morphio 3.0.0__tar.gz → 3.1.0__tar.gz

{MorphIO-3.0.0 → MorphIO-3.1.0}/.github/workflows/coverage_test.yaml

@@ -1,10 +1,13 @@
 name: coverage-test
 on: [pull_request, push]
+env:
+  CC: gcc-9
+  CXX: g++-9
 
 jobs:
     build:
         name: coverage-test
-        runs-on: ubuntu-18.04
+        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
 

{MorphIO-3.0.0 → MorphIO-3.1.0}/.github/workflows/publish-sdist-wheels.yml

@@ -13,7 +13,7 @@ env:
   CIBW_BUILD: 'cp3?-*'
   CIBW_SKIP: 'cp35-* cp39-* *-manylinux_i686'
   CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
-  CIBW_TEST_COMMAND: nosetests -s -v -P {project}/tests
+  CIBW_TEST_COMMAND: pytest -s -v {project}/tests
 
 jobs:
   build_wheels:
@@ -78,7 +78,7 @@ jobs:
           sudo apt install -y libhdf5-dev
           pip install -r tests/requirement_tests.txt
           pip install dist/*
-          nosetests -s -v -P tests
+          pytest -s -v tests
       - name: Store sdist as artifact
         uses: actions/upload-artifact@v2
         with:

{MorphIO-3.0.0 → MorphIO-3.1.0}/.gitignore

@@ -43,3 +43,7 @@ MorphIO.egg-info/
 .tags
 build/
 .*.swp
+*.idea
+ci/venv*
+cmake-build*
+env*

{MorphIO-3.0.0 → MorphIO-3.1.0}/CONTRIBUTING.md

@@ -130,7 +130,7 @@ Run the following command to build incrementally the project: `pip install -e .`
 
 ## Test
 
-Run the following command to run the Python unit-tests: `nosetests`
+Run the following command to run the Python unit-tests: `pytest tests`
 
 ## Coding conventions
 

MorphIO-3.1.0/MorphIO.egg-info/PKG-INFO

@@ -0,0 +1,98 @@
+Metadata-Version: 2.1
+Name: MorphIO
+Version: 3.1.0
+Summary: A neuron morphology IO library
+Home-page: https://github.com/BlueBrain/MorphIO/
+Author: Blue Brain Project, EPFL
+License: LGPLv3
+Description: |license| |build| |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
+        ================
+        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 GNU Lesser General Public License version 3. Refer to
+        COPYING.LESSER and COPYING for details.
+        
+        .. |license| image:: https://img.shields.io/pypi/l/morphio
+                        :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER
+        
+        .. |build| image:: https://travis-ci.com/BlueBrain/MorphIO.svg?token=KRP9rHiV52PC6mX3ACXp&branch=master
+                        :target: https://travis-ci.com/BlueBrain/MorphIO
+                        :alt: Build Status
+        
+        .. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest
+                     :target: https://morphio.readthedocs.io/
+                     :alt: documentation status
+        
+        
+Keywords: computational neuroscience,morphology,neuronneurolucidaneuromorphology
+Platform: UNKNOWN
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Description-Content-Type: text/x-rst
+Provides-Extra: docs

{MorphIO-3.0.0 → MorphIO-3.1.0}/MorphIO.egg-info/SOURCES.txt

@@ -193,19 +193,32 @@ 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/api.rst
 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/swc/neuromorpho.svg
+doc/source/images/swc/sequential.svg
+doc/source/images/swc/single.svg
+doc/source/images/swc/split.svg
+doc/source/images/swc/two_pt.svg
 examples/getting_started.ipynb
 examples/getting_started_mutable.ipynb
 include/morphio/endoplasmic_reticulum.h
@@ -280,7 +293,6 @@ src/vasc/properties.cpp
 src/vasc/section.cpp
 src/vasc/vasculature.cpp
 tests/CMakeLists.txt
-tests/__init__.py
 tests/main.cpp
 tests/requirement_tests.txt
 tests/test_0_API.py
@@ -294,10 +306,12 @@ tests/test_6_writers.py
 tests/test_7_modifiers.py
 tests/test_8_all_morphologies.py
 tests/test_9_surfaces.py
-tests/test_morphology.cpp
-tests/test_mut_morphology.cpp
+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
@@ -309,6 +323,7 @@ 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
@@ -318,6 +333,7 @@ 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

MorphIO-3.1.0/PKG-INFO

@@ -0,0 +1,98 @@
+Metadata-Version: 2.1
+Name: MorphIO
+Version: 3.1.0
+Summary: A neuron morphology IO library
+Home-page: https://github.com/BlueBrain/MorphIO/
+Author: Blue Brain Project, EPFL
+License: LGPLv3
+Description: |license| |build| |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
+        ================
+        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 GNU Lesser General Public License version 3. Refer to
+        COPYING.LESSER and COPYING for details.
+        
+        .. |license| image:: https://img.shields.io/pypi/l/morphio
+                        :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER
+        
+        .. |build| image:: https://travis-ci.com/BlueBrain/MorphIO.svg?token=KRP9rHiV52PC6mX3ACXp&branch=master
+                        :target: https://travis-ci.com/BlueBrain/MorphIO
+                        :alt: Build Status
+        
+        .. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest
+                     :target: https://morphio.readthedocs.io/
+                     :alt: documentation status
+        
+        
+Keywords: computational neuroscience,morphology,neuronneurolucidaneuromorphology
+Platform: UNKNOWN
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Description-Content-Type: text/x-rst
+Provides-Extra: docs

MorphIO-3.1.0/README.rst

@@ -0,0 +1,85 @@
+|license| |build| |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
+================
+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 GNU Lesser General Public License version 3. Refer to
+COPYING.LESSER and COPYING for details.
+
+.. |license| image:: https://img.shields.io/pypi/l/morphio
+                :target: https://github.com/BlueBrain/morphio/blob/master/COPYING.LESSER
+
+.. |build| image:: https://travis-ci.com/BlueBrain/MorphIO.svg?token=KRP9rHiV52PC6mX3ACXp&branch=master
+                :target: https://travis-ci.com/BlueBrain/MorphIO
+                :alt: Build Status
+
+.. |docs| image:: https://readthedocs.org/projects/morphio/badge/?version=latest
+             :target: https://morphio.readthedocs.io/
+             :alt: documentation status
+

{MorphIO-3.0.0 → MorphIO-3.1.0}/binds/python/bind_misc.cpp

@@ -8,6 +8,7 @@
 #include <morphio/types.h>
 #include <morphio/version.h>
 
+#include "../../include/morphio/enums.h"
 #include "bind_enums.h"
 
 namespace py = pybind11;
@@ -20,6 +21,7 @@ void bind_misc(py::module& m) {
           "Set the maximum number of warnings to be printed on screen\n"
           "0 will print no warning\n"
           "-1 will print them all");
+    m.def("set_raise_warnings", &morphio::set_raise_warnings, "Whether to raise warning as errors");
     m.def("set_ignored_warning",
           static_cast<void (*)(morphio::Warning, bool)>(&morphio::set_ignored_warning),
           "Ignore/Unignore a specific warning message",
@@ -55,8 +57,16 @@ void bind_misc(py::module& m) {
         .value("axon", morphio::enums::SectionType::SECTION_AXON)
         .value("basal_dendrite", morphio::enums::SectionType::SECTION_DENDRITE)
         .value("apical_dendrite", morphio::enums::SectionType::SECTION_APICAL_DENDRITE)
-        // .value("glia_process", morphio::enums::SectionType::SECTION_GLIA_PROCESS)
-        // .value("glia_endfoot", morphio::enums::SectionType::SECTION_GLIA_ENDFOOT)
+        .value("custom5", morphio::enums::SectionType::SECTION_CUSTOM_5)
+        .value("custom6", morphio::enums::SectionType::SECTION_CUSTOM_6)
+        .value("custom7", morphio::enums::SectionType::SECTION_CUSTOM_7)
+        .value("custom8", morphio::enums::SectionType::SECTION_CUSTOM_8)
+        .value("custom9", morphio::enums::SectionType::SECTION_CUSTOM_9)
+        .value("custom10", morphio::enums::SectionType::SECTION_CUSTOM_10)
+        .value("glia_perivascular_process",
+               morphio::enums::SectionType::SECTION_GLIA_PERIVASCULAR_PROCESS)
+        .value("glia_process", morphio::enums::SectionType::SECTION_GLIA_PROCESS)
+        .value("all", morphio::enums::SectionType::SECTION_ALL)
         .export_values();
 
     py::enum_<morphio::enums::VascularSectionType>(m, "VasculatureSectionType")

{MorphIO-3.0.0 → MorphIO-3.1.0}/ci/coverage_test.sh

@@ -4,15 +4,23 @@
 
 set -euxo pipefail
 
+if [ $# -ge 1 ]; then
+  EXTRA_OPTIONS=$1
+else
+  EXTRA_OPTIONS=""
+fi
+
 BUILD_DIR=build/build-coverage
 
 rm -rf "$BUILD_DIR"
 mkdir -p "$BUILD_DIR"
-cd "$BUILD_DIR"
+pushd "$BUILD_DIR"
+
 cmake                           \
     -DCMAKE_BUILD_TYPE=Debug    \
     -DHIGHFIVE_EXAMPLES=OFF     \
     -DHIGHFIVE_UNIT_TESTS=OFF   \
     -G"Unix Makefiles"          \
+    ${EXTRA_OPTIONS}            \
     ../..
 make -j all coverage

{MorphIO-3.0.0 → MorphIO-3.1.0}/ci/cpp_test.sh

@@ -6,16 +6,18 @@
 
 set -euxo pipefail
 
+BUILD_DIR=build/cpp_test
+
 if [ $# -ge 1 ]; then
   EXTRA_OPTIONS=$1
 else
   EXTRA_OPTIONS=""
 fi
 
-rm -rf build
-mkdir build
-pushd build
-cmake -DMorphIO_CXX_WARNINGS=ON -G "${CMAKE_GENERATOR:-Unix Makefiles}" ${EXTRA_OPTIONS} -j 2 ..
-cmake --build .
+rm -rf $BUILD_DIR
+mkdir -p $BUILD_DIR
+pushd $BUILD_DIR
+cmake -DMorphIO_CXX_WARNINGS=ON -G "${CMAKE_GENERATOR:-Unix Makefiles}" ${EXTRA_OPTIONS} ../..
+cmake --build . -j
 ctest -VV
 popd

{MorphIO-3.0.0 → MorphIO-3.1.0}/ci/python_test.sh

@@ -21,6 +21,5 @@ pip install .
 pip install -r tests/requirement_tests.txt
 
 CURRENT=$(pwd)
-
 cd ..
-nosetests -P ${CURRENT}/tests
+pytest ${CURRENT}/tests

MorphIO-3.1.0/doc/README.md

@@ -0,0 +1,16 @@
+### Local doc building
+
+For building documentation locally, make sure you have `sphinx-bluebrain-theme` and `doxygen`.
+
+```bash
+pip install sphinx-bluebrain-theme
+```
+
+and
+
+```bash
+# for Linux
+sudo apt install doxygen
+# for MacOS
+brew install doxygen
+```

MorphIO-3.1.0/doc/source/glia.rst

@@ -0,0 +1,16 @@
+Glia
+====
+
+MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the
+`H5 specification <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
+
+.. code-block:: python
+
+    import morphio
+
+    # Immutable
+    immutable_glia = morphio.GlialCell("astrocyte.h5")
+
+    # Mutable
+    empty_glia = morphio.mut.GlialCell()
+    mutable_glia = morphio.mut.GlialCell("astrocyte.h5")