Merge branch 'development' into feat-provide-jnml-wrapper

Author: sanjayankur31

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
 
     steps:
@@ -36,10 +36,10 @@ jobs:
         echo "github.ref is: ${{ github.ref }}"
         echo "github.base_ref is: ${{ github.base_ref }}"
 
+
     - name: Upgrade pip, install deps
       run: |
         python -m pip install --upgrade pip
-        pip install 'numpy<2.0.0' # due to lingering issues with other modules
         pip install .[dev]
 
     - name: List packages so far

pyneuroml/plot/PlotMorphologyVispy.py

@@ -1699,6 +1699,8 @@ def create_mesh(
             k = numpy.cross(orig_vec, dir_vector)
             mag_k = numpy.linalg.norm(k)
 
+            vertices = seg_mesh.get_vertices()
+
             if mag_k != 0.0:
                 k = k / mag_k
                 theta = math.acos(
@@ -1708,13 +1710,11 @@ def create_mesh(
                 logger.debug(f"k is {k}, theta is {theta}")
                 rot_matrix = rotate(math.degrees(theta), k).T
                 rot_obj = Rotation.from_matrix(rot_matrix[:3, :3])
+                rotated_vertices = rot_obj.apply(vertices)
             else:
-                logger.debug("k is [0..], using zeros for rotation matrix")
-                rot_matrix = numpy.zeros((3, 3))
-                rot_obj = Rotation.from_matrix(rot_matrix)
+                logger.debug("k is [0..], skipping rotation")
+                rotated_vertices = vertices
 
-            vertices = seg_mesh.get_vertices()
-            rotated_vertices = rot_obj.apply(vertices)
             translator = numpy.array(
                 [offset[0] + prox.x, offset[1] + prox.y, offset[2] + prox.z]
             )

setup.cfg

@@ -17,6 +17,7 @@ classifiers=
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering
 
 [options]