morphio 2.1.4__tar.gz → 2.1.5__tar.gz

{MorphIO-2.1.4 → MorphIO-2.1.5}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: MorphIO
-Version: 2.1.4
+Version: 2.1.5
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: NSE Team - Blue Brain Project

{MorphIO-2.1.4 → MorphIO-2.1.5}/MorphIO.egg-info/SOURCES.txt

@@ -525,6 +525,7 @@ tests/data/disconnected_neurite.swc
 tests/data/iterators.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/nrn_ordering.swc
 tests/data/reversed_NRN_neurite_order.swc

{MorphIO-2.1.4 → MorphIO-2.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: MorphIO
-Version: 2.1.4
+Version: 2.1.5
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: NSE Team - Blue Brain Project

{MorphIO-2.1.4 → MorphIO-2.1.5}/src/mut/morphology.cpp

@@ -267,8 +267,12 @@ void Morphology::sanitize(const morphio::plugin::DebugInfo& debugInfo)
 {
     morphio::plugin::ErrorMessages err(debugInfo._filename);
 
-    for (auto it = depth_begin(); it != depth_end(); ++it) {
+    auto it = depth_begin();
+    while (it != depth_end()) {
         std::shared_ptr<Section> section_ = *it;
+
+        // Incrementing iterator here before we potentially delete the section
+        ++it;
         unsigned int sectionId = section_->id();
 
         if (section_->isRoot())

{MorphIO-2.1.4 → MorphIO-2.1.5}/src/version.cpp

@@ -3,5 +3,5 @@
 #include <morphio/types.h>
 namespace morphio
 {
-  const std::string VERSION("2.1.4");
+  const std::string VERSION("2.1.5.dev2+g6899b1d");
 }

MorphIO-2.1.5/tests/data/nested_single_children.asc

@@ -0,0 +1,19 @@
+("CellBody"
+  (CellBody)
+  (0 0 0 1)
+)
+
+( (Color Blue)
+  (Axon)
+  (0 0 0 1)
+  (0 0 1 1)
+  (
+    (0 0 2 1)
+    (
+      (0 0 3 1)
+      (
+        (0 0 4 1)
+      )
+    )
+  )
+)

{MorphIO-2.1.4 → MorphIO-2.1.5}/tests/test_2_neurolucida.py

@@ -255,6 +255,18 @@ def test_empty_sibling():
     assert_array_equal(annotation.points, [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
     assert_array_equal(annotation.diameters, [2, 2, 2])
 
+def test_nested_single_child():
+    with captured_output() as (_, err):
+        with ostream_redirect(stdout=True, stderr=True):
+            n = Morphology(os.path.join(_path, 'nested_single_children.asc'))
+    assert_array_equal(n.root_sections[0].points,
+                       [[0., 0., 0.],
+                        [0., 0., 1.],
+                        [0., 0., 2.],
+                        [0., 0., 3.],
+                        [0., 0., 4.]])
+
+
 
 
 def test_section_single_point():