Merge pull request #84 from brainglobe/morphio_fix

Explicitly load neuron via morphio before passing to neuromorph

.github/workflows/test_and_deploy.yml

@@ -49,6 +49,7 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
 
   build_sdist_wheels:
     name: Build source distribution

morphapi/morphology/morphology.py

@@ -3,6 +3,8 @@
 from pathlib import Path
 
 import neurom as nm
+from morphio import Morphology as MorphioMorphology
+from morphio import Option
 from neurom.core.dataformat import COLS
 from vedo import merge
 from vedo.colors import color_map
@@ -77,7 +79,11 @@ def load_from_swc(self):
         if self.neuron_name is None:
             self.neuron_name = self.data_file.name
 
-        nrn = nm.load_morphology(self.data_file)
+        morphio_input = MorphioMorphology(
+            str(self.data_file),
+            options=Option.allow_unifurcated_section_change,
+        )
+        nrn = nm.load_morphology(morphio_input)
         self.morphology = nrn
 
         try:

pyproject.toml

@@ -10,8 +10,9 @@ dependencies = [
     "brainglobe-atlasapi >=2.0.1",
     "brainglobe-space >=1.0.0",
     "imagecodecs; python_version>='3.9'",
-    "neurom>=3,<4",
+    "neurom>=3",
     "numpy",
+    "morphio>=3.4.0",
     "pandas",
     "pyyaml>=5.3",
     "requests",