morphio 3.3.2__tar.gz → 3.3.3__tar.gz

{MorphIO-3.3.2 → MorphIO-3.3.3}/.github/workflows/check-sdist.yml

@@ -14,10 +14,10 @@ jobs:
         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-3.3.2 → MorphIO-3.3.3}/.github/workflows/publish-sdist-wheels.yml

@@ -3,7 +3,7 @@ on: [pull_request, push]
 
 env:
   CIBW_BUILD_VERBOSITY: 3
-  CIBW_BUILD: 'cp3?-*'
+  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
@@ -66,7 +66,7 @@ jobs:
           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 (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.0
+          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
 

{MorphIO-3.3.2 → MorphIO-3.3.3}/.github/workflows/run-tests.yml

@@ -3,7 +3,7 @@ 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
@@ -13,10 +13,11 @@ jobs:
       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-3.3.2 → MorphIO-3.3.3}/.gitignore

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

{MorphIO-3.3.2 → 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-3.3.2 → MorphIO-3.3.3}/.readthedocs.yaml

@@ -14,8 +14,18 @@ submodules:
 # 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"
 
-conda:
-  environment: doc/environment.yml
+sphinx:
+  configuration: doc/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

{MorphIO-3.3.2 → 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/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-3.3.2 → 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-3.3.2 → MorphIO-3.3.3/MorphIO.egg-info}/PKG-INFO

@@ -1,11 +1,14 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.3.2
+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/>`_
@@ -96,5 +99,6 @@ Description: |license| |build| |docs|
 Keywords: computational neuroscience,morphology,neuron,neurolucida,neuromorphology
 Platform: UNKNOWN
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Provides-Extra: docs

{MorphIO-3.3.2 → MorphIO-3.3.3}/MorphIO.egg-info/SOURCES.txt

@@ -129,39 +129,6 @@ setup.py
 3rdparty/lexertl14/include/lexertl/parser/tree/sequence_node.hpp
 3rdparty/lexertl14/include/lexertl/partition/charset.hpp
 3rdparty/lexertl14/include/lexertl/partition/equivset.hpp
-3rdparty/pybind11/CMakeLists.txt
-3rdparty/pybind11/include/pybind11/attr.h
-3rdparty/pybind11/include/pybind11/buffer_info.h
-3rdparty/pybind11/include/pybind11/cast.h
-3rdparty/pybind11/include/pybind11/chrono.h
-3rdparty/pybind11/include/pybind11/common.h
-3rdparty/pybind11/include/pybind11/complex.h
-3rdparty/pybind11/include/pybind11/eigen.h
-3rdparty/pybind11/include/pybind11/embed.h
-3rdparty/pybind11/include/pybind11/eval.h
-3rdparty/pybind11/include/pybind11/functional.h
-3rdparty/pybind11/include/pybind11/iostream.h
-3rdparty/pybind11/include/pybind11/numpy.h
-3rdparty/pybind11/include/pybind11/operators.h
-3rdparty/pybind11/include/pybind11/options.h
-3rdparty/pybind11/include/pybind11/pybind11.h
-3rdparty/pybind11/include/pybind11/pytypes.h
-3rdparty/pybind11/include/pybind11/stl.h
-3rdparty/pybind11/include/pybind11/stl_bind.h
-3rdparty/pybind11/include/pybind11/detail/class.h
-3rdparty/pybind11/include/pybind11/detail/common.h
-3rdparty/pybind11/include/pybind11/detail/descr.h
-3rdparty/pybind11/include/pybind11/detail/init.h
-3rdparty/pybind11/include/pybind11/detail/internals.h
-3rdparty/pybind11/include/pybind11/detail/typeid.h
-3rdparty/pybind11/tools/FindCatch.cmake
-3rdparty/pybind11/tools/FindEigen3.cmake
-3rdparty/pybind11/tools/FindPythonLibsNew.cmake
-3rdparty/pybind11/tools/check-style.sh
-3rdparty/pybind11/tools/libsize.py
-3rdparty/pybind11/tools/mkdoc.py
-3rdparty/pybind11/tools/pybind11Config.cmake.in
-3rdparty/pybind11/tools/pybind11Tools.cmake
 CMake/CodeCoverage.cmake
 CMake/CompilerFlags.cmake
 CMake/MorphIOConfig.cmake
@@ -186,42 +153,41 @@ binds/python/bindings_utils.h
 binds/python/morphio.cpp
 binds/python/generated/.clang-format
 binds/python/generated/docstrings.h
-ci/check_clang_format.sh
-ci/check_generated_docstrings.sh
-ci/coverage_test.sh
-ci/cpp_test.sh
-ci/python_test.sh
-doc/Makefile
-doc/README.md
-doc/environment.yml
-doc/source/Doxyfile
-doc/source/DoxygenLayout.xml
-doc/source/conf.py
-doc/source/cpp.rst
-doc/source/footer.html
-doc/source/glia.rst
-doc/source/header.html
-doc/source/index.rst
-doc/source/install.rst
-doc/source/markers.rst
-doc/source/mitochondria.rst
-doc/source/morphology.rst
-doc/source/python.rst
-doc/source/reticulum.rst
-doc/source/specification.rst
-doc/source/specification_neurolucida.rst
-doc/source/warnings.rst
-doc/source/_templates/doxygen_page.rst_t
-doc/source/doxygen/.gitignore
-doc/source/images/section_segment.svg
-doc/source/images/sections.svg
-doc/source/images/swc/sequential.svg
-doc/source/images/swc/sphere.svg
-doc/source/images/swc/split.svg
-doc/source/images/swc/three_pt.svg
-doc/source/images/swc/two_pt.svg
-examples/getting_started.ipynb
-examples/getting_started_mutable.ipynb
+binds/python/pybind11/CMakeLists.txt
+binds/python/pybind11/LICENSE
+binds/python/pybind11/include/pybind11/attr.h
+binds/python/pybind11/include/pybind11/buffer_info.h
+binds/python/pybind11/include/pybind11/cast.h
+binds/python/pybind11/include/pybind11/chrono.h
+binds/python/pybind11/include/pybind11/common.h
+binds/python/pybind11/include/pybind11/complex.h
+binds/python/pybind11/include/pybind11/eigen.h
+binds/python/pybind11/include/pybind11/embed.h
+binds/python/pybind11/include/pybind11/eval.h
+binds/python/pybind11/include/pybind11/functional.h
+binds/python/pybind11/include/pybind11/gil.h
+binds/python/pybind11/include/pybind11/iostream.h
+binds/python/pybind11/include/pybind11/numpy.h
+binds/python/pybind11/include/pybind11/operators.h
+binds/python/pybind11/include/pybind11/options.h
+binds/python/pybind11/include/pybind11/pybind11.h
+binds/python/pybind11/include/pybind11/pytypes.h
+binds/python/pybind11/include/pybind11/stl.h
+binds/python/pybind11/include/pybind11/stl_bind.h
+binds/python/pybind11/include/pybind11/detail/class.h
+binds/python/pybind11/include/pybind11/detail/common.h
+binds/python/pybind11/include/pybind11/detail/descr.h
+binds/python/pybind11/include/pybind11/detail/init.h
+binds/python/pybind11/include/pybind11/detail/internals.h
+binds/python/pybind11/include/pybind11/detail/type_caster_base.h
+binds/python/pybind11/include/pybind11/detail/typeid.h
+binds/python/pybind11/include/pybind11/stl/filesystem.h
+binds/python/pybind11/tools/FindCatch.cmake
+binds/python/pybind11/tools/FindEigen3.cmake
+binds/python/pybind11/tools/FindPythonLibsNew.cmake
+binds/python/pybind11/tools/pybind11Common.cmake
+binds/python/pybind11/tools/pybind11NewTools.cmake
+binds/python/pybind11/tools/pybind11Tools.cmake
 include/morphio/dendritic_spine.h
 include/morphio/endoplasmic_reticulum.h
 include/morphio/enums.h
@@ -234,7 +200,6 @@ include/morphio/morphology.h
 include/morphio/properties.h
 include/morphio/section.h
 include/morphio/section_base.h
-include/morphio/section_base.tpp
 include/morphio/section_iterators.hpp
 include/morphio/soma.h
 include/morphio/tools.h
@@ -258,7 +223,6 @@ include/morphio/vasc/vasculature.h
 morphio/__init__.py
 morphio/mut/__init__.py
 morphio/vasculature/__init__.py
-scripts/check-clang-format-all
 src/CMakeLists.txt
 src/dendritic_spine.cpp
 src/endoplasmic_reticulum.cpp
@@ -291,93 +255,8 @@ src/readers/morphologyHDF5.cpp
 src/readers/morphologyHDF5.h
 src/readers/morphologySWC.cpp
 src/readers/morphologySWC.h
-src/readers/utilsHDF5.h
 src/readers/vasculatureHDF5.cpp
 src/readers/vasculatureHDF5.h
 src/vasc/properties.cpp
 src/vasc/section.cpp
-src/vasc/vasculature.cpp
-tests/CMakeLists.txt
-tests/main.cpp
-tests/requirement_tests.txt
-tests/test_0_API.py
-tests/test_10_vasculature.py
-tests/test_1_swc.py
-tests/test_2_neurolucida.py
-tests/test_3_h5.py
-tests/test_4_immut.py
-tests/test_5_mut.py
-tests/test_6_writers.py
-tests/test_7_modifiers.py
-tests/test_8_all_morphologies.py
-tests/test_9_surfaces.py
-tests/test_immutable_morphology.cpp
-tests/test_morphology_readers.cpp
-tests/test_mutable_morphology.cpp
-tests/utils.py
-tests/contrib/catch.hpp
-tests/data/annotations.asc
-tests/data/astrocyte.h5
-tests/data/circle_contour.asc
-tests/data/complexe.swc
-tests/data/disconnected_neurite.swc
-tests/data/invalid-incomplete.asc
-tests/data/iterators.asc
-tests/data/marker-with-string.asc
-tests/data/markers.asc
-tests/data/mono-type.asc
-tests/data/multiple_point_section.asc
-tests/data/multiple_soma.swc
-tests/data/nested_single_children.asc
-tests/data/neurite_wrong_root_point.swc
-tests/data/no_soma.swc
-tests/data/nrn-order-already-sorted.h5
-tests/data/nrn_ordering.swc
-tests/data/pia.asc
-tests/data/reversed_NRN_neurite_order.swc
-tests/data/sections-block.asc
-tests/data/simple-with-font.asc
-tests/data/simple-with-image-coord.asc
-tests/data/simple.asc
-tests/data/simple.swc
-tests/data/simple.unknown
-tests/data/simple2.asc
-tests/data/single_point_root.asc
-tests/data/soma_cylinders.swc
-tests/data/soma_multiple_frustums.swc
-tests/data/soma_single_frustum.swc
-tests/data/soma_three_points_cylinder.swc
-tests/data/spine.asc
-tests/data/three_point_soma.swc
-tests/data/h5/empty.h5
-tests/data/h5/merged.h5
-tests/data/h5/non-valid.h5
-tests/data/h5/vasculature-broken-section-type.h5
-tests/data/h5/vasculature1.h5
-tests/data/h5/vasculature2.h5
-tests/data/h5/v1/Neuron-no-soma.h5
-tests/data/h5/v1/Neuron.h5
-tests/data/h5/v1/endoplasmic-reticulum.h5
-tests/data/h5/v1/glia.h5
-tests/data/h5/v1/glia_empty_perimeters.h5
-tests/data/h5/v1/glia_soma_only.h5
-tests/data/h5/v1/glia_wrong_sized_perimeters.h5
-tests/data/h5/v1/h5v1.4.h5
-tests/data/h5/v1/incorrect_point_columns.h5
-tests/data/h5/v1/incorrect_structure_columns.h5
-tests/data/h5/v1/make-dendritic-spine.py
-tests/data/h5/v1/metadata_group_only.h5
-tests/data/h5/v1/mitochondria.h5
-tests/data/h5/v1/monodim.h5
-tests/data/h5/v1/simple-broken-section-type.h5
-tests/data/h5/v1/simple-dendritric-spine.h5
-tests/data/h5/v1/simple-negative-section-type.h5
-tests/data/h5/v1/simple-two-point-soma.h5
-tests/data/h5/v1/simple.h5
-tests/data/h5/v1/single-neurite.h5
-tests/data/h5/v1/soma_after_dendrite.h5
-tests/data/h5/v1/soma_no_neurites.h5
-tests/data/h5/v1/three-point-soma-two-offset.h5
-tests/data/h5/v1/two_child_unmerged.h5
-tests/data/h5/v1/unknown_section_type_structure.h5
-tests/data/h5/v2/Neuron.h5
+src/vasc/vasculature.cpp

{MorphIO-3.3.2/MorphIO.egg-info → MorphIO-3.3.3}/PKG-INFO

@@ -1,11 +1,14 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.3.2
+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/>`_
@@ -96,5 +99,6 @@ Description: |license| |build| |docs|
 Keywords: computational neuroscience,morphology,neuron,neurolucida,neuromorphology
 Platform: UNKNOWN
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 Provides-Extra: docs

{MorphIO-3.3.2 → MorphIO-3.3.3}/README.rst

@@ -1,3 +1,6 @@
+.. image:: doc/source/logo/BBP-MorphIO.jpg
+
+
 |license| |build| |docs|
 
 MorphIO
@@ -6,7 +9,7 @@ MorphIO
 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/>`_

MorphIO-3.3.3/binds/python/CMakeLists.txt

@@ -0,0 +1,17 @@
+if (NOT EXTERNAL_PYBIND11)
+    add_subdirectory(pybind11 EXCLUDE_FROM_ALL)
+endif()
+
+pybind11_add_module(_morphio SYSTEM
+    morphio.cpp
+    bind_immutable.cpp
+    bindings_utils.cpp
+    bind_misc.cpp
+    bind_mutable.cpp
+    bind_vasculature.cpp
+)
+
+target_link_libraries(_morphio
+    PRIVATE morphio_static
+    PRIVATE pybind11::module
+)

{MorphIO-3.3.2 → MorphIO-3.3.3}/binds/python/bind_immutable.cpp

@@ -87,6 +87,12 @@ void bind_immutable_module(py::module& m) {
             "Returns a list with all points from all sections (soma points are not included)\n"
             "Note: points belonging to the n'th section are located at indices:\n"
             "[Morphology.sectionOffsets(n), Morphology.sectionOffsets(n+1)[")
+
+        .def_property_readonly(
+            "n_points",
+            [](const morphio::Morphology& obj) { return obj.points().size(); },
+            "Returns the number of points from all sections (soma points are not included)")
+
         .def_property_readonly(
             "diameters",
             [](const morphio::Morphology& morpho) {
@@ -108,14 +114,14 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly(
             "section_offsets",
             [](const morphio::Morphology& morpho) { return as_pyarray(morpho.sectionOffsets()); },
-            "Returns a list with offsets to access data of a specific section in the points\n"
-            "and diameters arrays.\n"
+            "Returns a list with N+1 offsets to access data of a specific section in the points\n"
+            "and diameters arrays (size N).\n"
             "\n"
-            "Example: accessing diameters of n'th section will be located in the DIAMETERS\n"
-            "array from DIAMETERS[sectionOffsets(n)] to DIAMETERS[sectionOffsets(n+1)-1]\n"
+            "Example: accessing diameters of n'th section will be located in the diameters\n"
+            "array: diameters[section_offsets[n]: section_offsets[n + 1]]\n"
             "\n"
-            "Note: for convenience, the last point of this array is the points array size\n"
-            "so that the above example works also for the last section.")
+            "Note: for convenience, the last element of this array is equal to the length of the\n"
+            "points/diameters arrays so that the above example works also for the last section.")
         .def_property_readonly(
             "section_types",
             [](const morphio::Morphology& morph) {
@@ -264,6 +270,12 @@ void bind_immutable_module(py::module& m) {
             "points",
             [](morphio::Section* section) { return span_array_to_ndarray(section->points()); },
             "Returns list of section's point coordinates")
+
+        .def_property_readonly(
+            "n_points",
+            [](const morphio::Section& section) { return section.points().size(); },
+            "Returns the number of points in section")
+
         .def_property_readonly(
             "diameters",
             [](morphio::Section* section) { return span_to_ndarray(section->diameters()); },
@@ -273,6 +285,15 @@ void bind_immutable_module(py::module& m) {
             [](morphio::Section* section) { return span_to_ndarray(section->perimeters()); },
             "Returns list of section's point perimeters")
 
+        .def("is_heterogeneous",
+             &morphio::Section::isHeterogeneous,
+             "Returns true if the tree downtream (downstream = true) or upstream (downstream = "
+             "false)\n"
+             "has the same type as the current section.",
+             py::arg("downstream") = true)
+
+        .def("has_same_shape", &morphio::Section::hasSameShape)
+
         // Iterators
         .def(
             "iter",
@@ -342,6 +363,8 @@ void bind_immutable_module(py::module& m) {
             "      - a relative distance of 1 means the mitochondrial point is at the "
             "end of the neuronal section\n")
 
+        .def("has_same_shape", &morphio::MitoSection::hasSameShape)
+
         // Iterators
         .def(
             "iter",

{MorphIO-3.3.2 → MorphIO-3.3.3}/binds/python/bind_mutable.cpp

@@ -309,6 +309,8 @@ void bind_mutable_module(py::module& m) {
             },
             "Returns the neurite section Ids of all points of this section")
 
+        .def("has_same_shape", &morphio::mut::MitoSection::hasSameShape)
+
         .def("append_section",
              static_cast<std::shared_ptr<morphio::mut::MitoSection> (morphio::mut::MitoSection::*)(
                  const morphio::Property::MitochondriaPointLevel&)>(
@@ -392,6 +394,14 @@ void bind_mutable_module(py::module& m) {
         .def_property_readonly("children",
                                &morphio::mut::Section::children,
                                "Returns a list of children IDs")
+        .def("is_heterogeneous",
+             &morphio::mut::Section::isHeterogeneous,
+             "Returns true if the tree downtream (downstream = true) or upstream (downstream = "
+             "false)\n"
+             "has the same type as the current section.",
+             py::arg("downstream") = true)
+        .def("has_same_shape", &morphio::mut::Section::hasSameShape)
+
         // Iterators
         .def(
             "iter",