Add test

Author: pgleeson

.github/workflows/non_omv.yml

@@ -0,0 +1,30 @@
+name: Non OMV tests
+
+on:
+  push:
+    branches: [ master, development, experimental ]
+  pull_request:
+    branches: [ master, development, experimental ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.12" ]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: Run Python scripts
+      run: |
+        echo "Running non OMV tests..."
+        cd Python
+        pip install -r requirements.txt
+        ./test.sh

neuromlmodel.py

@@ -90,7 +90,7 @@ def add_neuroml_model(
 if __name__ == "__main__":
     plotter = pv.Plotter()
 
-    add_neuroml_model(plotter, "NeuroPAL_All_straightened.net.nml", somas_only=True)
+    add_neuroml_model(plotter, "c302_D_Full.net.nml", somas_only=False)
     plotter.set_background("white")
     plotter.add_axes()
 

requirements.txt

@@ -0,0 +1,7 @@
+# Worm3DViewer Requirements
+pyvista
+stpyvista
+
+libneuroml
+pyneuroml
+ruff 

virtualworm.py

@@ -6,46 +6,38 @@
 NEURONS_OBJ_FILE = "neurons.obj"
 
 
-def add_virtualworm_muscles(plotter):
+def add_virtualworm_muscles(plotter, scale=20, translate=(-40, 0, 0)):
     print("Adding virtual worm file %s..." % BODY_WALL_MUSCLE_OBJ_FILE)
     mesh = pv.read(BODY_WALL_MUSCLE_OBJ_FILE)
-    mesh.scale(20, inplace=True)
-    mesh.translate((-40, 0, 0), inplace=True)
 
-    plotter.add_mesh(mesh, smooth_shading=True, color="green")
+    mesh.scale(scale, inplace=True)
+    mesh.translate((translate), inplace=True)
 
+    conn = mesh.connectivity("all")
 
-def add_virtualworm_neurons(plotter):
-    print("Adding virtual worm file %s..." % NEURONS_OBJ_FILE)
-    mesh2 = pv.read(NEURONS_OBJ_FILE)
-    mesh2.scale(20, inplace=True)
-    mesh2.translate((-80, 0, 0), inplace=True)
+    plotter.add_mesh(conn, smooth_shading=True, color="green")
 
-    plotter.add_mesh(mesh2, smooth_shading=True, color="orange")
 
-    """
-    conn = mesh.connectivity('all')
-    print(conn)
-    # Format scalar bar text for integer values.
-    scalar_bar_args = dict(
-        fmt='%.f',
+def add_virtualworm_neurons(plotter, scale=20, translate=(-80, 0, 0)):
+    print("Adding virtual worm file %s..." % NEURONS_OBJ_FILE)
+    mesh2 = pv.read(NEURONS_OBJ_FILE)
+    mesh2.scale(scale, inplace=True)
+    mesh2.translate(translate, inplace=True)
+
+    # plotter.add_mesh(mesh2, smooth_shading=True, color="orange")
+    conn = mesh2.connectivity("all")
+    plotter.add_mesh(
+        conn,
+        smooth_shading=True,
+        cmap="jet",
     )
 
-    cpos = [(10.5, 12.2, 18.3), (0.0, 0.0, 0.0), (0.0, 1.0, 0.0)]
-
-    
-    conn.plot(
-        categories=True,
-        cmap='jet',
-        scalar_bar_args=scalar_bar_args,
-        cpos=cpos,
-    )"""
-
 
 if __name__ == "__main__":
     pl = pv.Plotter()
 
     add_virtualworm_muscles(pl)
+    add_virtualworm_neurons(pl)
 
     pl.set_background("white")
     pl.add_axes()