CXX>:/permissive-;/W4;/w44062;/w44242;/w44254;/w44265>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=/permissive-,/W4,/w44062,/w44242,/w44254,/w44265>",
+                "_PRESET_WARNERR": "$<$<COMPILE_LANGUAGE:C,CXX>:/WX>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=/WX>",
+                "_PRESET_ASAN": "/fsanitize=address",
+                "_PRESET_UBSAN": "/fsanitize=undefined", // not currently supported
+                "_PRESET_TSAN": "/fsanitize=thread", // not currently supported
+                "_PRESET_DEBUGCHECKS": "/D_ITERATOR_DEBUG_LEVEL=1"
+            },
+            "condition": {
+                "type": "equals",
+                "lhs": "${hostSystemName}",
+                "rhs": "Windows"
+            }
+        },
+        {
+            // For clang-cl, use the same general presets as for MSVC with some minor changes.
+            "name": "clang-cl presets",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_PRESET_CFLAGS": "/utf-8",
+                "_PRESET_CXXFLAGS": "/utf-8",
+                "_PRESET_CUDAFLAGS": "-Xcompiler=/utf-8",
+                "_PRESET_WARN": "$<$<COMPILE_LANGUAGE:C,CXX>:/permissive-;/W4;/w44062;/w44242;/w44254;/w44265>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=/permissive-,/W4,/w44062,/w44242,/w44254,/w44265>",
+                "_PRESET_WARNERR": "$<$<COMPILE_LANGUAGE:C,CXX>:/WX>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=/WX>",
+                "_PRESET_ASAN": "/fsanitize=address",
+                "_PRESET_UBSAN": "-fsanitize=undefined -fsanitize-trap=undefined -fsanitize=implicit-integer-arithmetic-value-change",
+                "_PRESET_TSAN": "-fsanitize=thread", // not currently supported
+                "_PRESET_DEBUGCHECKS": "/D_ITERATOR_DEBUG_LEVEL=1"
+            },
+            "condition": {
+                "type": "equals",
+                "lhs": "${hostSystemName}",
+                "rhs": "Windows"
+            }
+        },
+        {
+            // For GCC, enable the highest warning level and pedantic mode.
+            "name": "GCC presets",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_PRESET_CFLAGS": "",
+                "_PRESET_CXXFLAGS": "",
+                "_PRESET_CUDAFLAGS": "",
+                "_PRESET_WARN": "$<$<COMPILE_LANGUAGE:C,CXX>:-Wall;-Wextra;-pedantic>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall,-Wextra,-pedantic>",
+                "_PRESET_WARNERR": "$<$<COMPILE_LANGUAGE:C,CXX>:-Werror>",  // avoid -Werror for CUDA host compilers for now
+                "_PRESET_ASAN": "-fsanitize=address -fno-omit-frame-pointer",
+                "_PRESET_UBSAN": "-fsanitize=undefined -fno-omit-frame-pointer -fsanitize-undefined-trap-on-error",
+                "_PRESET_TSAN": "-fsanitize=thread",
+                "_PRESET_DEBUGCHECKS": "-D_GLIBCXX_DEBUG"
+            }
+        },
+        {
+            // For Clang, enable the highest warning level and pedantic mode.
+            "name": "Clang presets",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_PRESET_CFLAGS": "",
+                "_PRESET_CXXFLAGS": "",
+                "_PRESET_CUDAFLAGS": "",
+                "_PRESET_WARN": "$<$<COMPILE_LANGUAGE:C,CXX>:-Wall;-Wextra;-pedantic>$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall,-Wextra,-pedantic>",
+                "_PRESET_WARNERR": "$<$<COMPILE_LANGUAGE:C,CXX>:-Werror>",  // avoid -Werror for CUDA host compilers for now
+                "_PRESET_ASAN": "-fsanitize=address -fno-omit-frame-pointer",
+                "_PRESET_UBSAN": "-fsanitize=undefined -fno-omit-frame-pointer -fsanitize-trap=undefined -fsanitize=implicit-integer-arithmetic-value-change",
+                "_PRESET_TSAN": "-fsanitize=thread",
+                // cf. https://libcxx.llvm.org/Hardening.html
+                "_PRESET_DEBUGCHECKS": "-D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_DEBUG"
+            }
+        },
+
+        {
+            "name": "ASan",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_ASAN": "$env{_PRESET_ASAN}"
+            }
+        },
+        {
+            "name": "UBSan",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_UBSAN": "$env{_PRESET_UBSAN}"
+            }
+        },
+        {
+            "name": "TSan",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_TSAN": "$env{_PRESET_TSAN}"
+            }
+        },
+        {
+            "name": "library debug checks",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_DEBUGCHECKS": "$env{_PRESET_DEBUGCHECKS} $env{_PRESET_DEBUGCHECKS2}"
+            }
+        },
+        {
+            "name": "high warning level",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_WARN": "$env{_PRESET_WARN}"
+            }
+        },
+        {
+            "name": "warnings as errors",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_WARNERR": "$env{_PRESET_WARNERR}"
+            }
+        },
+
+        {
+            "name": "libstdc++ for Clang",
+            "hidden": true,
+            "inherits": "compiler presets",
+            "environment": {
+                "_USE_PRESET_STDLIB": "-stdlib=libstdc++",
+                "_CUDA_USE_PRESET_STDLIB": "-Xcompiler=-stdlib=libstdc++",
+                "_PRESET_DEBUGCHECKS2": "-D_GLIBCXX_DEBUG"
+            }
+        },
+
+        {
+            "name": "force MSVC",
+            "hidden": true,
+            "inherits": "MSVC presets",
+            "environment": {
+                "CC": "cl",
+                "CXX": "cl"
+            },
+            "condition": {
+                "type": "equals",
+                "lhs": "${hostSystemName}",
+                "rhs": "Windows"
+            }
+        },
+        {
+            "name": "force clang-cl",
+            "hidden": true,
+            "inherits": "clang-cl presets",
+            "environment": {
+                "CC": "clang-cl",
+                "CXX": "clang-cl"
+            },
+            "condition": {
+                "type": "equals",
+                "lhs": "${hostSystemName}",
+                "rhs": "Windows"
+            }
+        },
+        {
+            "name": "force GCC",
+            "hidden": true,
+            "inherits": "GCC presets",
+            "environment": {
+                "CC": "gcc",
+                "CXX": "g++"
+            }
+        },
+        {
+            "name": "force Clang",
+            "hidden": true,
+            "inherits": "Clang presets",
+            "environment": {
+                "CC": "clang",
+                "CXX": "clang++"
+            }
+        }
+    ],
+    "buildPresets": [
+    ],
+    "testPresets": [
+        {
+            "name": "defaults",
+            "hidden": true,
+            "output": {
+                "outputOnFailure": true
+            },
+            "execution": {
+                "noTestsAction": "error",
+                "stopOnFailure": true
+            }
+        }
+    ]
+}