morphio 3.4.2__tar.gz → 3.5.1__tar.gz

morphio-3.5.1/.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@11d5960a326750d5838078e36cf38b85af677262 # v4
+        with:
+          submodules: 'true'
+          persist-credentials: false
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        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-3.5.1/.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: 1
+  CIBW_BUILD: 'cp*'
+  CIBW_SKIP: '*-manylinux_i686 *-win32 *musllinux* cp314t-* cp315*'
+  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-24.04, ubuntu-24.04-arm, windows-2022, macos-14, macos-15-intel]
+
+    steps:
+      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4
+        with:
+          submodules: 'true'
+          persist-credentials: false
+
+      - name: Install Python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        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@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
+        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-$(uname -m)/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"
+          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
+          # 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
+
+          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-`uname -m`/install
+          python -m cibuildwheel --output-dir dist
+
+      - name: Cache HDF5 On Windows
+        if: runner.os == 'Windows'
+        id: cache-hdf5-windows
+        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
+        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'
+        # 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: |
+          # vc141 was removed, add it back here: https://github.com/actions/runner-images/issues/9701
+          Set-Location "C:\Program Files (x86)\Microsoft Visual Studio\Installer\"
+          $InstallPath = "C:\Program Files\Microsoft Visual Studio\2022\Enterprise"
+          $componentsToAdd= @(
+            "Microsoft.VisualStudio.Component.VC.v141.x86.x64"
+            "Microsoft.VisualStudio.Component.VC.v141.x86.x64.Spectre"
+            )
+          [string]$workloadArgs = $componentsToAdd | ForEach-Object {" --add " +  $_}
+          $Arguments = ('/c', "vs_installer.exe", 'modify', '--installPath', "`"$InstallPath`"",$workloadArgs, '--quiet', '--norestart', '--nocache')
+          # should be run twice
+          $process = Start-Process -FilePath cmd.exe -ArgumentList $Arguments -Wait -PassThru -WindowStyle Hidden
+          $process = Start-Process -FilePath cmd.exe -ArgumentList $Arguments -Wait -PassThru -WindowStyle Hidden
+
+      - name: Build wheels Windows
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: |
+          C:\windows\system32\tar.exe xf C:\cache\hdf5\${{ env.WINDOWS_HDF5 }}\hdf5.zip
+          start /wait msiexec /a "%cd%\hdf\HDF5-${{ 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@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: dist-wheels-${{ matrix.os }}
+          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@11d5960a326750d5838078e36cf38b85af677262 # v4
+        with:
+          submodules: 'true'
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        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@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: dist-sdist
+          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]
+    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
+        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4
+        with:
+          pattern: dist-*
+          path: dist/
+          merge-multiple: true
+
+      - name: Display structure of downloaded files
+        run: ls -R
+        working-directory: dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

morphio-3.5.1/.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@11d5960a326750d5838078e36cf38b85af677262 # v4
+        with:
+          submodules: 'true'
+          persist-credentials: false
+
+      - name: Setup python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        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 language-pack-de
+
+      - 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: |
+          locale -a
+          ./ci/python_test.sh
+          ./ci/cpp_test.sh
+          ./ci/cpp_test.sh "-DMORPHIO_USE_DOUBLE=ON"

morphio-3.5.1/.readthedocs.yaml

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+# .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-24.04"
+  apt_packages:
+    - libhdf5-dev
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: doc/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

morphio-3.5.1/3rdparty/GSL_LITE/.editorconfig

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+[*]
+indent_style = space
+indent_size = 4

morphio-3.5.1/3rdparty/GSL_LITE/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

morphio-3.5.1/3rdparty/GSL_LITE/.gitignore

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+out/
+build*/
+.vs/