Adding tests on Netpyne

OpenSourceBrain · Apr 20, 2017 · bcd73fd · bcd73fd
1 parent 2c5f224
commit bcd73fd
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Showing 8 changed files with 45 additions and 8 deletions.
diff --git a/.gitignore b/.gitignore
@@ -41,3 +41,5 @@ generatedNeuroML2
 /NeuroML2/notebooks/*.hoc
 /NeuroML2/notebooks/LEMS_iv_L23_NoHotSpot.xml
 /NeuroML2/notebooks/iv_L23_NoHotSpot.net.nml
+/NeuroML2/*.json
+/NeuroML2/*_netpyne.py
diff --git a/.travis.yml b/.travis.yml
@@ -1,15 +1,18 @@
 # Framework for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
 
-sudo: false
+dist: trusty
+sudo: false  
 
 addons:
   apt:
     packages:
-       # Requirements for Brian
+    - python-matplotlib 
+    - python-tk
     - python-numpy 
     - python-scipy 
-    - python-matplotlib 
-    - python-sympy
+    - python-lxml
+    - libhdf5-7
+    - python-tables
 
 language: python
 python: 2.7
@@ -21,13 +24,12 @@ env:
     - OMV_ENGINE=PyNEURON
     - OMV_ENGINE=jNeuroML
     - OMV_ENGINE=jNeuroML_NEURON
+    - OMV_ENGINE=jNeuroML_NetPyNE
     - OMV_ENGINE=jNeuroML_validate
 
 install: 
     - pip install git+https://github.com/OpenSourceBrain/osb-model-validation
 
-    # Brian required by PyNEURON script also...
-    - omv install Brian
     # Need to pre install NEURON so nrnivmodl can be run targeting mod files in a different directory
     - omv install NEURON
     - cd NEURON/test

diff --git a/NeuroML2/.test.soma.jnml.omt b/NeuroML2/.test.soma.jnml.omt
@@ -15,5 +15,5 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 0
-        tolerance: 0.000279
+        tolerance: 0.000276
 
diff --git a/NeuroML2/.test.soma.jnmlnetpyne.omt b/NeuroML2/.test.soma.jnmlnetpyne.omt
@@ -0,0 +1,19 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_singleCompAllChans.xml
+engine: jNeuroML_NetPyNE
+
+mep: ../NEURON/test/.test.mep
+experiments:
+  spiking:
+    observables:
+      spike times:
+        file: 
+          path: jlems_sccct.dat
+          columns: [0,1]
+          scaling: [1000, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.000103
+
diff --git a/NeuroML2/.test.soma.jnmlnrn.omt b/NeuroML2/.test.soma.jnmlnrn.omt
@@ -15,5 +15,5 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 0
-        tolerance: 0.000106
+        tolerance: 0.000103
 
diff --git a/NeuroML2/.test.testSyns.jnml.omt b/NeuroML2/.test.testSyns.jnml.omt
@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_testSyns.xml 
+engine: jNeuroML
+
diff --git a/NeuroML2/.test.testSyns.jnmlnetpyne.omt b/NeuroML2/.test.testSyns.jnmlnetpyne.omt
@@ -0,0 +1,4 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_testSyns.xml 
+engine: jNeuroML_NetPyNE
diff --git a/NeuroML2/.test.testSyns.jnmlnrn.omt b/NeuroML2/.test.testSyns.jnmlnrn.omt
@@ -0,0 +1,5 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+
+target: LEMS_testSyns.xml 
+engine: jNeuroML_NEURON
+