Merge pull request #676 from MetaCell/feature/netpyne-102

Feature/netpyne 102

Author: ddelpiano

requirements.txt

@@ -45,7 +45,7 @@ multimethod==1.3
 nbconvert==5.6.1
 nbformat==5.0.6
 netpyne==1.0.3.1
-NEURON==8.0.2
+NEURON==8.2.2
 numpy==1.18.5
 oauthlib==3.0.1
 optuna==2.10.1

setup.py

@@ -48,6 +48,6 @@
         'sentry_sdk>=1.5.2',
         'dacite>=1.6.0',
         'h5py>=3.7.0',
-        'jsonpickle>=2.1.0'
+        'jsonpickle>=2.1.0',
     ],
 )

tests/backend/netpyne_model_importer_test.py

@@ -41,7 +41,7 @@ def setUpClass(cls):
         except:
             logging.error("Error loading mechanisms", exc_info=True)
 
-    @unittest.skip("Neuroml model import issue")
+    # @unittest.skip("Neuroml model import issue")
     def test_netpyne_exported_model_1(self):
       print("------------------------------------")
       print("Netpyne exported model sim run")
@@ -68,7 +68,7 @@ def test_netpyne_exported_model_1(self):
       params["modFolder"] = ""
       params["modPath"] = ""
       params["tab"] = "simulate"
-      
+
       print(params['jsonModelFolder'])
 
       netpyne = NetPyNEGeppetto()

tests/backend/netpyne_model_interpreter_test.py

@@ -80,31 +80,31 @@ def test_getGeppettoModelSimpleNetwork(self):
 
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut1(self):
         print("------------------------------------")
         print("Tutorial 1 Instantiation:")
         print("------------------------------------")
         from gui_tut1 import netParams, simConfig
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut2(self):
         print("------------------------------------")
         print("Tutorial 2 Instantiation:")
         print("------------------------------------")
         from gui_tut2 import netParams, simConfig
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut3(self):
         print("------------------------------------")
         print("Tutorial 3 Instantiation:")
         print("------------------------------------")
         from gui_tut3 import netParams, simConfig
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut4(self):
         print("------------------------------------")
         print("Tutorial 3 ip3high Instantiation:")
@@ -113,15 +113,15 @@ def test_tut4(self):
         from gui_tut3_ip3high import netParams, simConfig
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut5(self):
         print("------------------------------------")
         print("Tutorial 3 norxd Instantiation:")
         print("------------------------------------")
         from gui_tut3_norxd import netParams, simConfig
         self.getGeppettoModel(netParams, simConfig)
 
-    @unittest.skip("Neuron restart kernel issue")
+    # @unittest.skip("Neuron restart kernel issue")
     def test_tut6(self):
         print("------------------------------------")
         print("Tutorial 3 osc Instantiation:")

utilities/install.py

@@ -60,7 +60,7 @@ def clone(repository, folder=None, branch_or_tag=None, cwdp=DEPS_DIR, recursive=
 
         if exit_code != 0:
             raise SystemExit(f'Failed to clone repository {repository} into {folder}')
-        
+
     if not os.path.exists(os.path.join(cwdp, folder, '.git')):
         print(f'Skipping checkout of {repository}: folder is not a git repository')
         return
@@ -138,8 +138,8 @@ def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False,
         execute(cmd=['npm', 'ci'], cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR, 'js'))
         execute(cmd=['npm', 'run', 'build-dev' if development else 'build'],
                 cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR, 'js'))
-  
-    execute(cmd=['jupyter', 'nbextension', 'uninstall', 'jupyter_geppetto'])                                                                            
+
+    execute(cmd=['jupyter', 'nbextension', 'uninstall', 'jupyter_geppetto'])
     execute(cmd=['jupyter', 'nbextension', 'install', '--py', '--symlink', '--sys-prefix', 'jupyter_geppetto'])
     execute(cmd=['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'jupyter_geppetto'])
     execute(cmd=['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'widgetsnbextension'])
@@ -190,7 +190,7 @@ def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False,
         cprint("Installing test libraries")
         execute(cmd=['pip', 'install', '-r', 'requirements-test.txt'], cwd=ROOT_DIR)
         cprint("Testing NetPyNE")
-        # execute("python -m unittest netpyne_ui.tests.netpyne_model_interpreter_test".split())
+        execute("python -m pytest tests".split())
 
     cprint("Installing client packages")
     if not skipNpm: