fix(nsgr-netpyne): include model files in NSG zip also

For NEURON simulations, we only need the generated NEURON files, but for
NetPyNE, some bits are generated (channel mod files, for example), but
others are directly imported (networks/cells). So we need to ensure that
all of these files are also available to the main NetPyNE script.

Author: sanjayankur31

pyneuroml/nsgr/__init__.py

@@ -177,6 +177,13 @@ def run_on_nsg(
     generated_files = get_files_generated_after(
         start_time, ignore_suffixes=["xml", "nml"]
     )
+
+    # For NetPyNE, the channels are converted to NEURON mod files, but the
+    # network and cells are imported from the nml files.
+    # So we include all the model files too.
+    if engine == "jneuroml_netpyne":
+        generated_files.extend(model_file_list)
+
     logger.debug(f"Generated files are: {generated_files}")
 
     logger.info("Generating zip file")
@@ -199,7 +206,11 @@ def run_on_nsg(
                 if f.endswith("_netpyne.py"):
                     runner_file = f
             fpath = pathlib.Path(f)
-            moved_path = fpath.rename(nsg_dir / fpath)
+            moved_path = nsg_dir / fpath
+            # use os.renames because pathlib.Path.rename does not move
+            # recursively and so cannot move files within directories
+            os.renames(fpath, moved_path)
+
             archive.write(str(moved_path))
 
     logger.debug("Printing testParam.properties")