morphio 3.3.6__tar.gz → 3.3.7__tar.gz

{MorphIO-3.3.6 → 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-3.3.6 → 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-3.3.6 → 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:
@@ -21,7 +22,9 @@ 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

{MorphIO-3.3.6 → 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-3.3.6 → 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-3.3.6 → 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-3.3.6 → MorphIO-3.3.7}/CHANGELOG.md

@@ -1,3 +1,11 @@
+v3.3.7
+======
+* Change license from LGPL-3.0 to Apache-2.0 #467
+* Switch to HDF5 1.14 for all wheels
+* Add wheel building for python 3.12
+* Add wheel building for ARM64 Apple Silicon
+* Better write for soma types #411
+
 v3.3.6
 ======
 Improvements:

{MorphIO-3.3.6 → MorphIO-3.3.7}/CMakeLists.txt

@@ -1,4 +1,6 @@
 cmake_minimum_required(VERSION 3.2)
+#allow using of HDF5_ROOT for building with a custom HDF5 version
+cmake_policy(SET CMP0074 NEW)
 project(MorphIO VERSION 2.0.0)
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
@@ -52,20 +54,22 @@ if(BUILD_BINDINGS)
   add_subdirectory(binds/python)
 endif(BUILD_BINDINGS)
 
+include(GNUInstallDirs)
+
 install(
   DIRECTORY ${MORPHIO_INCLUDE_DIR}
-  DESTINATION include
+  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
   )
 
 install(
   EXPORT MorphIOTargets
   NAMESPACE MorphIO::
-  DESTINATION lib/cmake/MorphIO
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/MorphIO
   )
 
 install(
   FILES ${CMAKE_CURRENT_LIST_DIR}/CMake/MorphIOConfig.cmake
-  DESTINATION lib/cmake/MorphIO
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/MorphIO
   )
 
 

MorphIO-3.3.7/LICENSE.txt

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
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MorphIO-3.3.7/MorphIO.egg-info/PKG-INFO

@@ -0,0 +1,104 @@
+Metadata-Version: 2.1
+Name: MorphIO
+Version: 3.3.7
+Summary: A neuron morphology IO library
+Home-page: https://github.com/BlueBrain/MorphIO/
+Author: Blue Brain Project, EPFL
+License: Apache License 2.0
+Keywords: computational neuroscience,morphology,neuron,neurolucida,neuromorphology
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+Provides-Extra: docs
+License-File: LICENSE.txt
+License-File: AUTHORS.txt
+
+.. image:: doc/source/logo/BBP-MorphIO.jpg
+
+
+|license| |docs|
+
+MorphIO
+=======
+
+Documentation
+-------------
+
+MorphIO documentation is built and hosted on `readthedocs <http://morphio.readthedocs.org/>`_.
+
+* `latest snapshot <http://morphio.readthedocs.org/en/latest/>`_
+* `latest release <http://morphio.readthedocs.org/en/stable/>`_
+
+Introduction
+------------
+
+MorphIO is a library for reading and writing neuron morphology files. It supports the following
+formats:
+
+* SWC
+* ASC (aka. neurolucida)
+* H5 v1
+* H5 v2 is not supported anymore, see `H5v2`_
+
+It provides 3 C++ classes that are the starting point of every morphology analysis:
+
+* ``Soma``: contains the information related to the soma.
+
+* ``Section``: a section is the succession of points between two bifurcations. To the bare minimum
+  the ``Section`` object will contain the section type, the position and diameter of each point.
+
+* ``Morphology``: the morphology object contains general information about the loaded cell
+  but also provides accessors to the different sections.
+
+One important concept is that MorphIO is split into a *read-only* part and a *read/write* one.
+
+
+H5v2
+====
+
+Starting at version 2.6.0, the file format ``h5v2`` is no longer supported. If you have
+morphologies in this format, you can convert them to h5v1 with:
+
+.. code-block:: bash
+
+   pip install "morphio<2.6" "morph-tool==2.3.0"
+
+and then:
+
+.. code-block:: bash
+
+   # single file, OUTPUT must end with `.h5`
+   morph-tool convert file INPUTFILE OUTPUT
+   # bulk conversion
+   morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+
+
+Contributing
+============
+If you want to improve the project or you see any issue, every contribution is welcome.
+Please check the `contribution guidelines <https://github.com/BlueBrain/morphio/blob/master/CONTRIBUTING.md>`_ for more
+information.
+
+Acknowledgements
+================
+The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
+
+This research was supported by the EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
+
+License
+=======
+MorphIO is licensed under the terms of the Apache License 2.0.
+See LICENSE.txt for further details.
+
+Copyright (c) 2013-2023 Blue Brain Project/EPFL
+
+.. |license| image:: https://img.shields.io/pypi/l/morphio
+                :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER
+
+.. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest
+             :target: https://morphio.readthedocs.io/
+             :alt: documentation status
+