Merge pull request #5 from OpenSourceBrain/development

Tests on mac and mac14 too, mainly to check EDEN behaviour
OpenSourceBrain · May 2, 2024 · 9310c9d · 9310c9d
2 parents cbba4d0 + 0059494
commit 9310c9d
Show file tree

Hide file tree

Showing 16 changed files with 285 additions and 112 deletions.
diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -9,26 +9,31 @@ 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: [ 3.7, 3.9 ]
+        python-version: [ "3.10" ]
         engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_validate, jNeuroML_validatev1, jNeuroML_EDEN ]
+        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
-        pip install scipy sympy matplotlib cython pandas tables
 
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |

diff --git a/.gitignore b/.gitignore
@@ -55,3 +55,4 @@ neuroConstruct/generatedNeuroML2/*.js
 *_code.gen.c
 *_code.gen.so
 arm64
+/neuroConstruct/generatedNeuroML2/ACnet2.net.nml__flattened.xml
diff --git a/neuroConstruct/generatedNeuroML2/.test.jnmleden.omt b/neuroConstruct/generatedNeuroML2/.test.jnmleden.omt
@@ -14,7 +14,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.0010167414427688726
+        tolerance: 0.0010208952879688757
   Current clamp basket:
     observables:
       spike times:
@@ -25,4 +25,4 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.00029262095123372775
+        tolerance: 0.000292671703552327
diff --git a/neuroConstruct/generatedNeuroML2/.test.two.jnmleden.omt b/neuroConstruct/generatedNeuroML2/.test.two.jnmleden.omt
@@ -15,7 +15,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.017343922603342065
+        tolerance: 0.01734388742304312
   bask0:
     observables:
       spike times:
@@ -26,4 +26,4 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.0017869092394359062
+        tolerance: 0.001786960295444412
diff --git a/neuroConstruct/generatedNeuroML2/ACnet2.net.nml b/neuroConstruct/generatedNeuroML2/ACnet2.net.nml
@@ -1,9 +1,9 @@
 <?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_v2beta3.xsd" id="network_ACnet2">
+<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.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="network_ACnet2">
 
     <notes>
 
-Network structure (NeuroML 2beta3) for project: ACnet2 saved with neuroConstruct v1.7.1 on: 13:25:26, 17-Jun-14
+Network structure (NeuroML 2.3.1) for project: ACnet2 saved with neuroConstruct v1.7.5 on: 14:13:13, 02-May-24
 
 Cell Group: basket_soma contains 1 cells
 Cell Group: pyramidal_soma contains 1 cells
@@ -24,13 +24,9 @@ Cell Group: pyramidal_soma contains 1 cells
     <include href="Na_bask.channel.nml"/>
     <include href="Na_pyr.channel.nml"/>
     <include href="pyr_4_sym_soma.cell.nml"/>
-
     <pulseGenerator id="Input_3" delay="100.0ms" duration="500.0ms" amplitude="2.0E-4uA"/>
-
 
-
     <pulseGenerator id="Input_2" delay="100.0ms" duration="500.0ms" amplitude="1.0E-4uA"/>
-
 
     <network id="network_ACnet2" type="networkWithTemperature" temperature="6.3 degC">
 

diff --git a/neuroConstruct/generatedNeuroML2/Ca_conc.nml b/neuroConstruct/generatedNeuroML2/Ca_conc.nml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <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" id="Ca_conc">
-
+        
     <notes>NeuroML file describing intracellular Calcium dynamics, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
-
+        
     <fixedFactorConcentrationModel id="Ca_conc" restingConc="0.0mM" decayConstant="0.1s" ion="ca" rho="9543.150099999999mol_per_m_per_A_per_s"/>
-
+    
 </neuroml>
diff --git a/neuroConstruct/generatedNeuroML2/Ca_pyr.channel.nml b/neuroConstruct/generatedNeuroML2/Ca_pyr.channel.nml
@@ -1,70 +1,106 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <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" id="Ca_pyr">
-
+        
     <notes>NeuroML file containing a single Calcium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
-
+        
     <ionChannel id="Ca_pyr" conductance="10pS" type="ionChannelHH" species="ca">
-
-        <notes>NeuroML file containing a single Calcium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
 
+        <notes>NeuroML file containing a single Calcium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+
+
         <annotation>
+
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+
                 <rdf:Description rdf:about="Ca_pyr">
+
 
                     <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+
                         <rdf:Bag>
+
                             <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+
                             <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+
                         </rdf:Bag>
+
                     </bqmodel:isDescribedBy>
-
-
+                                    
+                    
                     <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+
                         <rdf:Bag>
+
                             <rdf:li>Ca channels</rdf:li>
+
                             <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+
                         </rdf:Bag>
+
                     </bqbiol:isVersionOf>
-
+                                    
                 </rdf:Description>
+
             </rdf:RDF>
+
         </annotation>
-
+                
         <gate id="m" type="gateHHrates" instances="2">
+
             <forwardRate type="HHSigmoidRate" rate="1.6e3per_s" scale="0.01389V" midpoint="5e-03V"/>
+
             <reverseRate type="HHExpLinearRate" rate="1e2per_s" scale="-0.005V" midpoint="-8.9e-3V"/>
+
         </gate>
-
+                
         <gate id="h" type="gateHHtauInf" instances="1">
+
             <timeCourse type="Ca_pyr_h_tau_tau"/>
+
             <steadyState type="Ca_pyr_h_inf_inf"/>
+
         </gate>
-
+
+
     </ionChannel>
-
+        
     <ComponentType name="Ca_pyr_h_tau_tau" extends="baseVoltageDepTime">
+
         <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
-
+                
         <Dynamics>
+
             <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
             <DerivedVariable name="t" exposure="t" dimension="time" value="(0.2) * TIME_SCALE"/>
+
         </Dynamics>
-
+            
     </ComponentType>
-
+        
     <ComponentType name="Ca_pyr_h_inf_inf" extends="baseVoltageDepVariable">
+
         <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
-
+                
         <Dynamics>
+
             <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
             <ConditionalDerivedVariable name="x" exposure="x" dimension="none">
+
                 <Case condition="V  .gt. ( -0.06 )" value=" (exp (-50*(V + 0.06))) "/>
+
                 <Case value=" 1"/>
+
             </ConditionalDerivedVariable>
+
         </Dynamics>
-
+            
     </ComponentType>
-
+    
 </neuroml>
diff --git a/neuroConstruct/generatedNeuroML2/Kahp_pyr.channel.nml b/neuroConstruct/generatedNeuroML2/Kahp_pyr.channel.nml
@@ -1,69 +1,106 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <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" id="Kahp_pyr">
-
+        
     <notes>NeuroML file containing a single Calcium-dependent Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
-
+        
     <ionChannel id="Kahp_pyr" conductance="10pS" type="ionChannelHH" species="k">
-
-        <notes>NeuroML file containing a single Calcium-dependent Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
 
+        <notes>NeuroML file containing a single Calcium-dependent Potassium Channel description, from the Hippocampal CA3 neuron model presented in Traub et al., 1991.</notes>
+
+
         <annotation>
+
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+
                 <rdf:Description rdf:about="Kahp_pyr">
+
 
                     <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+
                         <rdf:Bag>
+
                             <rdf:li>Traub, R. D., Wong, R. K., Miles, R., and Michelson, H. (1991). A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. Journal of neurophysiology, 66(2), 635-50.</rdf:li>
+
                             <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1663538"/>
+
                         </rdf:Bag>
+
                     </bqmodel:isDescribedBy>
-
-
+                                    
+                    
                     <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+
                         <rdf:Bag>
+
                             <rdf:li>K channels</rdf:li>
+
                             <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/NeuronProp.aspx?id=259&amp;mo=1&amp;re=&amp;pr=C"/>
+
                         </rdf:Bag>
+
                     </bqbiol:isVersionOf>
-
+                                    
                 </rdf:Description>
+
             </rdf:RDF>
+
         </annotation>
-
+                
         <gate id="z" type="gateHHrates" instances="1">
+
             <forwardRate type="Kahp_pyr_z_alpha_rate"/>
+
             <reverseRate type="Kahp_pyr_z_beta_rate"/>
+
         </gate>
-
+
+
     </ionChannel>
-
+        
     <ComponentType name="Kahp_pyr_z_alpha_rate" extends="baseVoltageConcDepRate">
+
         <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+
         <Constant name="CONC_SCALE" dimension="concentration" value="1 mM"/>
-
+                
         <Dynamics>
+
             <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
             <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+
             <ConditionalDerivedVariable name="r" exposure="r" dimension="per_time">
+
                 <Case condition="ca_conc  .lt. ( 500.0 )" value="( 0.4 * ca_conc ) / TIME_SCALE"/>
+
                 <Case value="( 200) / TIME_SCALE"/>
+
             </ConditionalDerivedVariable>
+
         </Dynamics>
-
+            
     </ComponentType>
-
+        
     <ComponentType name="Kahp_pyr_z_beta_rate" extends="baseVoltageConcDepRate">
+
         <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 V"/>
+
         <Constant name="CONC_SCALE" dimension="concentration" value="1 mM"/>
-
+                
         <Dynamics>
+
             <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+
             <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+
             <DerivedVariable name="r" exposure="r" dimension="per_time" value="(20) / TIME_SCALE"/>
+
         </Dynamics>
-
+            
     </ComponentType>
-
+    
 </neuroml>