Merge pull request #2 from OpenSourceBrain/development

Regenerated

Author: pgleeson

.github/workflows/omv-ci.yml

@@ -18,10 +18,10 @@ jobs:
         engine: [ jNeuroML_validate ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 

ISN.py

@@ -518,7 +518,7 @@ def generate(scale_populations = 1,
         levels = {'IPSC': synAmpaEE.erev, 'EPSC':synGabaIE.erev}
 
         for l in levels:
-            cell_index = levels.keys().index(l)
+            cell_index = list(levels.keys()).index(l)
 
             pop = 'popExc2'
             plot = 'IClamp_i_%s'%(l)

NeuroML2/ISN_net.net.nml.h5

@@ -16742,6 +16742,8 @@
 
         <channelDensity ionChannel="ca" id="ca_soma" condDensity = "5e-5 S_per_cm2" ion="ca" segmentGroup="soma_group" erev="140.67523 mV"/>
 
+        <spikeThresh value="10mV"/>
+
         <specificCapacitance  value="1 uF_per_cm2" />
 
         <initMembPotential value="-75.0 mV"/>

NeuroML2/ISN_net/L23_NoHotSpot.cell.nml

@@ -16742,6 +16742,8 @@
 
         <channelDensity ionChannel="ca" id="ca_soma" condDensity = "5e-5 S_per_cm2" ion="ca" segmentGroup="soma_group" erev="140.67523 mV"/>
 
+        <spikeThresh value="10mV"/>
+
         <specificCapacitance  value="1 uF_per_cm2" />
 
         <initMembPotential value="-75.0 mV"/>

NeuroML2/ISN_net_PointNeurons.net.nml.h5

@@ -16726,6 +16726,7 @@
                 <channelDensity id="it_soma" ionChannel="it" condDensity="0.0003 S_per_cm2" erev="140.67523 mV" segmentGroup="soma_group" ion="ca"/>
                 <channelDensity id="ca_dends" ionChannel="ca" condDensity="5e-5 S_per_cm2" erev="140.67523 mV" segmentGroup="dendrite_group" ion="ca"/>
                 <channelDensity id="ca_soma" ionChannel="ca" condDensity="5e-5 S_per_cm2" erev="140.67523 mV" segmentGroup="soma_group" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.04928685549 uF_per_cm2"/>
                 <initMembPotential value="-75.0 mV"/>
             </membraneProperties>

NeuroML2/LEMS_ISN_net.xml

@@ -15991,6 +15991,7 @@ Tuning procedure metadata:
                 <channelDensity id="it_soma" ionChannel="it" condDensity="0.0003 S_per_cm2" erev="140.67523 mV" segmentGroup="soma_group" ion="ca"/>
                 <channelDensity id="ca_dends" ionChannel="ca" condDensity="5e-5 S_per_cm2" erev="140.67523 mV" segmentGroup="dendrite_group" ion="ca"/>
                 <channelDensity id="ca_soma" ionChannel="ca" condDensity="5e-5 S_per_cm2" erev="140.67523 mV" segmentGroup="soma_group" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="0.897586517256 uF_per_cm2"/>
                 <initMembPotential value="-75.0 mV"/>
             </membraneProperties>