minor fixes.

subconn with KeyError raise that is slightly more descriptive
batch and netParams supporting '.' traversal
updated the secList to not break when a section (generally axon) without pt3d exists

netpyne/batch/batch.py

@@ -192,6 +192,8 @@ def save(self, filename):
             sim.saveJSON(filename, dataSave)
 
     def setCfgNestedParam(self, paramLabel, paramVal):
+        if '.' in paramLabel: #TODO [email protected] 195196 replace with my crawler code?
+            paramLabel = paramLabel.split('.')
         if isinstance(paramLabel, tuple):
             container = self.cfg
             for ip in range(len(paramLabel) - 1):

netpyne/network/subconn.py

@@ -238,7 +238,13 @@ def subcellularConn(self, allCellTags, allPopTags):
 
                         gridY = subConnParam['density']['gridY']
                         gridSigma = subConnParam['density']['gridValues']
-                        somaX, somaY, _ = posFromLoc(postCell.secs['soma'], 0.5)  # get cell pos move method to Cell!
+                         #TODO [email protected] 241247 'soma' is not always the name of the soma section
+                        try:
+                            somaX, somaY, _ = posFromLoc(postCell.secs['soma'], 0.5)  # get cell pos move method to Cell!
+                        except KeyError:
+                            raise KeyError(
+                                "Error in subcellularConn: there is no section named soma in cell {}".format(postCell.gid)
+                            )
                         if 'fixedSomaY' in subConnParam['density']:  # is fixed cell soma y, adjust y grid accordingly
                             fixedSomaY = subConnParam['density'].get('fixedSomaY')
                             gridY = [

netpyne/specs/netParams.py

@@ -694,7 +694,7 @@ def addCellParamsSecList(self, label, secListName, somaDist=None, somaDistY=None
             return
 
         secList = []
-        for secName, sec in cellRule.secs.items():
+        for secName, sec in cellRule['secs'].items():
             if 'pt3d' in sec['geom']:
                 pt3d = sec['geom']['pt3d']
                 midpoint = int(len(pt3d) / 2)
@@ -708,8 +708,8 @@ def addCellParamsSecList(self, label, secListName, somaDist=None, somaDistY=None
                         secList.append(secName)
 
             else:
-                print('Error adding secList: Sections do not contain 3d points')
-                return
+                #TODO [email protected] 711713 more descriptive message, don't break on axon.
+                print("Error adding {} to {}: {} does not contain 3d points".format(secName, secListName, secName))
 
         cellRule.secLists[secListName] = list(secList)
 
@@ -832,6 +832,8 @@ def todict(self):
         return replaceDictODict(self.__dict__)
 
     def setNestedParam(self, paramLabel, paramVal):
+        if '.' in paramLabel: #TODO [email protected] 835836 replace with my crawler code?
+            paramLabel = paramLabel.split('.')
         if isinstance(paramLabel, list):
             container = self
             for ip in range(len(paramLabel) - 1):