Merge pull request #1 from OpenSourceBrain/development

Tests with pynn 0.10.1
OpenSourceBrain · Mar 28, 2023 · f4dc4e1 · f4dc4e1
2 parents a62c089 + 1bbcc1d
commit f4dc4e1
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Showing 15 changed files with 238 additions and 39 deletions.
diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -11,25 +11,44 @@ jobs:
 
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [ 3.7 ]
-        engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML]
+        python-version: [ "3.8",  "3.9" ]
+        engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version:  ${{ matrix.python-version }}
+
     - name: Install OMV
       run: |
-        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation 
+        
     - name: Install additional packages
       run: |
         pip install scipy sympy matplotlib cython tables
+                  
+        pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+
+        
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |
         omv all -V --engine=${{ matrix.engine }}
+        
+    - name: Regenerate
+      run: |
+        omv install PyNN # required for regeneration...
+        omv install pyNeuroML # required for regeneration...
+        omv install jNeuroML
+        export JNML_HOME=/home/runner/jnml/jNeuroMLJar
+        export PATH=$JNML_HOME:$PATH
+        ./regenerate.sh
+      
+
     - name: OMV final version info
       run: |
         omv list -V # list installed engines
diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml
@@ -1,7 +1,7 @@
 <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_v2.3.xsd" id="ConnectionsTest">
     <notes>
     This NeuroML 2 file has been generated from: 
-        PyNN v0.9.6
+        PyNN v0.10.1
         libNeuroML v0.4.2
         pyNeuroML v0.7.6
     </notes>
@@ -17,38 +17,38 @@
             <property tag="radius" value="5"/>
             <property tag="color" value="0 0.6 0"/>
             <instance id="0">
-                <location x="40.34175597194811" y="-56.591291366920451" z="-52.704297599046448"/>
+                <location x="87.867091429339169" y="36.566883841576825" z="23.819394994835253"/>
             </instance>
             <instance id="1">
-                <location x="27.96964049341377" y="20.619331756707048" z="-40.861803830870279"/>
+                <location x="-22.414732648986103" y="-33.959789395443416" z="-90.377208907138694"/>
             </instance>
             <instance id="2">
-                <location x="-8.822322646973713" y="-79.443343688098949" z="-10.011891220669566"/>
+                <location x="54.996078669841175" y="63.22244265268138" z="8.332732747183268"/>
             </instance>
             <instance id="3">
-                <location x="-21.849212000552342" y="65.752552974467363" z="-27.538654076756487"/>
+                <location x="-73.045184370403433" y="15.931090520535406" z="-47.20047085637156"/>
             </instance>
             <instance id="4">
-                <location x="-38.26786504445414" y="76.745597854841847" z="-42.373649722922991"/>
+                <location x="11.886080666355546" y="-72.950647718983646" z="55.989089396806754"/>
             </instance>
         </population>
         <population id="pop_post" component="IF_cond_alpha_pop_post" size="5" type="populationList">
             <property tag="radius" value="5"/>
             <property tag="color" value="0 0.2 0.6"/>
             <instance id="0">
-                <location x="19.648700064194369" y="173.856015370791141" z="13.332375422194209"/>
+                <location x="32.097856025221816" y="177.715247089212056" z="-61.948698498499269"/>
             </instance>
             <instance id="1">
-                <location x="-25.653976862017934" y="186.933936247131953" z="55.394154045388987"/>
+                <location x="-74.115635174364087" y="241.910458891653718" z="3.906619842172132"/>
             </instance>
             <instance id="2">
-                <location x="8.878043164817528" y="218.933571545824407" z="-52.732081800665419"/>
+                <location x="54.387445031828904" y="192.588501616654327" z="-11.472415749409581"/>
             </instance>
             <instance id="3">
-                <location x="-21.626477676017085" y="169.336848396064056" z="23.243945074367289"/>
+                <location x="-14.603226514170453" y="171.734277722969381" z="-35.411273746924962"/>
             </instance>
             <instance id="4">
-                <location x="-10.321197646621894" y="230.787142220533354" z="93.051345121134659"/>
+                <location x="21.253482956578583" y="278.993049504672911" z="6.694332496085975"/>
             </instance>
         </population>
         <projection id="pop_pre__TO__pop_post" presynapticPopulation="pop_pre" postsynapticPopulation="pop_post" synapse="syn__pop_pre__TO__pop_post">

diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml
@@ -1,7 +1,7 @@
 <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_v2.3.xsd" id="Inputs">
     <notes>
     This NeuroML 2 file has been generated from: 
-        PyNN v0.9.6
+        PyNN v0.10.1
         libNeuroML v0.4.2
         pyNeuroML v0.7.6
     </notes>

diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml
@@ -2,7 +2,7 @@
 
     <!-- 
     This LEMS file has been generated from: 
-        PyNN v0.9.6
+        PyNN v0.10.1
         libNeuroML v0.4.2
         pyNeuroML v0.7.6
      -->

diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml
@@ -2,7 +2,7 @@
 
     <!-- 
     This LEMS file has been generated from: 
-        PyNN v0.9.6
+        PyNN v0.10.1
         libNeuroML v0.4.2
         pyNeuroML v0.7.6
      -->
@@ -22,38 +22,44 @@
 
         <Display id="pop_IF_curr_alpha_v" title="pop_IF_curr_alpha v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
             <Line id="pop_IF_curr_alpha v: cell 42" quantity="pop_IF_curr_alpha/0/IF_curr_alpha_pop_IF_curr_alpha/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
+            <Line id="pop_IF_curr_alpha v: cell 43" quantity="pop_IF_curr_alpha/1/IF_curr_alpha_pop_IF_curr_alpha/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="pop_IF_curr_alpha v: cell 44" quantity="pop_IF_curr_alpha/2/IF_curr_alpha_pop_IF_curr_alpha/v" scale="1mV" color="#98e752" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_IF_curr_exp_v" title="pop_IF_curr_exp v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_IF_curr_exp v: cell 43" quantity="pop_IF_curr_exp/0/IF_curr_exp_pop_IF_curr_exp/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="pop_IF_curr_exp v: cell 45" quantity="pop_IF_curr_exp/0/IF_curr_exp_pop_IF_curr_exp/v" scale="1mV" color="#bca074" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_IF_cond_alpha_v" title="pop_IF_cond_alpha v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_IF_cond_alpha v: cell 44" quantity="pop_IF_cond_alpha/0/IF_cond_alpha_pop_IF_cond_alpha/v" scale="1mV" color="#98e752" timeScale="1ms"/>
+            <Line id="pop_IF_cond_alpha v: cell 46" quantity="pop_IF_cond_alpha/0/IF_cond_alpha_pop_IF_cond_alpha/v" scale="1mV" color="#632794" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_IF_cond_exp_v" title="pop_IF_cond_exp v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_IF_cond_exp v: cell 45" quantity="pop_IF_cond_exp/0/IF_cond_exp_pop_IF_cond_exp/v" scale="1mV" color="#bca074" timeScale="1ms"/>
+            <Line id="pop_IF_cond_exp v: cell 48" quantity="pop_IF_cond_exp/1/IF_cond_exp_pop_IF_cond_exp/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
+            <Line id="pop_IF_cond_exp v: cell 49" quantity="pop_IF_cond_exp/2/IF_cond_exp_pop_IF_cond_exp/v" scale="1mV" color="#df5954" timeScale="1ms"/>
+            <Line id="pop_IF_cond_exp v: cell 47" quantity="pop_IF_cond_exp/0/IF_cond_exp_pop_IF_cond_exp/v" scale="1mV" color="#52c8bf" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_EIF_cond_exp_isfa_ista_v" title="pop_EIF_cond_exp_isfa_ista v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_EIF_cond_exp_isfa_ista v: cell 46" quantity="pop_EIF_cond_exp_isfa_ista/0/EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista/v" scale="1mV" color="#632794" timeScale="1ms"/>
+            <Line id="pop_EIF_cond_exp_isfa_ista v: cell 50" quantity="pop_EIF_cond_exp_isfa_ista/0/EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista/v" scale="1mV" color="#bf0239" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_HH_cond_exp_v" title="pop_HH_cond_exp v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_HH_cond_exp v: cell 47" quantity="pop_HH_cond_exp/0/HH_cond_exp_pop_HH_cond_exp/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
+            <Line id="pop_HH_cond_exp v: cell 51" quantity="pop_HH_cond_exp/0/HH_cond_exp_pop_HH_cond_exp/v" scale="1mV" color="#3f9fe8" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_post1_v" title="pop_post1 v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_post1 v: cell 48" quantity="pop_post1/0/IF_cond_exp_pop_post1/v" scale="1mV" color="#df5954" timeScale="1ms"/>
+            <Line id="pop_post1 v: cell 52" quantity="pop_post1/0/IF_cond_exp_pop_post1/v" scale="1mV" color="#dda9d2" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_post2_v" title="pop_post2 v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-70" ymax="10">
-            <Line id="pop_post2 v: cell 49" quantity="pop_post2/0/IF_cond_alpha_pop_post2/v" scale="1mV" color="#52c8bf" timeScale="1ms"/>
+            <Line id="pop_post2 v: cell 53" quantity="pop_post2/0/IF_cond_alpha_pop_post2/v" scale="1mV" color="#85ad96" timeScale="1ms"/>
         </Display>
 
         <OutputFile id="OF_pop_IF_curr_alpha_v" fileName="pop_IF_curr_alpha_v.dat">
             <OutputColumn id="pop_IF_curr_alpha_0_IF_curr_alpha_pop_IF_curr_alpha_v" quantity="pop_IF_curr_alpha/0/IF_curr_alpha_pop_IF_curr_alpha/v"/> 
+            <OutputColumn id="pop_IF_curr_alpha_1_IF_curr_alpha_pop_IF_curr_alpha_v" quantity="pop_IF_curr_alpha/1/IF_curr_alpha_pop_IF_curr_alpha/v"/> 
+            <OutputColumn id="pop_IF_curr_alpha_2_IF_curr_alpha_pop_IF_curr_alpha_v" quantity="pop_IF_curr_alpha/2/IF_curr_alpha_pop_IF_curr_alpha/v"/> 
         </OutputFile>
 
         <OutputFile id="OF_pop_IF_curr_exp_v" fileName="pop_IF_curr_exp_v.dat">
@@ -65,6 +71,8 @@
         </OutputFile>
 
         <OutputFile id="OF_pop_IF_cond_exp_v" fileName="pop_IF_cond_exp_v.dat">
+            <OutputColumn id="pop_IF_cond_exp_1_IF_cond_exp_pop_IF_cond_exp_v" quantity="pop_IF_cond_exp/1/IF_cond_exp_pop_IF_cond_exp/v"/> 
+            <OutputColumn id="pop_IF_cond_exp_2_IF_cond_exp_pop_IF_cond_exp_v" quantity="pop_IF_cond_exp/2/IF_cond_exp_pop_IF_cond_exp/v"/> 
             <OutputColumn id="pop_IF_cond_exp_0_IF_cond_exp_pop_IF_cond_exp_v" quantity="pop_IF_cond_exp/0/IF_cond_exp_pop_IF_cond_exp/v"/> 
         </OutputFile>
 
@@ -86,9 +94,13 @@
 
         <EventOutputFile id="Spikes_file_pop_IF_curr_alpha" fileName="pop_IF_curr_alpha.spikes" format="TIME_ID">
             <EventSelection id="0" select="pop_IF_curr_alpha/0/IF_curr_alpha_pop_IF_curr_alpha" eventPort="spike"/> 
+            <EventSelection id="1" select="pop_IF_curr_alpha/1/IF_curr_alpha_pop_IF_curr_alpha" eventPort="spike"/> 
+            <EventSelection id="2" select="pop_IF_curr_alpha/2/IF_curr_alpha_pop_IF_curr_alpha" eventPort="spike"/> 
         </EventOutputFile>
 
         <EventOutputFile id="Spikes_file_pop_IF_cond_exp" fileName="pop_IF_cond_exp.spikes" format="TIME_ID">
+            <EventSelection id="1" select="pop_IF_cond_exp/1/IF_cond_exp_pop_IF_cond_exp" eventPort="spike"/> 
+            <EventSelection id="2" select="pop_IF_cond_exp/2/IF_cond_exp_pop_IF_cond_exp" eventPort="spike"/> 
             <EventSelection id="0" select="pop_IF_cond_exp/0/IF_cond_exp_pop_IF_cond_exp" eventPort="spike"/> 
         </EventOutputFile>
 

diff --git a/NeuroML2/Positions.net.nml.h5 b/NeuroML2/Positions.net.nml.h5
diff --git a/NeuroML2/PyNN_NeuroML2_Export.net.nml b/NeuroML2/PyNN_NeuroML2_Export.net.nml
@@ -1,7 +1,7 @@
 <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_v2.3.xsd" id="PyNN_NeuroML2_Export">
     <notes>
     This NeuroML 2 file has been generated from: 
-        PyNN v0.9.6
+        PyNN v0.10.1
         libNeuroML v0.4.2
         pyNeuroML v0.7.6
     </notes>
@@ -16,10 +16,16 @@
     <expCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post1" tau_syn="5." e_rev="0."/>
     <alphaCondSynapse id="syn__pop_EIF_cond_exp_isfa_ista__TO__pop_post2" tau_syn="5." e_rev="0."/>
     <network id="PyNN_NeuroML2_Export">
-        <population id="pop_IF_curr_alpha" component="IF_curr_alpha_pop_IF_curr_alpha" size="1" type="populationList">
+        <population id="pop_IF_curr_alpha" component="IF_curr_alpha_pop_IF_curr_alpha" size="3" type="populationList">
             <instance id="0">
                 <location x="0." y="0." z="0."/>
             </instance>
+            <instance id="1">
+                <location x="1." y="0." z="0."/>
+            </instance>
+            <instance id="2">
+                <location x="2." y="0." z="0."/>
+            </instance>
         </population>
         <population id="pop_IF_curr_exp" component="IF_curr_exp_pop_IF_curr_exp" size="1" type="populationList">
             <instance id="0">
@@ -31,10 +37,16 @@
                 <location x="0." y="0." z="0."/>
             </instance>
         </population>
-        <population id="pop_IF_cond_exp" component="IF_cond_exp_pop_IF_cond_exp" size="1" type="populationList">
+        <population id="pop_IF_cond_exp" component="IF_cond_exp_pop_IF_cond_exp" size="3" type="populationList">
             <instance id="0">
                 <location x="0." y="0." z="0."/>
             </instance>
+            <instance id="1">
+                <location x="1." y="0." z="0."/>
+            </instance>
+            <instance id="2">
+                <location x="2." y="0." z="0."/>
+            </instance>
         </population>
         <population id="pop_EIF_cond_exp_isfa_ista" component="EIF_cond_exp_isfa_ista_pop_EIF_cond_exp_isfa_ista" size="1" type="populationList">
             <instance id="0">

diff --git a/PyNN/.test.input.brian2.omt b/PyNN/.test.input.brian2.omt
@@ -0,0 +1,26 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: InputsTest.py
+engine: PyNN_Brian2
+mep: .test.input.mep
+experiments:
+  v0:
+    observables:
+      spike times:
+        file: 
+          path: pop_pre_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: -50.1
+        tolerance: 0.00377714825306902460
+
+  spikes2:
+    observables:
+      spike times:
+        spiketimes file: 
+          path: pop_pre.spikes
+          format: TIME_ID
+          ids: 2
+        tolerance: 0.0031104199066874054
diff --git a/PyNN/.test.mep b/PyNN/.test.mep
@@ -10,4 +10,12 @@ experiments:
     pop_post2:
         expected:
             spike times: [56.94, 106.92999999999999, 203.78, 312.56, 421.68]
+
+    spike_rate_IF_curr_alpha_0:
+        expected:
+            spike rate: 31.274433150899135
+
+    spike_rate_IF_curr_alpha_1:
+        expected:
+            spike rate: 31.274433150899135
 
diff --git a/PyNN/.test.pynn9brian2.omt b/PyNN/.test.pynn9brian2.omt
@@ -0,0 +1,59 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: NeuroMLTest_PyNN0.9.py 
+engine: PyNN_Brian2
+mep: .test.mep
+experiments:
+  IF_curr_alpha:
+    observables:
+      spike times:
+        file: 
+          path: pop_IF_curr_alpha_0_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: -55
+        tolerance: 0.00030816640986148277
+  EIF_cond_exp_isfa_ista:
+    observables:
+      spike times:
+        file: 
+          path: pop_EIF_cond_exp_isfa_ista_0_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: -45
+        tolerance: 0.0003676020095576662
+  pop_post2:
+    observables:
+      spike times:
+        file: 
+          path: pop_post2_0_v.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: threshold
+          threshold: -63.5
+        tolerance: 0.0007024938531787697
+
+  spike_rate_IF_curr_alpha_0:
+    observables:
+      spike rate:
+        spiketimes file: 
+          path: pop_IF_curr_alpha.spikes
+          format: ID_TIME
+          scaling: 1
+          ids: 0
+        tolerance: 0.00015639662183320716
+
+  spike_rate_IF_curr_alpha_1:
+    observables:
+      spike rate:
+        spiketimes file: 
+          path: pop_IF_curr_alpha.spikes
+          format: ID_TIME
+          scaling: 1
+          ids: 1
+        tolerance: 0.00015639662183320716
diff --git a/PyNN/.test.pynn9nest.omt b/PyNN/.test.pynn9nest.omt
@@ -36,4 +36,24 @@ experiments:
         spike detection: 
           method: threshold
           threshold: -63.5
-        tolerance: 0.0001403
+        tolerance: 0.0001403
+
+  spike_rate_IF_curr_alpha_0:
+    observables:
+      spike rate:
+        spiketimes file: 
+          path: pop_IF_curr_alpha.spikes
+          format: ID_TIME
+          scaling: 1
+          ids: 0
+        tolerance: 0.00
+
+  spike_rate_IF_curr_alpha_1:
+    observables:
+      spike rate:
+        spiketimes file: 
+          path: pop_IF_curr_alpha.spikes
+          format: ID_TIME
+          scaling: 1
+          ids: 1
+        tolerance: 0.00