morphio 3.3.8__tar.gz

morphio-3.3.8/.clang-format

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+---
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BasedOnStyle: WebKit
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: false
+  AfterEnum: false
+  AfterExternBlock: false
+  AfterFunction: false
+  AfterNamespace: false
+  AfterStruct: false
+  AfterUnion: false
+  BeforeCatch: false
+  BeforeElse: false
+BreakBeforeBraces: Custom
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: true
+BreakStringLiterals: true
+ColumnLimit: 100
+CommentPragmas: '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros: [ foreach, ]
+IncludeCategories:
+  - Regex: '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority: 2
+  - Regex: '^(<|"(gtest|isl|json)/)'
+    Priority: 3
+  - Regex: '.*'
+    Priority: 1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentWidth: 4
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+Language: Cpp
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+PenaltyBreakAssignment: 40
+PenaltyBreakBeforeFirstCallParameter: 100
+PenaltyBreakComment: 60
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+PointerBindsToType: true
+ReflowComments: true
+SortIncludes: true
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: false
+SpaceBeforeInheritanceColon: false
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles: false # '< ' style
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false # '(' style
+SpacesInSquareBrackets: false
+Standard: Cpp11
+TabWidth: 4
+UseTab: Never
+...

morphio-3.3.8/.github/workflows/check-sdist.yml

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+name: Check that `sdist` builds and installs
+on: [pull_request, push]
+
+env:
+  apt_options: -o Acquire::Retries=3
+
+jobs:
+  build_sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+
+    # 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
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Build a source tarball
+        run:
+          python setup.py sdist
+
+      - name: Test tarball
+        run: |
+          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-3.3.8/.github/workflows/clang_format_check.yaml

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+name: clang-format-check
+on: [pull_request, push]
+
+env:
+  apt_options: -o Acquire::Retries=3
+
+jobs:
+  build:
+    name: clang-format-check
+    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
+
+    steps:
+        - name: Fetch repository
+          uses: actions/checkout@v3
+          with:
+             fetch-depth: 2
+        - name: Install packages
+          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-3.3.8/.github/workflows/coverage_test.yaml

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+name: coverage-test
+on: [pull_request, push]
+
+env:
+  CC: gcc-9
+  CXX: g++-9
+  apt_options: -o Acquire::Retries=3
+
+jobs:
+  build:
+    name: coverage-test
+    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
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Fetch repository
+        run: git fetch --prune --unshallow
+      - name: Get submodules
+        run: git submodule update --init --force --recursive
+      - name: Install packages
+        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

morphio-3.3.8/.github/workflows/docstring_check.yaml

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+name: docstring-check
+on: [pull_request, push]
+
+env:
+  apt_options: -o Acquire::Retries=3
+
+jobs:
+  build:
+    name: docstring-check
+    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
+
+    steps:
+      - name: Fetch repository
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+      - 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
+      - name: Check docstrings
+        run: |
+          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-12.so
+          ci/check_generated_docstrings.sh || true

morphio-3.3.8/.github/workflows/publish-sdist-wheels.yml

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+name: Publish sdist and wheels for macos, manylinux, and windows, publish to pypi if a release
+on: [pull_request, push]
+
+env:
+  apt_options: -o Acquire::Retries=3
+
+  CIBW_BUILD_VERBOSITY: 3
+  CIBW_BUILD: 'cp*'
+  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_HDF5_VERSION: 1.14.3
+  WINDOWS_HDF5: 1.14.2
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, windows-2022]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - 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_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH"
+          CIBW_BEFORE_BUILD: |
+            # CMake complains if the dependencies come from within the same tree
+            # as the source, so we'll just pretend they are elsewhere
+            mkdir -p /host/home/runner/work/src-cache
+            ln -s /host/home/runner/work/src-cache /opt/hdf5-static
+            bash ci/hdf5-build.sh /opt/hdf5-static
+
+        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-/install/
+
+          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
+        if: runner.os == 'macOS'
+        env:
+          CIBW_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH CMAKE_OSX_ARCHITECTURES MACOSX_DEPLOYMENT_TARGET"
+          CIBW_BEFORE_BUILD: |
+            # 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 $PWD/src-cache /Users/runner/work/src-cache
+            bash ci/hdf5-build.sh /Users/runner/work/src-cache
+        run: |
+          # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
+          export STATIC_HDF5=True
+
+          # x86_64 macOS allows for cross compilation; first we do arm64,
+          # only for the 11.0 target; and store in the cache the compiled code...
+          export CIBW_ARCHS_MACOS="arm64"
+          export CMAKE_OSX_ARCHITECTURES="arm64"
+          export MACOSX_DEPLOYMENT_TARGET="11.0"
+          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
+          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 CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
+          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 }}-${{ env.WINDOWS_HDF5 }}
+
+      - name: Fill Windows Cache
+        if: runner.os == 'Windows' && steps.cache-hdf5-windows.outputs.cache-hit != 'true'
+        continue-on-error: false
+        shell: cmd
+        run: |
+          mkdir C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}
+          curl -L -o C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}\hdf5.zip https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.2/bin/windows/hdf5-1.14.2-Std-win10_64-vs16.zip
+
+      - name: Build wheels Windows
+        if: runner.os == 'Windows'
+        shell: cmd
+        # the v140 toolchain is used, so that fewer vc_redist installs are required
+        # some of the information is available here:
+        # https://docs.microsoft.com/en-us/cpp/build/building-on-the-command-line
+        # but tracking down the 14.0 magic number (and especially newer ones isn't always easy)
+        # this has a partial table:
+        # https://devblogs.microsoft.com/cppblog/side-by-side-minor-version-msvc-toolsets-in-visual-studio-2017/
+        run: |
+          C:\windows\system32\tar.exe xf C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}\hdf5.zip
+          start /wait msiexec /a "%cd%\hdf\HDF5-${{ 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\${{ env.WINDOWS_HDF5 }}\cmake
+
+          python -m cibuildwheel --output-dir dist
+
+      - name: Store wheel as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/*.whl
+
+  build_sdist:
+    name: Build sdist
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Build a source tarball
+        run:
+          python setup.py sdist
+
+      - name: Test tarball
+        run: |
+          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
+
+      - name: Store sdist as artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/*.tar.gz
+
+  upload_artifacts:
+    name: Upload wheels to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+
+    steps:
+      - name: Download artifacts produced during the build_wheels and build_sdist jobs
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: Display structure of downloaded files
+        run: ls -R
+        working-directory: dist
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}
+          packages_dir: dist/

morphio-3.3.8/.github/workflows/run-tests.yml

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+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 }}
+    runs-on: ${{ matrix.os }}
+
+    # 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
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        compiler:
+          - {CC: clang, CXX: clang++}
+          - {CC: gcc, CXX: g++}
+        exclude:
+          - os: macos-latest
+            compiler: {CC: gcc, CXX: g++}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          submodules: 'true'
+
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install packages on Linux
+        if: runner.os == 'Linux'
+        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'
+        run: |
+            # { work around https://github.com/actions/setup-python/issues/577
+            #brew update
+            #brew --version
+            export HOMEBREW_NO_AUTO_UPDATE=1
+            # }
+            brew install cmake || true  # macos image has cmake installed, but a new version may exist; ignore it if so
+            brew install hdf5
+
+      - name: Build and run unittests
+        env:
+          CC: ${{ matrix.compiler.CC }}
+          CXX: ${{ matrix.compiler.CXX }}
+        run: |
+          ./ci/python_test.sh
+          ./ci/cpp_test.sh
+          ./ci/cpp_test.sh "-DMORPHIO_USE_DOUBLE=ON"

morphio-3.3.8/.gitignore

@@ -0,0 +1,50 @@
+# Python wheels
+*.whl
+
+.eggs/
+bin/
+src/version.cpp
+morphio.egg-info/
+MorphIO.egg-info/
+.venv
+
+*.pyc
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Custom
+.tags
+build/
+.*.swp
+*.idea
+ci/venv*
+cmake-build*
+env*
+venv-clang-format/

morphio-3.3.8/.gitmodules

@@ -0,0 +1,18 @@
+[submodule "3rdparty/HighFive"]
+	path = 3rdparty/HighFive
+	url = https://github.com/BlueBrain/HighFive.git
+[submodule "3rdparty/pybind11"]
+	path = binds/python/pybind11
+	url = https://github.com/pybind/pybind11.git
+[submodule "3rdparty/GSL_LITE"]
+	path = 3rdparty/GSL_LITE
+	url = https://github.com/martinmoene/gsl-lite.git
+[submodule "3rdparty/lexertl14"]
+	path = 3rdparty/lexertl14
+	url = https://github.com/BenHanson/lexertl14
+[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-3.3.8/.readthedocs.yaml

@@ -0,0 +1,31 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+submodules:
+  include: all
+  recursive: true
+
+# it appears that the conda `cmake` finds `conda` installed packages
+# fine, but if cmake is installed through `pyproject.toml`, that CMake
+# doesn't find HDF5, if the hdf5 headers are available by the system, then
+# it works
+build:
+  os: "ubuntu-20.04"
+  apt_packages:
+    - libhdf5-dev
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: doc/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

morphio-3.3.8/3rdparty/CMakeLists.txt

@@ -0,0 +1,19 @@
+find_package(HDF5 REQUIRED)
+
+if (NOT EXTERNAL_HIGHFIVE)
+  set(HIGHFIVE_EXAMPLES OFF CACHE BOOL "" FORCE)
+  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)
+  add_subdirectory(HighFive)
+  target_include_directories(HighFive SYSTEM INTERFACE)
+endif()
+
+add_subdirectory(GSL_LITE)
+target_include_directories(gsl-lite SYSTEM INTERFACE)
+
+add_library(lexertl INTERFACE)
+target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)
+
+add_subdirectory(ghc_filesystem)
+