morphio 3.3.5__tar.gz → 3.3.7__tar.gz

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/check-sdist.yml

@@ -1,6 +1,9 @@
 name: Check that `sdist` builds and installs
 on: [pull_request, push]
 
+env:
+  apt_options: -o Acquire::Retries=3
+
 jobs:
   build_sdist:
     name: Build sdist
@@ -14,10 +17,10 @@ jobs:
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.10'
 
       - name: Build a source tarball
         run:
@@ -25,7 +28,8 @@ jobs:
 
       - name: Test tarball
         run: |
-          sudo apt install -y libhdf5-dev
+          sudo apt-get ${{env.apt_options}} update -y
+          sudo apt-get ${{env.apt_options}} install -y libhdf5-dev
           pip install -r tests/requirement_tests.txt
           pip install dist/*
           pytest -s -v tests

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/clang_format_check.yaml

@@ -1,6 +1,9 @@
 name: clang-format-check
 on: [pull_request, push]
 
+env:
+  apt_options: -o Acquire::Retries=3
+
 jobs:
   build:
     name: clang-format-check
@@ -14,9 +17,9 @@ jobs:
           uses: actions/checkout@v3
           with:
              fetch-depth: 2
-        - name: Install apt
-          run: sudo apt-get update -y
         - name: Install packages
-          run: sudo apt-get install python3-venv
+          run: |
+            sudo apt-get ${{env.apt_options}} update -y
+            sudo apt-get ${{env.apt_options}} install -y python3-venv
         - name: check_clang_format
           run: ci/check_clang_format.sh

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/coverage_test.yaml

@@ -4,6 +4,7 @@ on: [pull_request, push]
 env:
   CC: gcc-9
   CXX: g++-9
+  apt_options: -o Acquire::Retries=3
 
 jobs:
   build:
@@ -21,11 +22,13 @@ jobs:
       - name: Get submodules
         run: git submodule update --init --force --recursive
       - name: Install packages
-        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev lcov
+        run: |
+          sudo apt-get ${{env.apt_options}} update -y
+          sudo apt-get ${{env.apt_options}} install -y build-essential libhdf5-dev lcov
       - name: Build and run unittests
         run: ci/coverage_test.sh
       - name: Upload Coverage to Coveralls
         uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: build/build-coverage/coverage.info.cleaned
+          path-to-lcov: build/build-coverage/coverage.info

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/docstring_check.yaml

@@ -1,6 +1,9 @@
 name: docstring-check
 on: [pull_request, push]
 
+env:
+  apt_options: -o Acquire::Retries=3
+
 jobs:
   build:
     name: docstring-check
@@ -15,7 +18,9 @@ jobs:
         with:
           submodules: recursive
       - name: Install packages
-        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-12
+        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
       - name: Check docstrings
         run: |
           export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-12.so

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/publish-sdist-wheels.yml

@@ -2,11 +2,16 @@ name: Publish sdist and wheels for macos, manylinux, and windows, publish to pyp
 on: [pull_request, push]
 
 env:
+  apt_options: -o Acquire::Retries=3
+
   CIBW_BUILD_VERBOSITY: 3
   CIBW_BUILD: 'cp*'
-  CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32 cp311-macosx_x86_64'
+  CIBW_SKIP: 'cp35-* cp36-* cp37-* *-manylinux_i686 *-musllinux_* *-win32'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: pytest -s -v {project}/tests
+  UNIXY_AEC_VERSION: 1.0.4
+  UNIXY_HDF5_VERSION: 1.14.2
+  WINDOWS_HDF5: 1.14.2
 
 jobs:
   build_wheels:
@@ -24,71 +29,90 @@ jobs:
         with:
           submodules: 'true'
 
-      - uses: actions/setup-python@v4
-        name: Install Python
+      - name: Install Python
+        uses: actions/setup-python@v4
         with:
-          python-version: '3.7'
+          python-version: '3.10'
 
       - name: Install cibuildwheel
         run: |
           python -m pip install cibuildwheel
 
+      - name: Cache HDF5 On Linux/macOS
+        if: runner.os == 'Linux' || runner.os == 'macOS'
+        uses: actions/cache@v3
+        id: cache-hdf5-posix
+        env:
+          cache-name: cache-hdf5-posix
+        with:
+          path: src-cache/
+          key: ${{ runner.os }}-build-${{ env.cache-name }}
+
       - name: Build wheels on Linux
         if: runner.os == 'Linux'
         env:
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
           CIBW_BEFORE_ALL: |
-            AEC_VERSION="1.0.4"
-            HDF5_VERSION="1.12.1"
-
-            yum update -y
             yum -y install zlib-devel
-            pushd /tmp
-
-            echo "Downloading & unpacking aec ${AEC_VERSION}"
-            curl -fsSLO https://gitlab.dkrz.de/k202009/libaec/uploads/ea0b7d197a950b0c110da8dfdecbb71f/libaec-${AEC_VERSION}.tar.gz
-            tar zxf libaec-$AEC_VERSION.tar.gz
-
-            echo "Building & installing libaec"
-            pushd libaec-$AEC_VERSION
-            ./configure
-            make -j 2
-            make install
-            ldconfig
-            popd
-
-            echo "Downloading & unpacking HDF5 ${HDF5_VERSION}"
-            curl -fsSLO "https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION%.*}/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz"
-            tar -xzvf hdf5-$HDF5_VERSION.tar.gz
-
-            echo "Building & installing HDF5"
-            pushd hdf5-$HDF5_VERSION
-            ./configure                      \
-              --prefix=/usr                  \
-              --enable-build-mode=production \
-              --with-szlib                   \
-              --enable-tools=no              \
-              --enable-tests=no
-            make -j 2
-            make install
-            ldconfig
-            popd
+
+            # CMake complains if the dependencies come from within the same tree
+            # as the source, so we'll just pretend they are elsewhere
+            mkdir -p $PWD/src-cache
+            ln -s $PWD/src-cache /opt/src-cache
+
+            bash ci/hdf5-build.sh /opt/src-cache
+
         run: |
+          export HDF5_ROOT=/opt/src-cache/install-
+          export CIBW_ENVIRONMENT_PASS=HDF5_ROOT
+
           python -m cibuildwheel --output-dir dist
 
       - name: Build wheels Mac OS
         if: runner.os == 'macOS'
         env:
-          MACOSX_DEPLOYMENT_TARGET: '10.13'
+          CIBW_ENVIRONMENT_PASS: "HDF5_ROOT CMAKE_OSX_ARCHITECTURES MACOSX_DEPLOYMENT_TARGET"
           CIBW_BEFORE_BUILD: |
-            #brew update
-            #brew --version
-            export HOMEBREW_NO_AUTO_UPDATE=1
-            export HDF5_DIR="$(brew --prefix hdf5)";
-            brew install hdf5
+            # CMake complains if the dependencies come from within the same tree
+            # as the source, so we'll just pretend they are elsewhere
+            mkdir -p $PWD/src-cache
+            ln -s $PWD/src-cache /Users/runner/work/src-cache
+
+            bash ci/hdf5-build.sh /Users/runner/work/src-cache
         run: |
+          # x86_64 macOS allows for cross compilation; first we do arm64,
+          # only for the 11.0 target; and store in the cache the compiled code...
+          export CIBW_ARCHS_MACOS="arm64"
+          export CMAKE_OSX_ARCHITECTURES="arm64"
+          export MACOSX_DEPLOYMENT_TARGET="11.0"
+          export HDF5_ROOT=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS
+          python -m cibuildwheel --output-dir dist
+
+          # ...and now we do both targets for x86_64
+          export CIBW_ARCHS_MACOS="x86_64"
+          export CMAKE_OSX_ARCHITECTURES="x86_64"
+          unset MACOSX_DEPLOYMENT_TARGET
+          export HDF5_ROOT=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS
           python -m cibuildwheel --output-dir dist
 
+      - name: Cache HDF5 On Windows
+        if: runner.os == 'Windows'
+        id: cache-hdf5-windows
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-hdf5-windows
+        with:
+          path: C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}
+          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ env.WINDOWS_HDF5 }}
+
+      - name: Fill Windows Cache
+        if: runner.os == 'Windows' && steps.cache-hdf5-windows.outputs.cache-hit != 'true'
+        continue-on-error: false
+        shell: cmd
+        run: |
+          mkdir C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}
+          curl -L -o C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}\hdf5.zip https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.2/bin/windows/hdf5-1.14.2-Std-win10_64-vs16.zip
+
       - name: Build wheels Windows
         if: runner.os == 'Windows'
         shell: cmd
@@ -99,13 +123,12 @@ jobs:
         # this has a partial table:
         # https://devblogs.microsoft.com/cppblog/side-by-side-minor-version-msvc-toolsets-in-visual-studio-2017/
         run: |
-          curl -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/bin/hdf5-1.12.0-Std-win10_64-vs16.zip
-          C:\windows\system32\tar.exe xf hdf5-1.12.0-Std-win10_64-vs16.zip
-          start /wait msiexec /a "%cd%\hdf\HDF5-1.12.0-win64.msi" /qn TARGETDIR="c:\hdf5\"
+          C:\windows\system32\tar.exe xf C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}\hdf5.zip
+          start /wait msiexec /a "%cd%\hdf\HDF5-${{ env.WINDOWS_HDF5 }}-win64.msi" /qn TARGETDIR="c:\hdf5\"
 
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.1
 
-          set HDF5_DIR=C:\hdf5\HDF_Group\HDF5\1.12.0\cmake
+          set HDF5_DIR=C:\hdf5\HDF_Group\HDF5\${{ env.WINDOWS_HDF5 }}\cmake
 
           python -m cibuildwheel --output-dir dist
 
@@ -125,10 +148,10 @@ jobs:
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.7
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: '3.10'
 
       - name: Build a source tarball
         run:
@@ -136,7 +159,8 @@ jobs:
 
       - name: Test tarball
         run: |
-          sudo apt install -y libhdf5-dev
+          sudo apt-get ${{env.apt_options}} update -y
+          sudo apt-get ${{env.apt_options}} install -y libhdf5-dev
           pip install -r tests/requirement_tests.txt
           pip install dist/*
           pytest -s -v tests
@@ -166,7 +190,7 @@ jobs:
         working-directory: dist
 
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

{MorphIO-3.3.5 → MorphIO-3.3.7}/.github/workflows/run-tests.yml

@@ -1,6 +1,9 @@
 name: Run tests
 on: [pull_request, push]
 
+env:
+  apt_options: -o Acquire::Retries=3
+
 jobs:
   build:
     name: Run tests on ${{ matrix.os }}.${{ matrix.compiler.CC }}
@@ -32,7 +35,9 @@ jobs:
 
       - name: Install packages on Linux
         if: runner.os == 'Linux'
-        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev
+        run: |
+          sudo apt-get ${{env.apt_options}} update -y
+          sudo apt-get ${{env.apt_options}} install -y build-essential libhdf5-dev
 
       - name: Install packages on MacOS
         if: runner.os == 'macOS'

{MorphIO-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/CMake/HighFiveConfig.cmake.in

@@ -15,8 +15,6 @@ if(TARGET HighFive)
     return()
 endif()
 
-@PACKAGE_INIT@
-
 # Get HighFive targets
 include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargets.cmake")
 
@@ -63,12 +61,8 @@ 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()
 
-if(NOT HighFive_FIND_QUIETLY)
-  message(STATUS "HIGHFIVE @PROJECT_VERSION@: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO)")
-endif()
+message(STATUS "HIGHFIVE @PROJECT_VERSION@: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO)")
 include("${CMAKE_CURRENT_LIST_DIR}/HighFiveTargetDeps.cmake")
 foreach(dependency HighFive_libheaders libdeps)
     copy_interface_properties(HighFive ${dependency})
 endforeach()
-
-check_required_components(HighFive)

{MorphIO-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/CMake/config/CompilerFlagsHelpers.cmake

@@ -35,7 +35,9 @@ 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-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/CMakeLists.txt

@@ -113,7 +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 AND NOT HighFive_FIND_QUIETLY)
+  if(HIGHFIVE_UNIT_TESTS)
     message(WARNING "Unit tests have been DISABLED.")
   endif()
   set(HIGHFIVE_UNIT_TESTS FALSE)

{MorphIO-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/doc/Doxyfile

@@ -865,7 +865,6 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/../include \
-                         @CMAKE_CURRENT_SOURCE_DIR@/installation.md \
                          @CMAKE_CURRENT_SOURCE_DIR@/../CHANGELOG.md \
                          @CMAKE_CURRENT_SOURCE_DIR@/../README.md
 

{MorphIO-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/include/highfive/H5Attribute.hpp

@@ -87,17 +87,9 @@ class Attribute: public Object, public PathTraits<Attribute> {
     template <typename T>
     void read(T& array) const;
 
-    /// \brief Read the attribute into a buffer.
-    ///
-    /// Note, this is the shallowest wrapper around `H5Aread`.
-    template <typename T>
-    void read(T* array, const DataType& mem_datatype) const;
-
     /// \brief Read the attribute into a buffer
-    ///
-    /// This overload deduces the memory datatype from `T`.
     template <typename T>
-    void read(T* array) const;
+    void read(T* array, const DataType& dtype = {}) const;
 
     ///
     /// Write the integrality N-dimension buffer to this attribute
@@ -109,19 +101,9 @@ class Attribute: public Object, public PathTraits<Attribute> {
     template <typename T>
     void write(const T& buffer);
 
-    /// \brief Write to this attribute from `buffer`.
-    ///
-    /// Note that this is the shallowest wrapper around `H5Awrite`. It's useful
-    /// if you need full control. If possible prefer `Attribute::write`.
-    template <typename T>
-    void write_raw(const T* buffer, const DataType& mem_dtype);
-
-    /// \brief Write to this attribute from `buffer`.
-    ///
-    /// This version attempts to automatically deduce the datatype
-    /// of the buffer. Note, that the file datatype is already set.
+    /// \brief Write a buffer to this attribute
     template <typename T>
-    void write_raw(const T* buffer);
+    void write_raw(const T* buffer, const DataType& dtype = {});
 
     /// \brief Get the list of properties for creation of this attribute
     AttributeCreateProps getCreatePropertyList() const {

{MorphIO-3.3.5 → MorphIO-3.3.7}/3rdparty/HighFive/include/highfive/bits/H5Attribute_misc.hpp

@@ -100,23 +100,19 @@ inline void Attribute::read(T& array) const {
 }
 
 template <typename T>
-inline void Attribute::read(T* array, const DataType& mem_datatype) const {
+inline void Attribute::read(T* array, const DataType& dtype) const {
     static_assert(!std::is_const<T>::value,
                   "read() requires a non-const structure to read data into");
+    using element_type = typename details::inspector<T>::base_type;
+    // Auto-detect mem datatype if not provided
+    const DataType& mem_datatype = dtype.empty() ? create_and_check_datatype<element_type>()
+                                                 : dtype;
 
     if (H5Aread(getId(), mem_datatype.getId(), static_cast<void*>(array)) < 0) {
         HDF5ErrMapper::ToException<AttributeException>("Error during HDF5 Read: ");
     }
 }
 
-template <typename T>
-inline void Attribute::read(T* array) const {
-    using element_type = typename details::inspector<T>::base_type;
-    const DataType& mem_datatype = create_and_check_datatype<element_type>();
-
-    read(array, mem_datatype);
-}
-
 template <typename T>
 inline void Attribute::write(const T& buffer) {
     const DataSpace& mem_space = getMemSpace();
@@ -141,18 +137,13 @@ inline void Attribute::write(const T& buffer) {
 }
 
 template <typename T>
-inline void Attribute::write_raw(const T* buffer, const DataType& mem_datatype) {
+inline void Attribute::write_raw(const T* buffer, const DataType& dtype) {
+    using element_type = typename details::inspector<T>::base_type;
+    const auto& mem_datatype = dtype.empty() ? create_and_check_datatype<element_type>() : dtype;
+
     if (H5Awrite(getId(), mem_datatype.getId(), buffer) < 0) {
         HDF5ErrMapper::ToException<DataSetException>("Error during HDF5 Write: ");
     }
 }
 
-template <typename T>
-inline void Attribute::write_raw(const T* buffer) {
-    using element_type = typename details::inspector<T>::base_type;
-    const auto& mem_datatype = create_and_check_datatype<element_type>();
-
-    write_raw(buffer, mem_datatype);
-}
-
 }  // namespace HighFive