OpenSourceBrain · pgleeson · May 15, 2024 · May 14, 2024 · May 14, 2024 · May 14, 2024
diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
@@ -17,10 +17,10 @@ jobs:
         python-version: [ 3.8, 3.9, "3.10" ]
 
     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 }}
 

diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -18,10 +18,10 @@ jobs:
 
 
     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 }}
 

diff --git a/.gitignore b/.gitignore
@@ -319,3 +319,4 @@ original.v.dat
 /CellTypesDatabase/models/GLIF/*txt
 /CellTypesDatabase/models/GLIF/*json
 arm64
+/CellTypesDatabase/models/.DS_Store
diff --git a/CellTypesDatabase/models/NeuroML2/497232312.net.nml b/CellTypesDatabase/models/NeuroML2/497232312.net.nml
@@ -4,7 +4,7 @@
     xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd"
     id = "NeuroML2_file_exported_from_NEURON">
 
-  <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.2.4 HEAD (1d87d5d39) 2024-02-09
+  <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.1.0 HEAD (047dd824) 2022-03-25
           Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
           Yale University and UCL 
   </notes>

diff --git a/CellTypesDatabase/models/NeuroML2/CaDynamics_all.nml b/CellTypesDatabase/models/NeuroML2/CaDynamics_all.nml
diff --git a/CellTypesDatabase/models/NeuroML2/CellTypesPerLayer.net.nml b/CellTypesDatabase/models/NeuroML2/CellTypesPerLayer.net.nml
@@ -1,6 +1,6 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="CellTypesPerLayer">
     <include href="ROTATED_Cell_473862496.cell.nml"></include>
-    <include href="ROTATED_Cell_472427533.cell.nml"></include>
+    <include href="ROTATED_Cell_329321704.cell.nml"></include>
     <include href="ROTATED_Cell_473871773.cell.nml"></include>
     <include href="ROTATED_Cell_473871592.cell.nml"></include>
     <network id="CellTypesPerLayer">
@@ -9,7 +9,7 @@
                 <location y="-100." x="0." z="0."/>
             </instance>
         </population>
-        <population id="Pop_ROTATED_Cell_472427533" type="populationList" component="ROTATED_Cell_472427533">
+        <population id="Pop_ROTATED_Cell_329321704" type="populationList" component="ROTATED_Cell_329321704">
             <instance id="0">
                 <location y="-295." x="300." z="0."/>
             </instance>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_329321704.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_329321704.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_329322394.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_329322394.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_471081668.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_471081668.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_471085845.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_471085845.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_471086533.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_471086533.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_471087975.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_471087975.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472299294.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472299294.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472299363.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472299363.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472300877.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472300877.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472301074.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472301074.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472304539.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472304539.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472304676.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472304676.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472306460.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472306460.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472306544.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472306544.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472306616.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472306616.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472349114.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472349114.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472352327.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472352327.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472363762.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472363762.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472421285.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472421285.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472424854.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472424854.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472427533.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472427533.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472430904.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472430904.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472434498.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472434498.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472440759.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472440759.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472442377.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472442377.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472447460.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472447460.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml
@@ -6796,7 +6796,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <member segment="495"/>
                 <member segment="496"/>
             </segmentGroup>
-            <segmentGroup id="ModelViewParmSubset_1">
+            <segmentGroup id="ModelViewParmSubset_235">
                 <include segmentGroup="soma_0"/>
             </segmentGroup>
             <segmentGroup id="dend">
@@ -6907,6 +6907,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
                 <channelDensity id="pas_dend" ionChannel="pas" condDensity="0.00012046511053782884 S_per_cm2" erev="-80.97549438476562 mV" segmentGroup="dend" ion="non_specific"/>
                 <channelDensityNernst id="Ca_HVA_soma" ionChannel="Ca_HVA" condDensity="5.857401378883121e-05 S_per_cm2" segmentGroup="soma" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_soma" ionChannel="Ca_LVA" condDensity="0.009555960646307055 S_per_cm2" segmentGroup="soma" ion="ca"/>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="soma"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="axon"/>
                 <specificCapacitance value="2.207587481 uF_per_cm2" segmentGroup="dend"/>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472451419.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472451419.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472455509.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472455509.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472912107.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472912107.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472912177.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472912177.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472915634.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472915634.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473465456.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473465456.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473465774.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473465774.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473561660.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473561660.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473561729.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473561729.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473834758.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473834758.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473835796.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473835796.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473860269.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473860269.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473862421.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473862421.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473862496.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473862496.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473862845.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473862845.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473863035.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473863035.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473863510.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473863510.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473863578.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473863578.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473871429.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473871429.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473871592.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473871592.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473871773.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473871773.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_473872986.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_473872986.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476630516.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476630516.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476637699.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476637699.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476637723.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476637723.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476637747.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476637747.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476637796.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476637796.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_476679102.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_476679102.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477313251.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477313251.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477494382.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477494382.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477510918.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477510918.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477510985.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477510985.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477838913.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477838913.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477839613.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477839613.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477840124.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477840124.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477876559.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477876559.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_477876583.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_477876583.cell.nml