swc issues and moogList

.github/workflows/githubaction.yml

@@ -0,0 +1,27 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        export DEBIAN_FRONTEND=noninteractive
+        sudo -E apt install -y cmake libgsl-dev g++ gcc git 
+        sudo -E apt install python3-tk python-tk
+        python -m pip install numpy matplotlib --user
+    - name: Build
+      run: |
+        python setup.py install

pybind11/Finfo.cpp

@@ -183,6 +183,7 @@ py::cpp_function __Finfo__::getDestFinfoSetterFunc2(const ObjId& oid,
         }
     }
 
+
     if(ftype1 == "Id") {
         if(ftype2 == "Id") {
             std::function<bool(Id, Id)> func = [oid, fname](Id a, Id b) {

python/rdesigneur/moogul.py

@@ -218,7 +218,7 @@ def drawForTheFirstTime( self, ax ):
 class MooNeuron( MooDrawable ):
     ''' Draws collection of line segments of defined dia and color'''
     def __init__( self,
-        neuronId,
+        mooObj,
         fieldInfo,
         field = 'Vm', 
         relativeObj = '.', 
@@ -235,12 +235,12 @@ def __init__( self,
                 colormap = colormap, lenScale = lenScale, 
                 diaScale = diaScale, autoscale = autoscale, 
                 valMin = valMin, valMax = valMax )
-        self.neuronId = neuronId
+        self.mooObj = mooObj
         self.updateCoords()
 
     def updateCoords( self ):
         ''' Obtains coords from the associated cell'''
-        self.compts_ = moose.wildcardFind( self.neuronId.path + "/#[ISA=CompartmentBase]" )
+        self.compts_ = self.mooObj
         # Matplotlib3d isn't able to do full rotations about an y axis,
         # which is what the NeuroMorpho models use, so
         # here we shuffle the axes around. Should be an option.

python/rdesigneur/rdesigneur.py

@@ -769,8 +769,8 @@ def _buildMoogli( self ):
             pair = i.elecpath + " " + i.geom_expr
             dendCompts = self.elecid.compartmentsFromExpression[ pair ]
             spineCompts = self.elecid.spinesFromExpression[ pair ]
-            dendObj, mooField = self._parseComptField( dendCompts, i, knownFields )
-            spineObj, mooField2 = self._parseComptField( spineCompts, i, knownFields )
+            dendObj, mooField = self._MoogparseComptField( dendCompts, i, knownFields )
+            spineObj, mooField2 = self._MoogparseComptField( spineCompts, i, knownFields )
             assert( mooField == mooField2 )
             mooObj3 = dendObj + spineObj
             numMoogli = len( mooObj3 )

python/rdesigneur/rmoogli.py

@@ -39,7 +39,7 @@ def makeMoogli( rd, mooObj, args, fieldInfo ):
                 valMin = ymin, valMax = ymax )
         viewer.addDrawable( reacSystem )
     else:
-        neuron = moogul.MooNeuron( rd.elecid, fieldInfo,
+        neuron = moogul.MooNeuron( mooObj, fieldInfo,
                 field = mooField, relativeObj = relObjPath,
                 valMin = ymin, valMax = ymax )
         print( "min = {}, max = {}".format(ymin, ymax) )