Merge pull request #734 from MetaCell/release/1.0.0-notebook-fix

Notebook fix sync fix

Author: enicolasgomez

Dockerfile

@@ -57,7 +57,8 @@ ENV NEURON_HOME=/opt/conda
 # For lfpykit 0.4
 # RUN wget -P $(pip show LFPykit | grep "Location:" | awk '{print $2"/lfpykit"}') https://www.parralab.org/nyhead/sa_nyhead.mat
 # For lpfykit 0.5
-RUN wget --no-check-certificate -P ${FOLDER}/workspace https://www.parralab.org/nyhead/sa_nyhead.mat
+ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
+RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
 
 USER $NB_UID
 

netpyne_ui/__init__.py

@@ -11,21 +11,23 @@
     "https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6"
 )
 
+HEAD_MODEL_FILE = os.getenv("NP_LFPYKIT_HEAD_FILE", "sa_nyhead.mat")
+
 def init_eeg():
     import sys
     from netpyne_ui.constants import HERE
     # FIXES library asking for input to download
     sys.stdin = open(os.path.join(HERE, "resources/stdin.txt"),'r') 
     from lfpykit.eegmegcalc import NYHeadModel
     try:
-        NYHeadModel() # Downloads the model if does not exist
+        NYHeadModel(HEAD_MODEL_FILE) # Downloads the model if does not exist
     except:
         logging.error("Error initializing the EEG head model", exc_info=True)
 
-from multiprocessing import Process
-thread = Process(target = init_eeg)
-thread.start()
-
+if not os.path.exists(HEAD_MODEL_FILE):
+    from multiprocessing import Process
+    thread = Process(target = init_eeg)
+    thread.start()
 
 RouteManager.add_controller(api.NetPyNEController)
 

netpyne_ui/mod_utils.py

@@ -1,3 +1,4 @@
+import logging
 import shutil
 import subprocess
 import os
@@ -26,24 +27,30 @@ def is_loaded_mechanisms():
         return True
 
 
-def loadModMechFiles(compileMod, modFolder):
+def loadModMechFiles(compileMod, modFolder, forceRecompile=False):
     # Create Symbolic link
 
-    if compileMod:
         try:
+
             owd = os.getcwd()
-            modPath = os.path.join(str(modFolder), "x86_64")
+            if compileMod:
+                
+                compiledModPath = os.path.join(str(modFolder), "x86_64")
 
-            if os.path.exists(modPath):
-                shutil.rmtree(modPath)
+                if os.path.exists(compiledModPath) and forceRecompile:
+                        logging.info("Forcing mod files to recompile in %s" % modFolder)
+                        shutil.rmtree(compiledModPath)
 
-            os.chdir(modFolder)
-            subprocess.call(["nrnivmodl"])
-            os.chdir('..')
+                if not os.path.exists(compiledModPath):
+                    logging.info("Compiling mod files in %s" % modFolder)
+                    os.chdir(modFolder)
+                    subprocess.call(["nrnivmodl"])
+                    os.chdir('..')
 
             try:
                 neuron.load_mechanisms(str(modFolder))
             except:
+                logging.exception("Error loading mechanisms")
                 raise
         finally:
             os.chdir(owd)

netpyne_ui/netpyne_geppetto.py

@@ -46,7 +46,6 @@
 
 os.chdir(constants.NETPYNE_WORKDIR_PATH)
 
-neuron.nrn_dll_loaded.append(os.path.join(NETPYNE_WORKDIR_PATH, 'mod'))  # Avoids to load workspace modfiles twice
 
 class NetPyNEGeppetto:
 
@@ -80,17 +79,6 @@ def __init__(self):
         if not simulations.local.is_running():
             [experiments.set_to_error(e) for e in running_exps]
 
-        # sys.stdin = open(os.path.join(constants.HERE, "stdin.txt"),'r') # FIXES library asking for input to download -- eg lfpykit models
-
-        # from ipykernel import kernelbase
-
-        # def raw_input(self, prompt=''):
-        #     return "y"
-        # kernelbase.Kernel.raw_input = raw_input
-
-        # from lfpykit.eegmegcalc import NYHeadModel
-        # NYHeadModel()
-
     def getData(self):
         return {
             "metadata": metadata,
@@ -550,7 +538,7 @@ def importModel(self, modelParameters):
             #   Shouldn't be specific to Import
             sim.clearAll()
         try:
-            loadModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'])
+            loadModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'], modelParameters.get("forceRecompile", True))
         except Exception:
             message = "Error while importing/compiling mods"
             logging.exception(message)
@@ -592,7 +580,7 @@ def importModel(self, modelParameters):
                 #   Only on import or better before every simulation or network instantiation?
                 sim.initialize()
             return utils.getJSONReply()
-        except Exception:
+        except:
             message = "Error while importing the NetPyNE model"
             logging.exception(message)
             return utils.getJSONError(message, sys.exc_info())
@@ -943,10 +931,10 @@ def getAvailableCellTypes(self):
             cell_types.add(p)
         return sorted(cell_types)
 
-    def getAvailableRxDSections(self, selectedRegion):
+    def getAvailableRxDSections(self, selectedRegion = None):
         sections = set([])
         sections.add('all')
-        if selectedRegion in self.netParams.rxdParams.regions and self.netParams.rxdParams.regions[selectedRegion].get('cells'):
+        if selectedRegion and selectedRegion in self.netParams.rxdParams.regions and self.netParams.rxdParams.regions[selectedRegion].get('cells'):
             if 'all' in self.netParams.rxdParams.regions[selectedRegion]['cells']:
                 for cellRule in self.netParams.cellParams:
                     for cellSect in self.netParams.cellParams[cellRule]['secs']:

utilities/install.py

@@ -125,7 +125,7 @@ def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False,
       cprint("Cloning workspace")
       clone(repository=WORKSPACE, branch_or_tag=workspace_branch, folder=WORKSPACE_DIR, cwdp=ROOT_DIR)
       cprint("Compiling workspace modules")
-      compile_mod()
+      #compile_mod()
 
     if not skipNpm and os.path.exists(os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR)):
         cprint("Building Jupyter Geppetto extension...")

webapp/components/definition/cellRules/NetPyNECellRules.js

@@ -338,6 +338,8 @@ export default class NetPyNECellRules extends React.Component {
   }
 
   componentDidUpdate (prevProps, prevState) {
+    if (this.props.commands !== prevProps.commands)
+      this.forceUpdate();
     // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable
     const newCellRuleName = this.hasSelectedCellRuleBeenRenamed(
       prevState,

webapp/components/definition/connectivity/NetPyNEConnectivityRules.js

@@ -103,6 +103,8 @@ export default class NetPyNEConnectivityRules extends Component {
   }
 
   componentDidUpdate (prevProps, prevState) {
+    if (this.props.commands !== prevProps.commands)
+      this.forceUpdate();
     // we need to check if any of the three entities have been renamed and if that's the case change the state for the selection variable
     const newConnectivityRuleName = this.hasSelectedConnectivityRuleBeenRenamed(
       prevState,

webapp/components/definition/plots/NetPyNEPlots.js

@@ -30,6 +30,11 @@ export default class NetPyNEPlots extends React.Component {
     this.handleNewPlot = this.handleNewPlot.bind(this);
   }
 
+  componentDidUpdate (prevProps, prevState) {
+    if (this.props.commands !== prevProps.commands)
+      this.forceUpdate();
+  }
+
   selectPlot (plot) {
     this.setState({ selectedPlot: plot });
   }

webapp/components/definition/stimulationTargets/NetPyNEStimulationTargets.js

@@ -94,6 +94,8 @@ export default class NetPyNEStimulationTargets extends Component {
   }
 
   componentDidUpdate (prevProps, prevState) {
+    if (this.props.commands !== prevProps.commands)
+      this.forceUpdate();
     const newStimulationTargetName = this.hasSelectedStimulationTargetBeenRenamed(
       prevState,
       this.state,

webapp/components/general/AdapterComponent.js

@@ -27,6 +27,8 @@ export default class AdapterComponent extends Component {
   }
 
   componentDidUpdate (prevProps, prevState) {
+    if (this.props.commands !== prevProps.commands)
+      this.forceUpdate();
     const newValue = this.props.convertFromPython(prevProps, prevState, this.props.value);
     if (newValue != undefined) {
       this.setState(newValue);