morphio 3.2.0__tar.gz → 3.3.2__tar.gz

{MorphIO-3.2.0 → MorphIO-3.3.2}/.github/workflows/check-sdist.yml

@@ -5,6 +5,10 @@ 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:

{MorphIO-3.2.0 → MorphIO-3.3.2}/.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-3.3.2/.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-3.3.2/.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-3.2.0 → MorphIO-3.3.2}/.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_VERBOSITY: 3
   CIBW_BUILD: 'cp3?-*'
-  CIBW_SKIP: 'cp35-* cp39-* *-manylinux_i686'
+  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 (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.0
+
+          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-3.2.0 → MorphIO-3.3.2}/.github/workflows/run-tests.yml

@@ -6,6 +6,9 @@ jobs:
     name: Run tests on ${{ matrix.os }}
     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]

MorphIO-3.3.2/.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .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:
+  apt_packages:
+    - libhdf5-dev
+
+conda:
+  environment: doc/environment.yml

MorphIO-3.3.2/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-3.3.2/CHANGELOG.md

@@ -0,0 +1,21 @@
+v3.3.1
+
+New Features:
+    * Dendritic spine (#321)
+
+Fixes:
+    * updated tests
+    * use std::make_unique (#333)
+    * don't compile c++ tests when creating python package (#332)
+    * remove unused AccessMode enum (#331)
+    * Imbue enums with numeric operations (#330)
+    * allow lowercase neurite names
+    * allow whitespace in CellBody neurite
+
+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-3.2.0 → MorphIO-3.3.2}/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-3.2.0 → MorphIO-3.3.2/MorphIO.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.2.0
+Version: 3.3.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -93,8 +93,8 @@ 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
+Description-Content-Type: text/markdown
 Provides-Extra: docs

{MorphIO-3.2.0 → MorphIO-3.3.2}/MorphIO.egg-info/SOURCES.txt

@@ -3,13 +3,15 @@
 .gitmodules
 .readthedocs.yaml
 .travis.yml
-CHANGLOG.md
+AUTHORS.txt
+CHANGELOG.md
 CMakeLists.txt
 CONTRIBUTING.md
 COPYING
 COPYING.LESSER
 MANIFEST.in
 README.rst
+pyproject.toml
 setup.py
 .github/workflows/check-sdist.yml
 .github/workflows/clang_format_check.yaml
@@ -220,6 +222,7 @@ doc/source/images/swc/three_pt.svg
 doc/source/images/swc/two_pt.svg
 examples/getting_started.ipynb
 examples/getting_started_mutable.ipynb
+include/morphio/dendritic_spine.h
 include/morphio/endoplasmic_reticulum.h
 include/morphio/enums.h
 include/morphio/errorMessages.h
@@ -238,6 +241,7 @@ include/morphio/tools.h
 include/morphio/types.h
 include/morphio/vector_types.h
 include/morphio/version.h
+include/morphio/mut/dendritic_spine.h
 include/morphio/mut/endoplasmic_reticulum.h
 include/morphio/mut/glial_cell.h
 include/morphio/mut/mito_section.h
@@ -256,6 +260,7 @@ morphio/mut/__init__.py
 morphio/vasculature/__init__.py
 scripts/check-clang-format-all
 src/CMakeLists.txt
+src/dendritic_spine.cpp
 src/endoplasmic_reticulum.cpp
 src/enums.cpp
 src/errorMessages.cpp
@@ -269,6 +274,7 @@ src/shared_utils.hpp
 src/soma.cpp
 src/vector_utils.cpp
 src/version.cpp.in
+src/mut/dendritic_spine.cpp
 src/mut/endoplasmic_reticulum.cpp
 src/mut/glial_cell.cpp
 src/mut/mito_section.cpp
@@ -315,8 +321,10 @@ 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
@@ -354,13 +362,15 @@ 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/h5v1.3.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

{MorphIO-3.2.0/MorphIO.egg-info → MorphIO-3.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.2.0
+Version: 3.3.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -93,8 +93,8 @@ 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
+Description-Content-Type: text/markdown
 Provides-Extra: docs

{MorphIO-3.2.0 → MorphIO-3.3.2}/binds/python/bind_immutable.cpp

@@ -1,16 +1,24 @@
 #include "bind_immutable.h"
 
+#include <pybind11/iostream.h>  // py::add_ostream_redirect
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
-#include <pybind11/iostream.h>  // py::add_ostream_redirect
 
+#include <morphio/dendritic_spine.h>
 #include <morphio/endoplasmic_reticulum.h>
 #include <morphio/enums.h>
 #include <morphio/glial_cell.h>
+#include <morphio/mut/dendritic_spine.h>
+#include <morphio/mut/endoplasmic_reticulum.h>
+#include <morphio/mut/glial_cell.h>
+#include <morphio/mut/mitochondria.h>
+//#include <morphio/mut/dendritic_spine.h>
 #include <morphio/mut/morphology.h>
 #include <morphio/soma.h>
 #include <morphio/types.h>
 
+#include <memory>  // std::make_unique
+
 #include "bind_enums.h"
 #include "bindings_utils.h"
 
@@ -28,8 +36,7 @@ void bind_immutable_module(py::module& m) {
              "options"_a = morphio::enums::Option::NO_MODIFIER)
         .def(py::init<morphio::mut::Morphology&>())
         .def(py::init([](py::object arg, unsigned int options) {
-                 return std::unique_ptr<morphio::Morphology>(
-                     new morphio::Morphology(py::str(arg), options));
+                 return std::make_unique<morphio::Morphology>(py::str(arg), options);
              }),
              "filename"_a,
              "options"_a = morphio::enums::Option::NO_MODIFIER,
@@ -151,9 +158,8 @@ void bind_immutable_module(py::module& m) {
 
     py::class_<morphio::GlialCell, morphio::Morphology>(m, "GlialCell")
         .def(py::init<const std::string&>())
-        .def(py::init([](py::object arg) {
-                 return std::unique_ptr<morphio::GlialCell>(new morphio::GlialCell(py::str(arg)));
-             }),
+        .def(py::init(
+                 [](py::object arg) { return std::make_unique<morphio::GlialCell>(py::str(arg)); }),
              "filename"_a,
              "Additional Ctor that accepts as filename any python object that implements __repr__ "
              "or __str__");
@@ -279,8 +285,9 @@ void bind_immutable_module(py::module& m) {
                 case IterType::UPSTREAM:
                     return py::make_iterator(section->upstream_begin(), section->upstream_end());
                 default:
-                    throw morphio::MorphioError("Only iteration types depth_first, breadth_first and "
-                                              "upstream are supported");
+                    throw morphio::MorphioError(
+                        "Only iteration types depth_first, breadth_first and "
+                        "upstream are supported");
                 }
             },
             py::keep_alive<0, 1>() /* Essential: keep object alive while iterator exists */,
@@ -347,8 +354,9 @@ void bind_immutable_module(py::module& m) {
                 case IterType::UPSTREAM:
                     return py::make_iterator(section->upstream_begin(), section->upstream_end());
                 default:
-                    throw morphio::MorphioError("Only iteration types depth_first, breadth_first and "
-                                                "upstream are supported");
+                    throw morphio::MorphioError(
+                        "Only iteration types depth_first, breadth_first and "
+                        "upstream are supported");
                 }
             },
             py::keep_alive<0, 1>() /* Essential: keep object alive while iterator exists */,
@@ -357,4 +365,105 @@ void bind_immutable_module(py::module& m) {
             "If id == -1, the iteration will be successively performed starting\n"
             "at each root section",
             "iter_type"_a = IterType::DEPTH_FIRST);
+
+    py::class_<morphio::DendriticSpine, morphio::Morphology>(m, "DendriticSpine")
+        .def(py::init([](py::object arg) {
+                 return std::make_unique<morphio::DendriticSpine>(py::str(arg));
+             }),
+             "filename"_a)
+        .def_property_readonly("root_sections",
+                               &morphio::DendriticSpine::rootSections,
+                               "Returns a list of all root sections "
+                               "(sections whose parent ID are -1)")
+        .def_property_readonly("sections",
+                               &morphio::DendriticSpine::sections,
+                               "Returns a vector containing all sections objects\n\n"
+                               "Notes:\n"
+                               "- Soma is not included\n"
+                               "- First section ID is 1 (0 is reserved for the soma)\n"
+                               "- To select sections by ID use: DendriticSpine::section(id)")
+
+        .def("section",
+             &morphio::DendriticSpine::section,
+             "Returns the Section with the given id\n"
+             "throw RawDataError if the id is out of range",
+             "section_id"_a)
+
+        // Property accessors
+        .def_property_readonly(
+            "points",
+            [](morphio::DendriticSpine* morpho) {
+                const auto& data = morpho->points();
+                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            },
+            "Returns a list with all points from all sections\n"
+            "Note: points belonging to the n'th section are located at indices:\n"
+            "[DendriticSpine.sectionOffsets(n), DendriticSpine.sectionOffsets(n+1)[")
+        .def_property_readonly(
+            "diameters",
+            [](const morphio::DendriticSpine& morpho) {
+                const auto& data = morpho.diameters();
+                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            },
+            "Returns a list with all diameters from all sections\n"
+            "Note: diameters belonging to the n'th section are located at indices:\n"
+            "[DendriticSpine.sectionOffsets(n), DendriticSpine.sectionOffsets(n+1)[")
+        .def_property_readonly(
+            "section_offsets",
+            [](const morphio::DendriticSpine& 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"
+            "\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"
+            "\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.")
+        .def_property_readonly(
+            "section_types",
+            [](const morphio::DendriticSpine& morph) {
+                const auto& data = morph.sectionTypes();
+                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            },
+            "Returns a vector with the section type of every section")
+        .def_property_readonly("connectivity",
+                               &morphio::DendriticSpine::connectivity,
+                               "Return the graph connectivity of the DendriticSpine "
+                               "where each section is seen as a node\nNote: -1 is the soma node")
+        .def_property_readonly("cell_family",
+                               &morphio::DendriticSpine::cellFamily,
+                               "Returns the cell family (neuron or glia)")
+        .def_property_readonly("post_synaptic_density",
+                               &morphio::DendriticSpine::postSynapticDensity,
+                               "Returns the post synaptic density values")
+        .def_property_readonly("version", &morphio::DendriticSpine::version, "Returns the version")
+
+        // Iterators
+        .def(
+            "iter",
+            [](morphio::DendriticSpine* morpho, IterType type) {
+                switch (type) {
+                case IterType::DEPTH_FIRST:
+                    return py::make_iterator(morpho->depth_begin(), morpho->depth_end());
+                case IterType::BREADTH_FIRST:
+                    return py::make_iterator(morpho->breadth_begin(), morpho->breadth_end());
+                case IterType::UPSTREAM:
+                default:
+                    throw morphio::MorphioError(
+                        "Only iteration types depth_first and breadth_first are supported");
+                }
+            },
+            py::keep_alive<0, 1>() /* Essential: keep object alive while iterator exists */,
+            "Section iterator that runs successively on every neurite\n"
+            "iter_type controls the order of iteration on sections of a given neurite. 2 values "
+            "can be passed:\n"
+            "- morphio.IterType.depth_first (default)\n"
+            "- morphio.IterType.breadth_first (default)\n",
+            "iter_type"_a = IterType::DEPTH_FIRST)
+        .def(
+            "write",
+            [](morphio::mut::DendriticSpine* morph, py::object arg) { morph->write(py::str(arg)); },
+            "filename"_a);
 }