morphio 3.3.0__tar.gz → 3.3.3__tar.gz

{MorphIO-3.3.0 → MorphIO-3.3.3}/.github/workflows/check-sdist.yml

@@ -5,15 +5,19 @@ 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@v2
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.6
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: 3.8
 
       - name: Build a source tarball
         run:

{MorphIO-3.3.0 → MorphIO-3.3.3}/.github/workflows/clang_format_check.yaml

@@ -5,6 +5,10 @@ jobs:
   build:
     name: clang-format-check
     runs-on: ubuntu-18.04
+
+    # 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@v1

MorphIO-3.3.3/.github/workflows/coverage_test.yaml

@@ -0,0 +1,31 @@
+name: coverage-test
+on: [pull_request, push]
+
+env:
+  CC: gcc-9
+  CXX: g++-9
+
+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@v2
+      - 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 update && sudo apt-get install 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

MorphIO-3.3.3/.github/workflows/docstring_check.yaml

@@ -0,0 +1,25 @@
+name: docstring-check
+on: [pull_request, push]
+
+jobs:
+  build:
+    name: docstring-check
+    runs-on: ubuntu-18.04
+
+    # 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@v2
+        with:
+          submodules: recursive
+      - name: Install packages
+        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-9
+      - name: Check docstrings
+        run: |
+          export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-9.so.1
+          ci/check_generated_docstrings.sh || true
+
+          export LIBCLANG_PATH=libLLVM-10.so.1
+          ci/check_generated_docstrings.sh || true

{MorphIO-3.3.0 → MorphIO-3.3.3}/.github/workflows/publish-sdist-wheels.yml

@@ -1,27 +1,23 @@
-name: Publish sdist and wheels macos-manylinux
-
-on:
-  push:
-    tags:
-      - 'v[0-9]+.[0-9]+.[0-9]+'
+name: Publish sdist and wheels for macos, manylinux, and windows, publish to pypi if a release
+on: [pull_request, push]
 
 env:
-  CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-  MACOSX_DEPLOYMENT_TARGET: '10.13'
-  CIBW_BUILD_VERBOSITY: 2
-  # Only build on Python 3.x
-  CIBW_BUILD: 'cp3?-*'
-  CIBW_SKIP: 'cp35-* cp39-* *-manylinux_i686'
+  CIBW_BUILD_VERBOSITY: 3
+  CIBW_BUILD: 'cp*'
+  CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: pytest -s -v {project}/tests
 
 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-18.04, macos-latest]
+        os: [ubuntu-20.04, macos-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v2
@@ -35,66 +31,98 @@ jobs:
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==1.6.4
+          python -m pip install cibuildwheel
+
       - name: Build wheels on Linux
         if: runner.os == 'Linux'
         env:
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
           CIBW_BEFORE_BUILD: 'yum update -y; yum -y install hdf5-devel'
         run: |
           python -m cibuildwheel --output-dir dist
+
       - name: Build wheels Mac OS
         if: runner.os == 'macOS'
         env:
+          MACOSX_DEPLOYMENT_TARGET: '10.13'
           CIBW_BEFORE_BUILD: |
             brew update
             brew --version
-            brew install cmake
             brew install hdf5
         run: |
           python -m cibuildwheel --output-dir dist
+
+      - 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: |
+          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\"
+
+          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
+
+          python -m cibuildwheel --output-dir dist
+
       - name: Store wheel as artifact
         uses: actions/upload-artifact@v2
         with:
           name: dist
-          path: 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@v2
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.6
+      - name: Set up Python 3.7
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: 3.7
+
       - name: Build a source tarball
         run:
           python setup.py sdist
+
       - name: Test tarball
         run: |
           sudo apt 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@v2
         with:
           name: dist
-          path: dist
+          path: dist/*.tar.gz
+
+  upload_artifacts:
+    name: Upload wheels to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
 
-  upload_wheels:
     runs-on: ubuntu-latest
     needs: [build_wheels, build_sdist]
-    name: Upload wheels to PyPI
+
     steps:
       - name: Download artifacts produced during the build_wheels and build_sdist jobs
         uses: actions/download-artifact@v2
         with:
           name: dist
-          path: dist
+          path: dist/
 
       - name: Display structure of downloaded files
         run: ls -R

{MorphIO-3.3.0 → MorphIO-3.3.3}/.github/workflows/run-tests.yml

@@ -3,17 +3,21 @@ on: [pull_request, push]
 
 jobs:
   build:
-    name: Run tests on ${{ matrix.os }}
+    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++
+          - {CC: clang, CXX: clang++}
+          - {CC: gcc, CXX: g++}
+        exclude:
+          - os: macos-latest
+            compiler: {CC: gcc, CXX: g++}
 
     steps:
       - name: Checkout repository

{MorphIO-3.3.0 → MorphIO-3.3.3}/.gitignore

@@ -47,3 +47,4 @@ build/
 ci/venv*
 cmake-build*
 env*
+venv-clang-format/

{MorphIO-3.3.0 → MorphIO-3.3.3}/.gitmodules

@@ -2,7 +2,7 @@
 	path = 3rdparty/HighFive
 	url = https://github.com/BlueBrain/HighFive.git
 [submodule "3rdparty/pybind11"]
-	path = 3rdparty/pybind11
+	path = binds/python/pybind11
 	url = https://github.com/pybind/pybind11.git
 [submodule "3rdparty/GSL_LITE"]
 	path = 3rdparty/GSL_LITE
@@ -10,3 +10,6 @@
 [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

MorphIO-3.3.3/.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-3.3.0 → MorphIO-3.3.3}/3rdparty/CMakeLists.txt

@@ -14,9 +14,3 @@ target_include_directories(gsl-lite SYSTEM INTERFACE)
 
 add_library(lexertl INTERFACE)
 target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)
-
-if(BUILD_BINDINGS)
-  add_subdirectory(pybind11)
-  target_include_directories(pybind11 SYSTEM INTERFACE
-    pybind11)
-endif()

MorphIO-3.3.3/AUTHORS.txt

@@ -0,0 +1,28 @@
+Adrien Devresse
+Ahmet Bilgili
+Aleksei Sanin
+Alexander Dietz
+Alexandru Săvulescu
+Andrew Hale
+Antonio Bellotta
+Arseny V. Povolotsky
+Ben Beasley
+Benoît Coste
+Chevtchenko Grigori
+Cyrille Favreau
+Daniel Nachbaur
+Eleftherios Zisis
+Fernando Pereira
+Jafet Villafranca
+Jean-Denis Courcol
+Juan Hernando Vieites
+Matthias Wolf
+Mike Gevaert (maintainer)
+Mohamed-Ghaith Kaabi
+Nicolas Cornu
+Pablo Toharia
+Raphael Dumusc
+Snigda Dagar
+Stefan Eilemann
+Thomas Delemontex
+Tristan Carel

MorphIO-3.3.3/CHANGELOG.md

@@ -0,0 +1,45 @@
+v3.3.3
+======
+
+New Features:
+* Vasculature section_offsets & section_connectivity (#352)
+* n_points method for immutable Morphology and Vasculature (#359)
+* is_heterogeneous method for checking downstream/upstream section type homogeneity (#360)
+
+Fixes:
+* Fixed documentation links (#350)
+* Python version check >=3.7 (#356)
+* Updated pybind11 submodule to v2.8.1 (#362)
+* Added exception for attempting to write unsupported section types into ascii (#370)
+* Wheels for newer python versions
+* fix operator<< instances (#364)
+
+v3.3.2
+======
+
+Fixes:
+* Fixed wheel uploading (#355)
+
+v3.3.1
+======
+
+New Features:
+* Dendritic spine. Morphology format spec changed from 1.2 to 1.3 (#321)
+
+Fixes:
+* Imbue enums with numeric operations (#330)
+* Remove unused AccessMode enum (#331)
+* Don't compile c++ tests when creating python package (#332)
+* Use std::make_unique (#333)
+* Updated tests (#340)
+* Allow lowercase neurite names
+* Allow whitespace in CellBody neurite
+* Excluded musslinux wheels from building (#354)
+
+Previously:
+* The first neurite point is no longer connected to the soma. It was previously
+  the case if the soma was a multiple points soma. This feature has been
+  removed as choosing to which point to connect is interpretation dependant and
+  should not be the responsability of an IO tool. This feature was already
+  discussed [here](https://github.com/BlueBrain/Brion/pull/94#issuecomment-248010437).
+  This will impact primarily the surface and volume computations.

{MorphIO-3.3.0 → MorphIO-3.3.3}/CMake/CompilerFlags.cmake

@@ -1,7 +1,16 @@
-# Taken from https://github.com/BlueBrain/hpc-coding-conventions/blob/master/cpp/cmake/bob.cmake#L192-L255
 if (WIN32)
-  set(FLAGS "${FLAGS} /DH5_BUILT_AS_DYNAMIC_LIB /EHsc /D_USE_MATH_DEFINES")
+  set(FLAGS "${FLAGS} /DH5_BUILT_AS_DYNAMIC_LIB")
+
+  # Exception handling
+  # s: Enables standard C++ stack unwinding.
+  # c: [assume] functions declared as extern "C" never throw a C++ exception.
+  set(FLAGS "${FLAGS} /EHsc")
+
+  # get access to M_PI constant
+  set(FLAGS "${FLAGS} /D_USE_MATH_DEFINES")
+
 elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  # Taken from https://github.com/BlueBrain/hpc-coding-conventions/blob/master/cpp/cmake/bob.cmake#L192-L255
   if(${PROJECT_NAME}_CXX_WARNINGS)
     set(FLAGS "${FLAGS} -Werror -Weverything")
     # Using std=c++11, no need for 98 compat
@@ -33,6 +42,7 @@ elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
       set(FLAGS "${FLAGS} -fcomment-block-commands=file")
     endif()
   endif()
+
 elseif(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
   if(${PROJECT_NAME}_CXX_WARNINGS)
     set(FLAGS "${FLAGS} -Wall")

{MorphIO-3.3.0 → MorphIO-3.3.3}/CMakeLists.txt

@@ -7,7 +7,9 @@ set(CMAKE_VERBOSE_MAKEFILE ON)
 
 option(BUILD_BINDINGS "Build the python bindings" ON)
 option(MorphIO_CXX_WARNINGS "Compile C++ with warnings" ON)
+option(EXTERNAL_CATCH2 "Use Catch2 from external source" OFF)
 option(EXTERNAL_HIGHFIVE "Use HighFive from external source" OFF)
+option(EXTERNAL_PYBIND11 "Use pybind11 from external source" OFF)
 option(MORPHIO_TESTS "Build tests" ON)
 option(MORPHIO_USE_DOUBLE "Use doubles instead of floats" OFF)
 
@@ -27,9 +29,15 @@ set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
 include(CompilerFlags)
 set(CMAKE_CXX_FLAGS "${FLAGS}")
 
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 if (EXTERNAL_HIGHFIVE)
   find_package(HighFive REQUIRED)
 endif()
+if (EXTERNAL_PYBIND11)
+  find_package(pybind11 REQUIRED CONFIG)
+endif()
 set(MORPHIO_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include/)
 
 add_subdirectory(3rdparty)
@@ -58,5 +66,11 @@ install(
 
 if (MORPHIO_TESTS)
   enable_testing()
+  if (EXTERNAL_CATCH2)
+    find_package(Catch2 REQUIRED)
+  else()
+    add_subdirectory(3rdparty/Catch2)
+    include(3rdparty/Catch2/contrib/Catch.cmake)
+  endif()
   add_subdirectory(tests)
 endif()

MorphIO-3.3.3/MANIFEST.in

@@ -0,0 +1,32 @@
+# MorphIO c++
+graft src
+graft include
+include CMakeLists.txt
+
+# MorphIO submodule dependencies
+include 3rdparty/GSL_LITE/CMakeLists.txt 3rdparty/GSL_LITE/gsl-lite.natvis
+recursive-include 3rdparty/GSL_LITE/cmake *
+recursive-include 3rdparty/GSL_LITE/include *
+
+include 3rdparty/HighFive/CMakeLists.txt
+recursive-include 3rdparty/HighFive/include *
+recursive-include 3rdparty/HighFive/CMake *
+recursive-include 3rdparty/HighFive/doc *
+
+include 3rdparty/lexertl14/CMakeLists.txt
+recursive-include 3rdparty/lexertl14/include/lexertl *
+
+# pybind11 for python bindings
+recursive-include binds/python/pybind11/include *
+recursive-include binds/python/pybind11/tools *.cmake
+include binds/python/pybind11/CMakeLists.txt
+include binds/python/pybind11/LICENSE
+
+# setuptools_scm forces all SCM files to be packaged into sdist
+# we need to manually exclude them to prevent their inclusion
+# see https://github.com/pypa/setuptools_scm/issues/190
+prune ci
+prune doc
+prune tests
+prune scripts
+prune examples

{MorphIO-3.3.0 → MorphIO-3.3.3/MorphIO.egg-info}/PKG-INFO

@@ -1,11 +1,14 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.3.0
+Version: 3.3.3
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
 License: LGPLv3
-Description: |license| |build| |docs|
+Description: .. image:: doc/source/logo/BBP-MorphIO.jpg
+        
+        
+        |license| |build| |docs|
         
         MorphIO
         =======
@@ -13,7 +16,7 @@ Description: |license| |build| |docs|
         Documentation
         -------------
         
-        MorphIO documentation is built and hosted on `readthedocs <http://morphio.readthedocs.org/>`.
+        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/>`_
@@ -93,8 +96,9 @@ Description: |license| |build| |docs|
                      :alt: documentation status
         
         
-Keywords: computational neuroscience,morphology,neuronneurolucidaneuromorphology
+Keywords: computational neuroscience,morphology,neuron,neurolucida,neuromorphology
 Platform: UNKNOWN
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
-Description-Content-Type: text/x-rst
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
 Provides-Extra: docs