Tests with netpyne format

.github/workflows/omv-ci.yml

@@ -26,9 +26,11 @@ jobs:
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
-        pip install scipy sympy matplotlib cython pandas tables
 
         pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+
+        pip install scipy sympy matplotlib cython pandas tables
+
 
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |

NetPyNE/HHSmall/HHSmall.py

@@ -98,3 +98,8 @@ def generate_netParams(*argv):
 simConfig.analysis['plotRaster'] = True  # Plot raster
 simConfig.analysis['plotTraces'] = {'include': [2]}  # Plot raster
 simConfig.analysis['plot2Dnet'] = True  # Plot 2D net cells and connections
+
+simConfig.validateNetParams=True
+
+cfg = simConfig
+netParams = generate_netParams(None)

NetPyNE/HHSmall/index.npjson

@@ -0,0 +1,6 @@
+{
+    "mod_folder": "../HHSmall",
+    "simConfig": "HHSmall.py",
+    "python_run": "init.py",
+    "netParams": "HHSmall.py"
+}

NetPyNE/HHSmall/init.py

@@ -0,0 +1,10 @@
+"""
+init.py
+
+Starting script to run NetPyNE-based model.
+"""
+
+from netpyne import sim
+
+cfg, netParams = sim.loadFromIndexFile('index.npjson')
+sim.createSimulateAnalyze(netParams, cfg)

NetPyNE/HybridTut/HybridTut.py

@@ -116,3 +116,5 @@
 simConfig.analysis['plotTraces'] = {'include': [1,51]} # plot recorded traces for this list of cells
 simConfig.analysis['plotRatePSD'] = {'include': ['allCells', 'PYR_HH', 'PYR_Izhi'], 'Fs': 200, 'smooth': 10} # plot recorded traces for this list of cells
 
+
+simConfig.validateNetParams=True

NetPyNE/TwoCells/LEMS_TwoCell_netpyne_data.json

@@ -677,7 +677,7 @@
         }
     },
     "netpyne_changeset": "",
-    "netpyne_version": "1.0.6",
+    "netpyne_version": "1.0.7",
     "simConfig": {
         "addSynMechs": true,
         "allowConnsWithWeight0": true,
@@ -702,7 +702,7 @@
         "dt": 0.01,
         "dump_coreneuron_model": false,
         "duration": 700.0,
-        "filename": "/Users/padraig/neuroConstruct/osb/showcase/NetPyNEShowcase/NeuroML2/TwoCells/LEMS_TwoCell_netpyne",
+        "filename": "LEMS_TwoCell_netpyne",
         "gatherOnlySimData": true,
         "gpu": false,
         "hParams": {
@@ -719,6 +719,7 @@
         "printPopAvgRates": false,
         "printRunTime": false,
         "printSynsAfterRule": false,
+        "progressBar": 2,
         "pt3dRelativeToCellLocation": true,
         "rand123GlobalIndex": null,
         "random123": false,

NetPyNE/TwoCells/index.npjson

@@ -0,0 +1,6 @@
+{
+    "mod_folder": "../TwoCells",
+    "simConfig": "reload2.py",
+    "python_run": "init.py",
+    "netParams": "reload2.py"
+}

NetPyNE/TwoCells/init.py

@@ -0,0 +1,10 @@
+"""
+init.py
+
+Starting script to run NetPyNE-based model.
+"""
+
+from netpyne import sim
+
+cfg, netParams = sim.loadFromIndexFile('index.npjson')
+sim.createSimulateAnalyze(netParams, cfg)

NetPyNE/TwoCells/loadNML.py

@@ -0,0 +1,8 @@
+from LEMS_TwoCell_netpyne import NetPyNESimulation
+
+n = NetPyNESimulation()
+n.generate_json_only()
+
+print("Validating: %s"%n.simConfig.validateNetParams)
+
+cfg = n.simConfig

NetPyNE/TwoCells/reload2.py

@@ -0,0 +1,64 @@
+# From https://github.com/harshagurnani/GoC_Varied_Inputs/blob/ankur/Tests/single_cell/test_single_cell_netpyne_load.py
+
+from pathlib import Path
+from netpyne import sim
+import json
+
+json_file = Path('LEMS_TwoCell_netpyne_data.json')
+netParams_dict = None
+simConfig_dict = None
+
+with json_file.open(mode='r') as f:
+    netpyne_info = json.load(f)
+
+    netParams_dict = netpyne_info['net']['params']
+    simConfig_dict = netpyne_info['simConfig']
+
+'''
+    simConfig_dict['saveJson'] = False # Prevent overwriting json gnerated by nml export
+    simConfig_dict['saveDat'] = True # Save data from this run
+    print('> Creating, simulating, analyzing...')
+    sim.createSimulateAnalyze(netParams=netParams_dict, simConfig=simConfig_dict,
+                                  output=False)
+
+print(' - simConfig_dict (%s) with keys: \n      %s'%(type(simConfig_dict),simConfig_dict.keys()))
+print(' - netParams_dict (%s) with keys: \n      %s'%(type(netParams_dict),netParams_dict.keys()))
+print(" - netParams_dict['cellParams']: \n      %s"%(netParams_dict['cellParams']))
+'''
+
+from netpyne.specs.simConfig import SimConfig
+from netpyne.specs.netParams import NetParams
+
+cfg = SimConfig(simConfig_dict)
+cfg.validateNetParams = True
+cfg.verbose = True
+
+
+for cell in netParams_dict['cellParams']:
+    for sec in netParams_dict['cellParams'][cell]['secs']:
+        if len(netParams_dict['cellParams'][cell]['secs'][sec]['ions'])==0:
+            netParams_dict['cellParams'][cell]['secs'][sec]['ions']['none']={'e':0,'i':0,"o":0}
+        for ion_name in netParams_dict['cellParams'][cell]['secs'][sec]['ions']:
+            ion = netParams_dict['cellParams'][cell]['secs'][sec]['ions'][ion_name]
+            if not 'o' in ion: ion['o'] = 0 
+            if not 'i' in ion: ion['i'] = 0 
+            print('>> %s - %s - %s'%(cell, sec, ion))
+
+netParams = NetParams(netParams_dict)
+
+print(' - simConfig (%s) with keys: \n      %s'%(type(cfg),cfg.todict().keys()))
+print(' - netParams (%s) with keys: \n      %s'%(type(netParams),netParams.todict().keys()))
+
+
+
+
+import netpyne
+#netpyne.sim.validator.validateNetParams = lambda a: (False, False)
+
+from netpyne.sim.validator import validateNetParams
+
+print('==============================')
+validateNetParams(netParams)
+print('==============================')
+
+print('> Done...')

NetPyNE/UI/HHCellNetwork.txt_data.json

@@ -170,7 +170,7 @@
         }
     },
     "netpyne_changeset": "",
-    "netpyne_version": "1.0.6",
+    "netpyne_version": "1.0.7",
     "simConfig": {
         "addSynMechs": true,
         "allowConnsWithWeight0": true,
@@ -212,6 +212,7 @@
         "printPopAvgRates": false,
         "printRunTime": false,
         "printSynsAfterRule": false,
+        "progressBar": 2,
         "pt3dRelativeToCellLocation": true,
         "rand123GlobalIndex": null,
         "random123": false,

NetPyNE/UI/helpers.py

@@ -18,6 +18,10 @@
 '''
 def convertAndImportLEMSSimulation(lemsFileName, verbose=True):
 
+    ## Why do these need to be set?? TODO: take out!
+    sim.nhosts = 5
+    sim.rank = 1
+
     fullLemsFileName = os.path.abspath(lemsFileName)
     if verbose:
         print(
@@ -43,7 +47,6 @@ def convertAndImportLEMSSimulation(lemsFileName, verbose=True):
         print("All keys: {}".format(netpyne_info.keys()))
         print("net keys: {}".format(netpyne_info['net'].keys()))
 
-
     sim.loadAll(json_filename)
 
     print("Loaded network into NetPyNE containing %s which would run for %s ms"%([d for d in sim.net.params.popParams.keys()], sim.cfg.duration))