updated exec and models

biosimulators_simularium/exec.py

@@ -41,10 +41,11 @@ def execute(
     # generate vtp
     vtp_filename = setup_config.get('vtp_filename', 'simulation.vtp')
     vtp_filepath: str = os.path.join(working_dir, vtp_filename)
-    generate_vtp_file(mesh, vtp_filepath)
+    generate_vtp_file(mesh, filename=vtp_filepath)
 
     # generate a simularium file
     return generate_simularium_file(
+        trajectory,
         working_dir,
         output_dir,
         agent_params,
@@ -55,9 +56,16 @@ def execute(
     )
 
 
-def generate_vtp_file(mesh: pv.PolyData, save_path):
-    # write the vtp file
-    return mesh.save(save_path)
+def generate_vtp_file(mesh: pv.PolyData, **kwargs):
+    """write a vtp file to `save_path` based on the `mesh`. Kwargs according to `pv.PolyData().save()` args.
+
+        Keyword Args:
+            filename:`str`: path in which to save the vtp file.
+            binary: bool = True,
+            texture: Any = None,
+            recompute_normals: Any
+    """
+    return mesh.save(kwargs['filename'])
 
 
 def generate_simularium_file(
@@ -128,10 +136,6 @@ def generate_simularium_file(
     return write_simularium_file(trajectory, simularium_filename=simularium_filepath, json=use_json)
 
 
-def generate_vtp_file(data=None):
-    pass
-
-
 def execute_generate(write_simularium, write_vtp, **kwargs):
     # TODO: implement callbacks
     pass

biosimulators_simularium/tests/fixtures/MinE/model.txt

@@ -22,7 +22,7 @@ define L_PARAM2		1.5	# half of cell length minus radius
 define NUMBER_MIND	4000	# number of MinD in cell
 define NUMBER_MINE	1400	# number of MinE in cell
 
-define TIME_STOP	10	 # stopping time
+define TIME_STOP	3	 # stopping time
 
 #define KICK_START	1	# start with MinD_ATP at an end
 

biosimulators_simularium/tests/fixtures/crowding/model.txt

@@ -18,7 +18,7 @@ boundaries z 0 20
 
 frame_thickness 0
 
-define TIME_STOP 10
+define TIME_STOP 3
 
 time_start 0
 time_stop TIME_STOP

biosimulators_simularium/tests/run.py

@@ -10,4 +10,4 @@
 
 mol_output = generate_output(dir_fp=MIN_E_DIR)
 mesh = generate_interpolated_mesh(mol_output=mol_output)
-print(mesh.point_normals)
+print(dir(mesh))