Merge pull request #2 from OpenSourceBrain/development

Test on linux & mac 14
OpenSourceBrain · Apr 9, 2024 · 281de79 · 281de79
2 parents a0a47e7 + d0f33bd
commit 281de79
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diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -2,9 +2,9 @@ name: Continuous builds
 
 on:
   push:
-    branches: [ main, development ]
+    branches: [ main, development, experimental ]
   pull_request:
-    branches: [ main, development ]
+    branches: [ main, development, experimental ]
 
 jobs:
   build:
@@ -14,15 +14,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9 ]
-        runs-on: [ ubuntu-latest, macos-latest,  macos-11 ]
-        engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_EDEN, jNeuroML_validate, EDEN, "EDEN:0.2.0" ]
+        runs-on: [ ubuntu-latest, macos-14 ]
+        engine:
+            - jNeuroML
+            - jNeuroML_NEURON
+            - jNeuroML_EDEN
+            - "jNeuroML_EDEN:0.2.3"
+            - jNeuroML_validate
+            - "EDEN:0.2.0"
+            - "EDEN:0.2.2"
+            - "EDEN:0.2.3"
 
+        python-version: [ "3.10" ]
+
     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/pip-install.yml b/.github/workflows/pip-install.yml
@@ -17,9 +17,9 @@ jobs:
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@
 x86_64
 *_nrn.py
 arm64
+/NeuroML2/hhcell.hoc
+/NeuroML2/report.*.txt
diff --git a/NeuroML2/.test.2007.jnmleden.omt b/NeuroML2/.test.2007.jnmleden.omt
@@ -14,4 +14,4 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0.000
+        tolerance: 3.667537832120739e-08  # due to slight difference on mac/linux of eden...
diff --git a/NeuroML2/.test.eden.omt b/NeuroML2/.test.eden.omt
@@ -12,4 +12,4 @@ experiments:
         spike detection:
           method: threshold
           threshold: 0
-        tolerance: 0
+        tolerance: 3.667537832120739e-08  # due to slight difference on mac/linux of eden...
diff --git a/NeuroML2/.test.ex5.eden.omt b/NeuroML2/.test.ex5.eden.omt
@@ -0,0 +1,28 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_NML2_Ex5_DetCell.xml 
+engine: jNeuroML_EDEN
+mep: .test.ex5.mep
+experiments:
+  v:
+    observables:
+      spike times:
+        file: 
+          path: ex5_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.0035033174501254887
+  m:
+    observables:
+      spike times:
+        file: 
+          path: ex5_vars.dat
+          columns: [0,1]
+          scaling: [1000, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.9
+        tolerance: 0.0035249957767891716
diff --git a/NeuroML2/.test.ex5.jnml.omt b/NeuroML2/.test.ex5.jnml.omt
@@ -0,0 +1,28 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_NML2_Ex5_DetCell.xml 
+engine: jNeuroML
+mep: .test.ex5.mep
+experiments:
+  v:
+    observables:
+      spike times:
+        file: 
+          path: ex5_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.005542225676726113
+  m:
+    observables:
+      spike times:
+        file: 
+          path: ex5_vars.dat
+          columns: [0,1]
+          scaling: [1000, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.9
+        tolerance: 0.005574638211610937
diff --git a/NeuroML2/.test.ex5.jnmlnrn.omt b/NeuroML2/.test.ex5.jnmlnrn.omt
@@ -0,0 +1,28 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_NML2_Ex5_DetCell.xml 
+engine: jNeuroML_NEURON
+mep: .test.ex5.mep
+experiments:
+  v:
+    observables:
+      spike times:
+        file: 
+          path: ex5_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0
+  m:
+    observables:
+      spike times:
+        file: 
+          path: ex5_vars.dat
+          columns: [0,1]
+          scaling: [1000, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0.9
+        tolerance: 0
diff --git a/NeuroML2/.test.ex5.mep b/NeuroML2/.test.ex5.mep
@@ -0,0 +1,9 @@
+system: Test Ex0
+
+experiments:
+    v:
+        expected:
+            spike times: [102.22, 118.46, 134.5, 150.51999999999998, 166.55, 182.57999999999998, 198.6, 214.63, 230.65, 246.68, 262.71, 278.72999999999996, 294.76000000000005, 310.79, 326.81, 342.84, 358.86, 374.89, 390.92, 406.94, 422.97, 439.0, 455.02, 471.05, 487.07, 503.09999999999997, 519.13, 535.15, 551.18, 567.2, 583.23, 599.26, 615.2800000000001, 631.3100000000001, 647.34, 663.3599999999999, 679.3900000000001, 695.41, 711.4399999999999, 727.4699999999999, 743.49, 759.52, 775.55, 791.57, 807.6, 823.62, 839.65, 855.68, 871.7, 887.73]
+    m:
+        expected:
+            spike times: [102.44, 118.69, 134.72, 150.75, 166.77, 182.79999999999998, 198.83, 214.85000000000002, 230.88, 246.9, 262.93, 278.96, 294.98, 311.01, 327.04, 343.06, 359.09000000000003, 375.11, 391.14, 407.16999999999996, 423.19, 439.22, 455.25, 471.27000000000004, 487.3, 503.32, 519.35, 535.38, 551.4, 567.43, 583.45, 599.48, 615.51, 631.5300000000001, 647.5600000000001, 663.59, 679.61, 695.64, 711.66, 727.6899999999999, 743.72, 759.74, 775.77, 791.8, 807.8199999999999, 823.85, 839.87, 855.9, 871.93, 887.95]
diff --git a/NeuroML2/LEMS_NML2_Ex5_DetCell.xml b/NeuroML2/LEMS_NML2_Ex5_DetCell.xml
@@ -0,0 +1,64 @@
+<Lems>
+
+    <!-- Example with Simple cell specifying segment details-->
+
+    <!-- This is a file which can be read and executed by the LEMS Interpreter.
+         It imports the LEMS definitions of the core NeuroML 2 Components,
+         imports in "pure" NeuroML 2 and contains some LEMS elements for running
+         a simulation -->
+
+
+    <Target component="sim1" reportFile="report.ex5.txt"/>
+
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+
+    <!-- Including file with a <neuroml> root, a "real" NeuroML 2 file -->
+    <Include file="NML2_SingleCompHHCell.nml"/>
+
+
+    <Simulation id="sim1" length="1000ms" step="0.01ms" target="net1">
+
+        <Display id="d1" title="Ex5: HH cell with simple morphology: voltage" timeScale="1ms" xmin="0" xmax="300" ymin="-90" ymax="50">
+                <Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#cccccc" timeScale="1ms"/>
+                <Line id="spiking" quantity="hhpop[0]/spiking" scale="0.1V"  color="#004040" timeScale="1ms"/>
+                <!--<Line id="l3" quantity="hhpop[0]/debugVal" scale="1V"  color="#999999" timeScale="1ms"/>-->
+        </Display>
+        <Display id="d2" title="Ex5: HH cell with simple morphology: rate variables" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1">
+                <Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#000000" timeScale="1ms"/>
+                <Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#ff0000" timeScale="1ms"/>
+                <Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>
+        </Display>
+        <Display id="d3" title="Ex5: HH cell with simple morphology: current densities" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1">
+                <Line id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#000000" timeScale="1ms"/>
+                <Line id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ff0000" timeScale="1ms"/>
+        </Display>
+        <Display id="d4" title="Ex5: HH cell with simple morphology: conductance densities" timeScale="1ms" xmin="0" xmax="300" ymin="-50" ymax="350">
+                <Line id="gna" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/gDensity" scale="1"  color="#000000" timeScale="1ms"/>
+                <Line id="gk" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/gDensity" scale="1"  color="#ff0000" timeScale="1ms"/>
+        </Display>
+
+
+        <OutputFile id="of0" fileName="ex5_v.dat">
+            <OutputColumn id="v" quantity="hhpop[0]/v"/>
+        </OutputFile>
+
+        <OutputFile id="of1" fileName="ex5_vars.dat">
+            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/>
+            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/>
+            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/>
+        </OutputFile>
+
+        <!-- Not supported by EDEN...
+        <OutputFile id="of2" fileName="results/ex5_curr_dens.dat">
+            <OutputColumn id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>
+            <OutputColumn id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/>
+        </OutputFile>-->
+
+
+    </Simulation>
+
+
+</Lems>
diff --git a/NeuroML2/NML2_SingleCompHHCell.nml b/NeuroML2/NML2_SingleCompHHCell.nml
@@ -0,0 +1,90 @@
+<?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 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
+         id="NML2_SingleCompHHCell">
+
+    <!-- Single compartment cell with HH channels -->
+
+    <!-- This is a "pure" NeuroML 2 file. It can be included in a LEMS file for use in a simulaton 
+    by the LEMS interpreter, see LEMS_NML2_Ex5_DetCell.xml -->     
+
+    <ionChannelHH id="passiveChan" conductance="10pS">
+        <notes>Leak conductance</notes>
+    </ionChannelHH>
+
+
+    <ionChannelHH id="naChan" conductance="10pS" species="na">
+        <notes>Na channel</notes>
+
+        <gateHHrates id="m" instances="3">
+            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
+            <reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
+        </gateHHrates>
+
+        <gateHHrates id="h" instances="1">
+            <forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
+            <reverseRate type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
+        </gateHHrates>
+
+    </ionChannelHH>
+
+
+    <ionChannelHH id="kChan" conductance="10pS" species="k">
+
+        <gateHHrates id="n" instances="4">
+            <forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
+            <reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
+        </gateHHrates>
+
+    </ionChannelHH>
+
+
+
+    <cell id="hhcell">
+
+        <morphology id="morph1">
+            <segment id="0" name="soma">
+                <proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 um^2-->
+                <distal x="0" y="0" z="0" diameter="17.841242"/>
+            </segment>
+
+            <segmentGroup id="soma_group">
+                <member segment="0"/>
+            </segmentGroup>
+
+        </morphology>
+
+        <biophysicalProperties id="bioPhys1">
+
+            <membraneProperties>
+
+                <channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV" ion="non_specific"/>
+                <channelDensity id="naChans" ionChannel="naChan" condDensity="120.0 mS_per_cm2" erev="50.0 mV" ion="na"/>
+                <channelDensity id="kChans" ionChannel="kChan" condDensity="360 S_per_m2" erev="-77mV" ion="k"/>
+
+                <spikeThresh value="-20mV"/>
+                <specificCapacitance value="1.0 uF_per_cm2"/>
+                <initMembPotential value="-65mV"/>
+
+            </membraneProperties>
+
+            <intracellularProperties>
+                <resistivity value="0.03 kohm_cm"/>   <!-- Note: not used in single compartment simulations -->
+            </intracellularProperties>
+
+        </biophysicalProperties>
+
+    </cell>
+
+    <pulseGenerator id="pulseGen1" delay="100ms" duration="800ms" amplitude="0.08nA"/>
+
+
+    <network id="net1">
+        <population id="hhpop" component="hhcell" size="1"/>
+        <explicitInput target="hhpop[0]" input="pulseGen1"/>
+    </network>
+
+</neuroml>
+
diff --git a/NeuroML2/clean.sh b/NeuroML2/clean.sh
@@ -1 +1,2 @@
-rm x86_64 *.c *.so *.dat
+rm -rf x86_64 arm64 
+mv *nrn.py LEMS*_eden.py *.c *.so *.dat *.mod *txt *.hoc /tmp