Merge pull request #15 from OpenSourceBrain/development

Adding <spikeThresh> for future nml validity
OpenSourceBrain · May 14, 2024 · ead235a · ead235a
2 parents 2413bba + 406fc17
commit ead235a
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Showing 32 changed files with 579 additions and 561 deletions.
diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml
@@ -16,10 +16,10 @@ jobs:
         python-version: [ 3.7, 3.9 ]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      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
@@ -9,22 +9,28 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
+    name: Py${{ matrix.python-version }}, ${{ matrix.engine}} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9 ]
+        python-version: [ "3.10" ]
         engine: [ NEURON, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate ]
+        runs-on: [ubuntu-latest, macos-latest ]
 
     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 }}
 
+    - name: Install HDF5 for pytables on macos-latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Install OMV
       run: |
         pip install git+https://github.com/OpenSourceBrain/osb-model-validation
@@ -35,7 +41,6 @@ jobs:
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |
         omv all -V --engine=${{ matrix.engine }}
-        more NMC/NeuroML2/report*
 
     - name: OMV final version info
       run: |

diff --git a/NMC/NeuroML2/.test.jnmleden.omt b/NMC/NeuroML2/.test.jnmleden.omt
@@ -15,4 +15,4 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 0
-        tolerance: 0.000860873175366194
+        tolerance: 0.000860898645740264
diff --git a/NMC/NeuroML2/LEMS_L1_HAC_cNAC187_1.xml b/NMC/NeuroML2/LEMS_L1_HAC_cNAC187_1.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
-    <Target component="L1_HAC_cNAC187_1" reportFile="report.l1.__SIMULATOR__.txt"/>
+    <Target component="L1_HAC_cNAC187_1" reportFile="report.L1_HAC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="cNAC187_L1_HAC_f8c9772d9d.stepcurrent3.net.nml"/>
     <Include file="cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml"/>
     <Include file="K_Tst.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="Ca_LVAst.channel.nml"/>
     <Include file="Ca.channel.nml"/>
-
-    <Simulation id="L1_HAC_cNAC187_1" length="3000ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="L1_HAC_cNAC187_1" length="3000.0ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" title="Membrane potentials of cells in Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
             <Line id="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0[0]: v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" fileName="L1_HAC_cNAC187_1.Pop_cNAC187_L1_HAC_f8c9772d9d_0_0.v.dat">
-            <OutputColumn id="v_Pop_cNAC187_L1_HAC_f8c9772d9d_0_0_0_cNAC187_L1_HAC_f8c9772d9d_0_0_v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v"/> 
+            <OutputColumn id="v_Pop_cNAC187_L1_HAC_f8c9772d9d_0_0_0_cNAC187_L1_HAC_f8c9772d9d_0_0_v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NMC/NeuroML2/LEMS_L23_LBC_cSTUT189_1.xml b/NMC/NeuroML2/LEMS_L23_LBC_cSTUT189_1.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
-    <Target component="L23_LBC_cSTUT189_1" reportFile="report.lbc.__SIMULATOR__.txt"/>
+    <Target component="L23_LBC_cSTUT189_1" reportFile="report.L23_LBC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="cSTUT189_L23_LBC_e6e8f83407.stepcurrent3.net.nml"/>
     <Include file="cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml"/>
     <Include file="K_Tst.channel.nml"/>
@@ -30,17 +30,16 @@
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="Ca_LVAst.channel.nml"/>
     <Include file="Ca.channel.nml"/>
-
-    <Simulation id="L23_LBC_cSTUT189_1" length="3000ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="L23_LBC_cSTUT189_1" length="3000.0ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" title="Membrane potentials of cells in Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
             <Line id="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0[0]: v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" fileName="L23_LBC_cSTUT189_1.Pop_cSTUT189_L23_LBC_e6e8f83407_0_0.v.dat">
-            <OutputColumn id="v_Pop_cSTUT189_L23_LBC_e6e8f83407_0_0_0_cSTUT189_L23_LBC_e6e8f83407_0_0_v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v"/> 
+            <OutputColumn id="v_Pop_cSTUT189_L23_LBC_e6e8f83407_0_0_0_cSTUT189_L23_LBC_e6e8f83407_0_0_v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NMC/NeuroML2/LEMS_L23_NBC_cNAC187_1.xml b/NMC/NeuroML2/LEMS_L23_NBC_cNAC187_1.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
-    <Target component="L23_NBC_cNAC187_1" reportFile="report.l23ncb.__SIMULATOR__.txt"/>
+    <Target component="L23_NBC_cNAC187_1" reportFile="report.L23_NBC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="cNAC187_L23_NBC_9d37c4b1f8.stepcurrent3.net.nml"/>
     <Include file="cNAC187_L23_NBC_9d37c4b1f8_0_0.cell.nml"/>
     <Include file="K_Tst.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="Ca_LVAst.channel.nml"/>
     <Include file="Ca.channel.nml"/>
-
-    <Simulation id="L23_NBC_cNAC187_1" length="3000ms" step="0.01ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="L23_NBC_cNAC187_1" length="3000.0ms" step="0.01ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" title="Membrane potentials of cells in Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
             <Line id="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0[0]: v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" fileName="L23_NBC_cNAC187_1.Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0.v.dat">
-            <OutputColumn id="v_Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0_0_cNAC187_L23_NBC_9d37c4b1f8_0_0_v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v"/> 
+            <OutputColumn id="v_Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0_0_cNAC187_L23_NBC_9d37c4b1f8_0_0_v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NMC/NeuroML2/LEMS_L23_PC_cADpyr229_1.xml b/NMC/NeuroML2/LEMS_L23_PC_cADpyr229_1.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
-    <Target component="L23_PC_cADpyr229_1" reportFile="report.l23.__SIMULATOR__.txt"/>
+    <Target component="L23_PC_cADpyr229_1" reportFile="report.L23_PC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="cADpyr229_L23_PC_5ecbf9b163.stepcurrent3.net.nml"/>
     <Include file="cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml"/>
     <Include file="pas.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="K_Pst.channel.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="Ca_LVAst.channel.nml"/>
-
-    <Simulation id="L23_PC_cADpyr229_1" length="3000ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="L23_PC_cADpyr229_1" length="3000.0ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" title="Membrane potentials of cells in Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
             <Line id="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0[0]: v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" fileName="L23_PC_cADpyr229_1.Pop_cADpyr229_L23_PC_5ecbf9b163_0_0.v.dat">
-            <OutputColumn id="v_Pop_cADpyr229_L23_PC_5ecbf9b163_0_0_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v"/> 
+            <OutputColumn id="v_Pop_cADpyr229_L23_PC_5ecbf9b163_0_0_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NMC/NeuroML2/LEMS_L5_TTPC1_cADpyr232_1.xml b/NMC/NeuroML2/LEMS_L5_TTPC1_cADpyr232_1.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
 
      -->
-    
+
     <!-- Specify which component to run -->
-    <Target component="L5_TTPC1_cADpyr232_1" reportFile="report.l5.__SIMULATOR__.txt"/>
+    <Target component="L5_TTPC1_cADpyr232_1" reportFile="report.L5_TTPC1.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="cADpyr232_L5_TTPC1_0fb1ca4724.stepcurrent3.net.nml"/>
     <Include file="cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml"/>
     <Include file="pas.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="K_Pst.channel.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="Ca_LVAst.channel.nml"/>
-
-    <Simulation id="L5_TTPC1_cADpyr232_1" length="3000ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="L5_TTPC1_cADpyr232_1" length="3000.0ms" step="0.025ms" target="network" seed="1234">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" title="Membrane potentials of cells in Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
             <Line id="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0[0]: v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" fileName="L5_TTPC1_cADpyr232_1.Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0.v.dat">
-            <OutputColumn id="v_Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_0_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v"/> 
+            <OutputColumn id="v_Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_0_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/NMC/NeuroML2/bAC217_L4_MC_5fa0a62bd0_0_0.cell.nml b/NMC/NeuroML2/bAC217_L4_MC_5fa0a62bd0_0_0.cell.nml
@@ -22579,6 +22579,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue value="1e4 * ((-0.869600 + 2.087000*exp((p--1000.000000)*-0.003000))*0.000371)" inhomogeneousParameter="PathLengthOver_apical"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance segmentGroup="basal" value="1.0 uF_per_cm2"/>
                 <specificCapacitance segmentGroup="apical" value="1.0 uF_per_cm2"/>
                 <specificCapacitance segmentGroup="axonal" value="1.0 uF_per_cm2"/>

diff --git a/NMC/NeuroML2/bNAC219_L1_DAC_a9ae5cbbf5_0_0.cell.nml b/NMC/NeuroML2/bNAC219_L1_DAC_a9ae5cbbf5_0_0.cell.nml
@@ -5323,6 +5323,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003000))*0.000049)" inhomogeneousParameter="PathLengthOver_apical"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance segmentGroup="basal" value="1.0 uF_per_cm2"/>
                 <specificCapacitance segmentGroup="apical" value="1.0 uF_per_cm2"/>
                 <specificCapacitance segmentGroup="axonal" value="1.0 uF_per_cm2"/>

diff --git a/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163.net.nml b/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163.net.nml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
     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"
+    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 7.8.2 HEAD (09b151ec) 2020-12-16
+  <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/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163.stepcurrent3.net.nml b/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163.stepcurrent3.net.nml
@@ -12,7 +12,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
     <network id="network" type="networkWithTemperature" temperature="34 degC">
         <population id="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" component="cADpyr229_L23_PC_5ecbf9b163_0_0" size="1" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stepcurrent3_hyp_input" population="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" component="stepcurrent3_hyp">