morphio 3.0.0__tar.gz → 3.0.2__tar.gz

{MorphIO-3.0.0 → MorphIO-3.0.2}/.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-3.0.2}/.gitignore

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

{MorphIO-3.0.0 → MorphIO-3.0.2}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.0.0
+Version: 3.0.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -49,6 +49,7 @@ Description: |license| |build| |docs|
         -  `Tips <#tips>`__
         
            -  `Maximum number of warnings <#maximum-number-of-warnings>`__
+           -  `Raise warnings as errors <#raise-warnings>`__
         
         -  `Specification <#specification>`__
         
@@ -415,7 +416,7 @@ Description: |license| |build| |docs|
         Glia
         ^^^^
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the
-        `H5 specification <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+        `H5 specification <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
         
         .. code-block:: python
         
@@ -428,6 +429,7 @@ Description: |license| |build| |docs|
             empty_glia = morphio.mut.GlialCell()
             mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
         
+        .. _mitochondria-readme:
         
         Mitochondria
         ^^^^^^^^^^^^
@@ -499,7 +501,7 @@ Description: |license| |build| |docs|
         Endoplasmic reticulum
         ^^^^^^^^^^^^^^^^^^^^^
         Endoplasmic reticulum can also be stored and written to H5 file. The specification is part of the
-        `BBP morphology documentation <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+        `BBP morphology documentation <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
         There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute
         is an array and each line refers to the value of the attribute for a specific neuronal section.
         
@@ -690,11 +692,20 @@ Description: |license| |build| |docs|
            # Warnings won't be displayed
            morphio.set_maximum_warnings(0)
         
+        Raise warnings
+        ~~~~~~~~~~~~~~
+        Because MorphIO warning is just output to stdout/stderr, one can switch to raise warnings as errors, so they can be
+        caught programmatically:
+        
+        .. code-block:: python
+        
+           morphio.set_raise_warnings(True)
+        
         
         Specification
         =============
         
-        See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
+        See https://morphio.readthedocs.io/en/latest/specification.html
         
         H5v2
         ====
@@ -719,7 +730,8 @@ Description: |license| |build| |docs|
         Contributing
         ============
         If you want to improve the project or you see any issue, every contribution is welcome.
-        Please check the `contribution guidelines <CONTRIBUTING.md>`_ for more information.
+        Please check the `contribution guidelines <https://github.com/BlueBrain/morphio/blob/master/CONTRIBUTING.md>`_ for more
+        information.
         
         Acknowledgements
         ================

{MorphIO-3.0.0 → MorphIO-3.0.2}/MorphIO.egg-info/SOURCES.txt

@@ -206,6 +206,11 @@ doc/source/specification.rst
 doc/source/specification_neurolucida.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
@@ -294,10 +299,12 @@ 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
@@ -318,6 +325,7 @@ 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-3.0.0 → MorphIO-3.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.0.0
+Version: 3.0.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -49,6 +49,7 @@ Description: |license| |build| |docs|
         -  `Tips <#tips>`__
         
            -  `Maximum number of warnings <#maximum-number-of-warnings>`__
+           -  `Raise warnings as errors <#raise-warnings>`__
         
         -  `Specification <#specification>`__
         
@@ -415,7 +416,7 @@ Description: |license| |build| |docs|
         Glia
         ^^^^
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the
-        `H5 specification <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+        `H5 specification <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
         
         .. code-block:: python
         
@@ -428,6 +429,7 @@ Description: |license| |build| |docs|
             empty_glia = morphio.mut.GlialCell()
             mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
         
+        .. _mitochondria-readme:
         
         Mitochondria
         ^^^^^^^^^^^^
@@ -499,7 +501,7 @@ Description: |license| |build| |docs|
         Endoplasmic reticulum
         ^^^^^^^^^^^^^^^^^^^^^
         Endoplasmic reticulum can also be stored and written to H5 file. The specification is part of the
-        `BBP morphology documentation <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+        `BBP morphology documentation <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
         There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute
         is an array and each line refers to the value of the attribute for a specific neuronal section.
         
@@ -690,11 +692,20 @@ Description: |license| |build| |docs|
            # Warnings won't be displayed
            morphio.set_maximum_warnings(0)
         
+        Raise warnings
+        ~~~~~~~~~~~~~~
+        Because MorphIO warning is just output to stdout/stderr, one can switch to raise warnings as errors, so they can be
+        caught programmatically:
+        
+        .. code-block:: python
+        
+           morphio.set_raise_warnings(True)
+        
         
         Specification
         =============
         
-        See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
+        See https://morphio.readthedocs.io/en/latest/specification.html
         
         H5v2
         ====
@@ -719,7 +730,8 @@ Description: |license| |build| |docs|
         Contributing
         ============
         If you want to improve the project or you see any issue, every contribution is welcome.
-        Please check the `contribution guidelines <CONTRIBUTING.md>`_ for more information.
+        Please check the `contribution guidelines <https://github.com/BlueBrain/morphio/blob/master/CONTRIBUTING.md>`_ for more
+        information.
         
         Acknowledgements
         ================

{MorphIO-3.0.0 → MorphIO-3.0.2}/README.rst

@@ -42,6 +42,7 @@ Table of content
 -  `Tips <#tips>`__
 
    -  `Maximum number of warnings <#maximum-number-of-warnings>`__
+   -  `Raise warnings as errors <#raise-warnings>`__
 
 -  `Specification <#specification>`__
 
@@ -408,7 +409,7 @@ Python:
 Glia
 ^^^^
 MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the
-`H5 specification <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+`H5 specification <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
 
 .. code-block:: python
 
@@ -421,6 +422,7 @@ MorphIO also support reading and writing glia (such as astrocytes) from/to disk
     empty_glia = morphio.mut.GlialCell()
     mutable_glia = morphio.mut.GlialCell("astrocyte.h5")
 
+.. _mitochondria-readme:
 
 Mitochondria
 ^^^^^^^^^^^^
@@ -492,7 +494,7 @@ Reading mithochondria from H5 files:
 Endoplasmic reticulum
 ^^^^^^^^^^^^^^^^^^^^^
 Endoplasmic reticulum can also be stored and written to H5 file. The specification is part of the
-`BBP morphology documentation <https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html>`__
+`BBP morphology documentation <https://developer.humanbrainproject.eu/docs/projects/morphology-documentation/latest/h5v1.html>`__
 There is one endoplasmic reticulum object per morphology. It contains 4 attributes. Each attribute
 is an array and each line refers to the value of the attribute for a specific neuronal section.
 
@@ -683,11 +685,20 @@ On can control the maximum number of warnings using the command:
    # Warnings won't be displayed
    morphio.set_maximum_warnings(0)
 
+Raise warnings
+~~~~~~~~~~~~~~
+Because MorphIO warning is just output to stdout/stderr, one can switch to raise warnings as errors, so they can be
+caught programmatically:
+
+.. code-block:: python
+
+   morphio.set_raise_warnings(True)
+
 
 Specification
 =============
 
-See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
+See https://morphio.readthedocs.io/en/latest/specification.html
 
 H5v2
 ====
@@ -712,7 +723,8 @@ and then:
 Contributing
 ============
 If you want to improve the project or you see any issue, every contribution is welcome.
-Please check the `contribution guidelines <CONTRIBUTING.md>`_ for more information.
+Please check the `contribution guidelines <https://github.com/BlueBrain/morphio/blob/master/CONTRIBUTING.md>`_ for more
+information.
 
 Acknowledgements
 ================

{MorphIO-3.0.0 → MorphIO-3.0.2}/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",
@@ -55,6 +57,12 @@ 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("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_process", morphio::enums::SectionType::SECTION_GLIA_PROCESS)
         // .value("glia_endfoot", morphio::enums::SectionType::SECTION_GLIA_ENDFOOT)
         .export_values();

{MorphIO-3.0.0 → MorphIO-3.0.2}/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-3.0.2}/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