morphio 3.2.0__tar.gz → 3.3.0__tar.gz

{MorphIO-3.2.0 → MorphIO-3.3.0/MorphIO.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.2.0
+Version: 3.3.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL

{MorphIO-3.2.0 → MorphIO-3.3.0}/MorphIO.egg-info/SOURCES.txt

@@ -315,8 +315,10 @@ 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

{MorphIO-3.2.0/MorphIO.egg-info → MorphIO-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 3.2.0
+Version: 3.3.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL

{MorphIO-3.2.0 → MorphIO-3.3.0}/binds/python/bind_misc.cpp

@@ -262,7 +262,11 @@ void bind_misc(py::module& m) {
         .def_property_readonly(
             "diameters",
             [](morphio::Property::Marker* marker) { return marker->_pointLevel._diameters; },
-            "Returns the list of diameters of the marker points");
+            "Returns the list of diameters of the marker points")
+        .def_property_readonly(
+            "section_id",
+            [](morphio::Property::Marker* marker) { return marker->_sectionId; },
+            "Returns the id of section that contains the marker");
 
     py::class_<morphio::Property::MitochondriaPointLevel>(
         m,

{MorphIO-3.2.0 → MorphIO-3.3.0}/doc/source/markers.rst

@@ -1,29 +1,38 @@
 NeuroLucida markers
 ===================
 
-A marker is an `s-expression <https://en.wikipedia.org/wiki/S-expression>`__ at the top level of the
+Specification
+*************
+A marker is an `s-expression <https://en.wikipedia.org/wiki/S-expression>`__ of the
 Neurolucida file that contains additional information about the morphology. For example:
 
 .. code-block:: lisp
 
-  ("pia"
+  ("pia" ;  String-named marker starts. Such marker can exist only at the top level.
     (Closed)
     (MBFObjectType 5)
     (0 1 2 3)
     (3 4 5 4)
     (6 7 8 5)
     (9 10 11 6)
-   )
+   ) ;  marker ends
 
-This PR adds a `Morphology.markers` attribute that stores the markers found in the file. A Marker
-object has 3 attributes:
-- label
-- points
-- diameters.
+or
 
-**Specification**
+.. code-block:: lisp
+
+    ; ...
+    ( -277.14  -119.13   -18.02     0.69)
+    ( -275.54  -119.99   -16.67     0.69)  ; some section point
+    (Cross  ;  common marker starts
+      (Color Orange)
+      (Name "Marker 3") ; this name will be ignored. 'Cross' will be used as the marker's label.
+      ( -271.87  -121.14   -16.27     0.69)  ; 1
+      ( -269.34  -122.29   -15.48     0.69)  ; 2
+    )  ;  marker ends
+    ; ...
 
-The following s-expressions are parsed:
+The following s-expressions are parsed as markers:
 
 * Any s-exp with a top level string. Like:
 
@@ -38,7 +47,7 @@ The following s-expressions are parsed:
       (9 10 11 6)
       )
 
-* An sexp with one of the following top level regular expression:
+* An sexp with one of the following regular expression:
 
     - Dot[0-9]*
     - Plus[0-9]*
@@ -84,17 +93,44 @@ The following s-expressions are parsed:
         ( -189.59    55.67    28.68     0.12)  ; 1
         )  ;  End of markers
 
-ℹ️ Markers can may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.
+* An 'Incomplete' sexp. Despite it's not the part of the known Neurolucida format, this tag is parsed as marker.
+
+    Example:
+
+    .. code-block:: lisp
+
+        : ...
+        ( -269.77  -129.47   -22.57     0.92)  ;
+        ( -268.17  -130.62   -24.75     0.92)  ;
+        ( -266.79  -131.77   -26.13     0.92)  ; last point before 'Incomplete' happens
+         Incomplete
+      ) ; end of branch
 
-**Usage**
+.. note::
+    Markers may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case,
+    diameters are set to 0.
+
+Usage
+*****
+
+An instance of morphology has `markers` list attribute that keeps the markers found in the file. A single marker
+object within this list is represented as an object with attributes:
+
+- ``section_id``, the id of the section that contains the marker, ``-1`` if there is no section
+- ``label``, the text label of the marker
+- ``points``, the marker points
+- ``diameters``, the marker diameters
+
+.. code-block:: python
 
-.. code-block::python
     cell = Morphology(os.path.join(_path, 'pia.asc'))
     all_markers = cell.markers
     pia = m.markers[0]
 
     # fetch the label marker with the `label` attribute
     assert_equal(pia.label, 'pia')
+    # fetch the marker's section id
+    assert_equal(pia.section_id, -1)
 
     # fetch the points with the `points` attribute
     assert_array_equal(pia.points,
@@ -106,22 +142,5 @@ The following s-expressions are parsed:
     # fetch the diameters with the `diameters` attribute
     assert_array_equal(pia.diameters, [3, 4, 5, 6])
 
-⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
-
-.. code-block:: lisp
-
-  ( (Color White)  ; [10,1]
-    (Dendrite)
-    ( -290.87  -113.09   -16.32     2.06)  ; Root
-    ( -290.87  -113.09   -16.32     2.06)  ; R, 1
-    (
-      ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
-      ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
-      (Cross  ;  [3,3]
-        (Color Orange)
-        (Name "Marker 3")
-        ( -271.87  -121.14   -16.27     0.69)  ; 1
-        ( -269.34  -122.29   -15.48     0.69)  ; 2
-      )  ;  End of markers
-    )
-   )
+.. warning::
+    Markers with string names are supported only at the top level. Other markers can be presented at any level.

MorphIO-3.3.0/doc/source/warnings.rst

@@ -0,0 +1,87 @@
+Warnings
+========
+
+MorphIO is trying to be as less rigid as possible in validating of morphologies. That's why most of problems with
+morphologies are come as warnings instead of errors. Because of that the output of MorphIO might be verbose.
+In order to minimize it you can set the maximum number of warnings, or ignore some of warnings. On the other hand
+if you want morphologies to be as valid as possible then you can tell MorphIO to interpret warnings as errors.
+
+Maximum number of warnings
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+The maximum number of warnings can be set as:
+
+.. code-block:: python
+
+   import morphio
+
+   # Will stop displaying warnings after 100 warnings
+   morphio.set_maximum_warnings(100)
+
+   # Will never stop displaying warnings
+   morphio.set_maximum_warnings(-1)
+
+   # Warnings won't be displayed
+   morphio.set_maximum_warnings(0)
+
+Ignore warnings
+~~~~~~~~~~~~~~~
+
+A type of warning can be ignored as shown below. For the complete list of warning types see :class:`morphio.Warning`.
+
+.. code-block:: python
+
+   # ignore single warning
+   morphio.set_ignored_warning(morphio.Warning.wrong_root_point, True)
+   # stop ignoring it
+   morphio.set_ignored_warning(morphio.Warning.wrong_root_point, False)
+   # ignore a list of warnings
+   morphio.set_ignored_warning([morphio.Warning.no_soma_found,
+                                morphio.Warning.zero_diameter], True)
+   # stop ignoring them
+   morphio.set_ignored_warning([morphio.Warning.no_soma_found,
+                                morphio.Warning.zero_diameter], False)
+
+For safety reasons you might want to disable warnings only for construction of morphology, and enable it back
+afterwards:
+
+.. code-block:: python
+
+   try:
+       morphio.set_ignored_warning(morphio.Warning.wrong_root_point, True)
+       m = morphio.Morphology('path/to/morph')
+   finally:
+       morphio.set_ignored_warning(morphio.Warning.wrong_root_point, False)
+
+
+Raise warnings
+~~~~~~~~~~~~~~
+If you want MorphIO to be rigid and fail on any morphology anomaly, you can switch to raise warnings as errors.
+This way they also can be caught programmatically.
+
+.. code-block:: python
+
+   morphio.set_raise_warnings(True)
+
+For safety reasons you might want to raise warnings only for construction of morphology, and disable it back
+afterwards:
+
+.. code-block:: python
+
+   try:
+       morphio.set_raise_warnings(True)
+       m = morphio.Morphology('path/to/morph')
+   finally:
+       morphio.set_raise_warnings(False)
+
+If you care only about some types of warnings then you need to ignore others:
+
+.. code-block:: python
+
+   try:
+       morphio.set_raise_warnings(True)
+       # warnings you are not interested in
+       morphio.set_ignored_warning([morphio.Warning.wrong_root_point, ...], True)
+       m = morphio.Morphology('path/to/morph')
+   finally:
+       morphio.set_ignored_warning([morphio.Warning.wrong_root_point, ...], False)
+       morphio.set_raise_warnings(False)

{MorphIO-3.2.0 → MorphIO-3.3.0}/include/morphio/properties.h

@@ -146,6 +146,7 @@ struct Annotation {
 struct Marker {
     PointLevel _pointLevel;
     std::string _label;
+    int32_t _sectionId;  // id of section that contains the marker
 };
 
 struct CellLevel {

{MorphIO-3.2.0 → MorphIO-3.3.0}/src/readers/morphologyASC.cpp

@@ -47,7 +47,7 @@ bool is_end_of_section(Token id) {
 bool skip_sexp(size_t id) {
     return (id == +Token::WORD || id == +Token::COLOR || id == +Token::GENERATED ||
             id == +Token::HIGH || id == +Token::INCOMPLETE || id == +Token::LOW ||
-            id == +Token::NORMAL || id == +Token::FONT || id == +Token::MARKER);
+            id == +Token::NORMAL || id == +Token::FONT);
 }
 }  // namespace
 
@@ -137,6 +137,7 @@ class NeurolucidaParser
             Property::Marker marker;
             marker._pointLevel = properties;
             marker._label = header.label;
+            marker._sectionId = header.parent_id;
             nb_.addMarker(marker);
             return_id = -1;
         } else if (header.token == Token::CELLBODY) {
@@ -280,6 +281,19 @@ class NeurolucidaParser
                 }
                 return true;
             } else if (is_end_of_branch(id)) {
+                if (id == Token::INCOMPLETE) {
+                    Property::Marker marker;
+                    marker._label = to_string(Token::INCOMPLETE);
+                    marker._sectionId = section_id;
+                    nb_.addMarker(marker);
+                    if (!is_end_of_section(Token(peek_id))) {
+                        throw RawDataError(err_.ERROR_UNEXPECTED_TOKEN(
+                            lex_.line_num(),
+                            lex_.peek()->str(),
+                            lex_.current()->str(),
+                            "'Incomplete' tag must finish the branch."));
+                    }
+                }
                 lex_.consume();
             } else if (id == Token::LSPINE) {
                 // skip spines
@@ -289,8 +303,16 @@ class NeurolucidaParser
                 lex_.consume(Token::RSPINE, "Must be end of spine");
             } else if (id == Token::LPAREN) {
                 if (skip_sexp(peek_id)) {
-                    // skip words/strings/markers
+                    // skip words/strings
                     lex_.consume_until_balanced_paren();
+                } else if (peek_id == +Token::MARKER) {
+                    Header marker_header;
+                    marker_header.parent_id = section_id;
+                    marker_header.token = Token::STRING;
+                    marker_header.label = lex_.peek()->str();
+                    lex_.consume_until(Token::LPAREN);
+                    parse_neurite_section(marker_header);
+                    lex_.consume(Token::RPAREN, "Marker should end with RPAREN");
                 } else if (peek_id == +Token::NUMBER) {
                     Point point;
                     floatType radius;

MorphIO-3.3.0/tests/data/invalid-incomplete.asc

@@ -0,0 +1,22 @@
+( (Color White)  ; [10,1]
+  (Dendrite)
+  ( -290.87  -113.09   -16.32     2.06)
+  ( -290.87  -113.09   -16.32     2.06)
+  (
+    ( -267.94  -128.61   -22.57     0.69)
+    ( -204.90  -157.63   -42.45     0.69)
+    (Cross  ;  [3,3]
+      (Color Orange)
+      (Name "Marker 3")
+      ( -223.67  -157.92   -42.45     0.69)  ; 1
+      ( -222.76  -154.18   -39.90     0.69)  ; 2
+    )  ;  End of markers
+     Incomplete
+    ( -206.90  -157.63   -42.45     0.69)
+  |
+    ( -269.77  -129.47   -22.57     0.92)  ; R-2-2, 1
+    ( -268.17  -130.62   -24.75     0.92)  ; R-2-2, 2
+    ( -266.79  -131.77   -26.13     0.92)  ; R-2-2, 3
+     Incomplete
+  )
+)

MorphIO-3.3.0/tests/data/markers.asc

@@ -0,0 +1,42 @@
+;	The file is created for C++ tests to increase coverage
+( (Color White)  ; [10,1]
+  (Dendrite)
+  ( -290.87  -113.09   -16.32     2.06)  ; Root
+  ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+  (
+    ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+    ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+    (Cross  ;  [3,3]
+      (Color Orange)
+      (Name "Marker 3")
+      ( -271.87  -121.14   -16.27     0.69)  ; 1
+      ( -269.34  -122.29   -15.48     0.69)  ; 2
+    )  ;  End of markers
+     Normal
+  |
+    ( -277.80  -120.28   -19.48     0.92)  ; R-2, 1
+    ( -276.65  -121.14   -20.20     0.92)  ; R-2, 2
+    (Cross  ;  [3,3]
+      (Color Orange)
+      (Name "Marker 3")
+      ( -279.41  -119.99   -18.00     0.46)  ; 1
+      ( -272.98  -126.60   -21.22     0.92)  ; 2
+    )  ;  End of markers
+    (
+      ( -267.94  -128.61   -22.57     0.69)  ; R-2-1, 1
+      ( -204.90  -157.63   -42.45     0.69)  ; R-2-1, 34
+      (Cross  ;  [3,3]
+        (Color Orange)
+        (Name "Marker 3")
+        ( -223.67  -157.92   -42.45     0.69)  ; 1
+        ( -222.76  -154.18   -39.90     0.69)  ; 2
+      )  ;  End of markers
+       Incomplete
+    |
+      ( -269.77  -129.47   -22.57     0.92)  ; R-2-2, 1
+      ( -268.17  -130.62   -24.75     0.92)  ; R-2-2, 2
+      ( -266.79  -131.77   -26.13     0.92)  ; R-2-2, 3
+       Incomplete
+    )  ;  End of split
+  )  ;  End of split
+)

{MorphIO-3.2.0 → MorphIO-3.3.0}/tests/test_2_neurolucida.py

@@ -5,6 +5,8 @@ import numpy as np
 from morphio import Morphology, RawDataError, SomaError, ostream_redirect
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
+import pytest
+
 from utils import _test_asc_exception, tmp_asc_file
 
 DATA_DIR = Path(__file__).parent / 'data'
@@ -445,84 +447,70 @@ def test_spine():
 def test_markers():
     '''Test that markers do not prevent file from being read correctly'''
 
-    with tmp_asc_file('''
-( (Color White)  ; [10,1]
-  (Dendrite)
-  ( -290.87  -113.09   -16.32     2.06)  ; Root
-  ( -290.87  -113.09   -16.32     2.06)  ; R, 1
-  (
-    ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
-    ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
-    (Cross  ;  [3,3]
-      (Color Orange)
-      (Name "Marker 3")
-      ( -271.87  -121.14   -16.27     0.69)  ; 1
-      ( -269.34  -122.29   -15.48     0.69)  ; 2
-    )  ;  End of markers
-     Normal
-  |
-    ( -277.80  -120.28   -19.48     0.92)  ; R-2, 1
-    ( -276.65  -121.14   -20.20     0.92)  ; R-2, 2
-    (Cross  ;  [3,3]
-      (Color Orange)
-      (Name "Marker 3")
-      ( -279.41  -119.99   -18.00     0.46)  ; 1
-      ( -272.98  -126.60   -21.22     0.92)  ; 2
-    )  ;  End of markers
-    (
-      ( -267.94  -128.61   -22.57     0.69)  ; R-2-1, 1
-      ( -204.90  -157.63   -42.45     0.69)  ; R-2-1, 34
-      (Cross  ;  [3,3]
-        (Color Orange)
-        (Name "Marker 3")
-        ( -223.67  -157.92   -42.45     0.69)  ; 1
-        ( -222.76  -154.18   -39.90     0.69)  ; 2
-      )  ;  End of markers
-       Incomplete
-    |
-      ( -269.77  -129.47   -22.57     0.92)  ; R-2-2, 1
-      ( -268.17  -130.62   -24.75     0.92)  ; R-2-2, 2
-      ( -266.79  -131.77   -26.13     0.92)  ; R-2-2, 3
-       Incomplete
-    )  ;  End of split
-  )  ;  End of split
-)
-''') as tmp_file:
-
-        n = Morphology(tmp_file.name)
-
-        assert len(n.root_sections) == 1
-
-        assert_array_equal(n.root_sections[0].points,
-                           np.array([[-290.87,  -113.09,   -16.32],
-                                     [-290.87,  -113.09,   -16.32],
-                                     ],
-                                    dtype=np.float32))
-
-        assert_array_equal(n.root_sections[0].children[0].points,
-                           np.array([[-290.87,  -113.09,   -16.32],
-                                     [-277.14,  -119.13,   -18.02],
-                                     [-275.54,  -119.99,   -16.67]],
-                                    dtype=np.float32))
-
-        assert_array_equal(n.root_sections[0].children[1].points,
-                           np.array([[-290.87,  -113.09,   -16.32],
-                                     [-277.80,  -120.28,   -19.48],
-                                     [-276.65,  -121.14,   -20.20]],
-                                    dtype=np.float32))
-
-        assert_array_equal(n.root_sections[0].children[1].children[0].points,
-                           np.array([[-276.65,  -121.14,   -20.20],
-                                     [-267.94,  -128.61,   -22.57],
-                                     [-204.90,  -157.63,   -42.45]],
-                                    dtype=np.float32))
-
-        assert_array_equal(n.root_sections[0].children[1].children[1].points,
-                           np.array([[-276.65,  -121.14,   -20.20],
-                                     [-269.77,  -129.47,   -22.57],
-                                     [-268.17,  -130.62,   -24.75],
-                                     [-266.79,  -131.77,   -26.13]],
-                                    dtype=np.float32))
+    n = Morphology(DATA_DIR / 'markers.asc')
+
+    assert len(n.markers) == 5
+    assert_array_equal(n.markers[0].points,
+                       np.array([[-271.87, -121.14, -16.27],
+                                 [-269.34, -122.29, -15.48]],
+                                dtype=np.float32))
+    assert_array_equal(n.markers[0].diameters,
+                       np.array([0.69, 0.69], dtype=np.float32))
+    assert n.markers[0].label == 'Cross'
+
+    assert_array_equal(n.markers[1].points,
+                       np.array([[-279.41, -119.99, -18.00],
+                                 [-272.98, -126.60, -21.22]],
+                                dtype=np.float32))
+    assert_array_equal(n.markers[1].diameters,
+                       np.array([0.46, 0.92], dtype=np.float32))
+    assert n.markers[1].label == 'Cross'
+
+    assert_array_equal(n.markers[2].points,
+                       np.array([[-223.67, -157.92, -42.45],
+                                 [-222.76, -154.18, -39.90]],
+                                dtype=np.float32))
+    assert_array_equal(n.markers[2].diameters,
+                       np.array([0.69, 0.69], dtype=np.float32))
+    assert n.markers[2].label == 'Cross'
+    assert n.markers[3].label == 'INCOMPLETE'
+    assert n.markers[3].section_id == 3
+    assert n.markers[4].label == 'INCOMPLETE'
+    assert n.markers[4].section_id == 4
+
+
+    assert len(n.root_sections) == 1
+
+    assert_array_equal(n.root_sections[0].points,
+                       np.array([[-290.87,  -113.09,   -16.32],
+                                 [-290.87,  -113.09,   -16.32],
+                                 ],
+                                dtype=np.float32))
+
+    assert_array_equal(n.root_sections[0].children[0].points,
+                       np.array([[-290.87,  -113.09,   -16.32],
+                                 [-277.14,  -119.13,   -18.02],
+                                 [-275.54,  -119.99,   -16.67]],
+                                dtype=np.float32))
+
+    assert_array_equal(n.root_sections[0].children[1].points,
+                       np.array([[-290.87,  -113.09,   -16.32],
+                                 [-277.80,  -120.28,   -19.48],
+                                 [-276.65,  -121.14,   -20.20]],
+                                dtype=np.float32))
+
+    assert_array_equal(n.root_sections[0].children[1].children[0].points,
+                       np.array([[-276.65,  -121.14,   -20.20],
+                                 [-267.94,  -128.61,   -22.57],
+                                 [-204.90,  -157.63,   -42.45]],
+                                dtype=np.float32))
+
+    assert_array_equal(n.root_sections[0].children[1].children[1].points,
+                       np.array([[-276.65,  -121.14,   -20.20],
+                                 [-269.77,  -129.47,   -22.57],
+                                 [-268.17,  -130.62,   -24.75],
+                                 [-266.79,  -131.77,   -26.13]],
+                                dtype=np.float32))
 
 
 def test_string_markers():
@@ -612,6 +600,13 @@ def test_neurolucida_markers():
             assert_array_almost_equal(neuron.markers[1].diameters,
                                       np.array([0.52], dtype=np.float32))
 
+
+def test_invalid_incomplete():
+    '''Test that any data after Incomplete is invalid.'''
+    with pytest.raises(RawDataError, match='Incomplete'):
+        Morphology(DATA_DIR / 'invalid-incomplete.asc')
+
+
 def test_skip_font():
     assert_array_equal(Morphology(DATA_DIR / 'simple-with-font.asc').points,
                        Morphology(DATA_DIR / 'simple.asc').points)

{MorphIO-3.2.0 → MorphIO-3.3.0}/tests/test_morphology_readers.cpp

@@ -147,6 +147,16 @@ TEST_CASE("LoadNeurolucidaMorphology", "[morphology]") {
     REQUIRE(m.diameters().size() == 14);
 }
 
+TEST_CASE("LoadNeurolucidaMorphologyMarkers", "[morphology]") {
+    const morphio::Morphology m("data/markers.asc");
+
+    REQUIRE(m.markers().size() == 5);
+
+    {  // file is an not a valid h5 file
+        CHECK_THROWS_AS(morphio::Morphology("data/invalid-incomplete.asc"), morphio::RawDataError);
+    }
+}
+
 TEST_CASE("LoadBadDimensionMorphology", "[morphology]") {
     REQUIRE_THROWS(morphio::Morphology("data/h5/v1/monodim.h5"));
 }

MorphIO-3.2.0/doc/source/warnings.rst

@@ -1,26 +0,0 @@
-Warnings
-========
-
-Maximum number of warnings
-~~~~~~~~~~~~~~~~~~~~~~~~~~
-On can control the maximum number of warnings using the command:
-
-.. code-block:: python
-
-   # Will stop displaying warnings after 100 warnings
-   morphio.set_maximum_warnings(100)
-
-   # Will never stop displaying warnings
-   morphio.set_maximum_warnings(-1)
-
-   # 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)