Merge pull request #112 from openworm/development

To v0.10.1; improved cellW2D

Author: pgleeson

.github/workflows/non_omv.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:        
         runs-on: [ubuntu-latest, macos-13, macos-latest ]
-        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
         exclude:
           - runs-on: macos-latest
             python-version: "3.8"
@@ -42,12 +42,6 @@ jobs:
         pip install WormNeuroAtlas
         pip list
         
-    - name: Test OpenWormReader with owmeta
-      if: ${{ matrix.python-version != '3.11' }}
-      run: |
-        pip install owmeta>=0.12.3
-        owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
-        python -m c302.OpenWormReader
 
     - name: Test WormNeuroAtlasReader
       run: |

c302/__version__.py

@@ -1 +1 @@
-__version__ = "0.10.0"
+__version__ = "0.10.1"

c302/cell_W2D.xml

@@ -1,20 +1,20 @@
 <Lems>
 
 <ComponentType name="cellW2D"
-    extends="baseCellMembPot"
+    extends="baseCellMembPotCap"
     description="Cell based on Worm2D model">
 
     <Parameter name="bias" dimension="none" description="..."/>
     <Parameter name="gain" dimension="none" description="..."/>
     <Parameter name="tau" dimension="time"/>
 
     <Constant name="COND_SCALE" dimension="conductance" value="1nS"/>
-    <DerivedParameter name="C" dimension="capacitance" value="tau*COND_SCALE"/>
 
     <!--
     Defined in baseCellMembPotCap:
     <Parameter name="C" dimension="capacitance"/>
     -->
+    <DerivedParameter name="C" dimension="capacitance" value="tau*COND_SCALE"/>
 
     <!-- Initial Conditions -->
     <Parameter name="state0" dimension="none"/>
@@ -65,11 +65,15 @@
 
 </ComponentType>
 
-<cellW2D id="GenericNeuronCell" tau="1s" bias="1" gain="1" state0=".5"/>
-<cellW2D id="GenericMuscleCell" tau="1s" bias="1" gain="1" state0=".5"/>
+<cellW2D id="GenericNeuronCell" tau="100ms" bias="1" gain="1" state0="0"/>
+<cellW2D id="GenericMuscleCell" tau="100ms" bias="1" gain="1" state0="0"/>
+
+<cellW2D id="GenericNeuronCellW2D" tau="1s" bias="1" gain="1" state0=".5"/>
+<cellW2D id="GenericMuscleCellW2D" tau="1s" bias="1" gain="1" state0=".5"/>
 
-<outputSynapse id="neuron_to_neuron_w2d"/>
-<outputSynapse id="neuron_to_muscle_w2d"/>
+<outputSynapse id="neuron_to_neuron_exc_w2d" sign="1"/>
+<outputSynapse id="neuron_to_neuron_inh_w2d" sign="-1"/>
+<outputSynapse id="neuron_to_muscle_w2d" sign="1"/>
 
 </Lems>
 

c302/custom_synapses.xml

@@ -12,6 +12,8 @@
                    extends="baseGradedSynapse"
                    description="For Worm2D...">
 
+        <Parameter name="sign" dimension="none"/>
+
         <Property name="weight" dimension="none" defaultValue="1"/>
 
         <Constant name="PAMP_SCALE" dimension="current" value="1pA"/>
@@ -24,7 +26,7 @@
 
         <Dynamics>
             <DerivedVariable name="outputpeer" dimension="none" select="peer/output"/>
-            <DerivedVariable name="i" exposure="i"  value="weight * outputpeer * PAMP_SCALE"/>
+            <DerivedVariable name="i" exposure="i"  value="weight * sign * outputpeer * PAMP_SCALE"/>
         </Dynamics>
     </ComponentType>
 

c302/parameters_W2D.py

@@ -71,7 +71,8 @@ def create_offsetcurrent(self):
         )
 
     def create_neuron_to_neuron_syn(self):
-        self.neuron_to_neuron_exc_syn = OutputSynapse(id="neuron_to_neuron_w2d")
+        self.neuron_to_neuron_exc_syn = OutputSynapse(id="neuron_to_neuron_exc_w2d")
+        self.neuron_to_neuron_inh_syn = OutputSynapse(id="neuron_to_neuron_inh_w2d")
 
         self.neuron_to_neuron_elec_syn = GapJunction(
             id="neuron_to_neuron_elec_syn",
@@ -101,7 +102,7 @@ def get_exc_syn(self, pre_cell, post_cell, type):
         return self.neuron_to_neuron_exc_syn
 
     def get_inh_syn(self, pre_cell, post_cell, type):
-        return self.neuron_to_neuron_exc_syn
+        return self.neuron_to_neuron_inh_syn
 
 
 from c302.bioparameters import NonNeuroMLCustomType