Merge pull request #122 from OpenSourceBrain/test_xpp

XPP updates: Add JNeuroMLXppEngine and pyNEURON_XPP_LEMS

.github/workflows/ci.yml

@@ -46,9 +46,11 @@ jobs:
           - jNeuroML_PyNN_NEURON
           - jNeuroML_validate
           - jNeuroML_validatev1
+          - jNeuroML_XPP
           - Py_neuroConstruct
           - pyNeuroML
           - pyNeuroML_validate_sbml
+          - pyNEURON_XPP_LEMS
           - jNeuroML_Moose
           - MOOSE:3.1.5
           - XPP

.gitignore

@@ -123,3 +123,8 @@ report*.txt
 /utilities/tests/*_eden.py
 arm64
 /*ken.sh
+/utilities/tests/LEMS_NML2_Ex9_FN.ode
+/utilities/tests/LEMS_nca.xml
+/utilities/tests/nca.model.xml
+/utilities/tests/NML2_SingleCompHHCell.nml__flattened.xml
+/utilities/tests/lems/simp2.dat

omv/engines/__init__.py

@@ -12,6 +12,7 @@
 # from omv.engines.jneuromlbrian import JNeuroMLBrianEngine
 from omv.engines.jneuromleden import JNeuroMLEdenEngine
 from omv.engines.jneuromlbrian2 import JNeuroMLBrian2Engine
+from omv.engines.jneuromlxpp import JNeuroMLXppEngine
 from omv.engines.jneuromlmoose import JNeuroMLMooseEngine
 from omv.engines.jneuromlvalidate import JNeuroMLValidateEngine
 from omv.engines.jneuromlvalidatev1 import JNeuroMLValidateV1Engine
@@ -43,6 +44,7 @@
 from omv.engines.pyneuroconstruct import PyneuroConstructEngine
 from omv.engines.pyneuroml_ import PyNeuroMLEngine
 from omv.engines.pyneuromlvalidatesbml import PyNeuroMLValidateSBMLEngine
+from omv.engines.pyneuromlxpp import PyNeuroMLXppEngine
 
 
 OMVEngines = {

omv/engines/jneuromlbrian.py

@@ -26,7 +26,7 @@ def install(version):
         if not JNeuroMLEngine.is_installed():
             JNeuroMLEngine.install(None)
         if not Brian1Engine.is_installed():
-            Brian1Engine.install(None)
+            Brian1Engine.install(version)
 
         JNeuroMLBrianEngine.path = JNeuroMLEngine.path + ":" + Brian1Engine.path
         JNeuroMLBrianEngine.environment_vars = {}

omv/engines/jneuromlnetpyne.py

@@ -31,7 +31,7 @@ def install(version):
                 verbosity=1,
             )
         if not NetPyNEEngine.is_installed():
-            NetPyNEEngine.install(None)
+            NetPyNEEngine.install(version)
             inform(
                 "%s installed NetPyNE (& NEURON)..." % JNeuroMLNetPyNEEngine.name,
                 indent=2,

omv/engines/jneuromlpynnnrn.py

@@ -32,7 +32,7 @@ def install(version):
                 verbosity=1,
             )
         if not PyNNNRNEngine.is_installed():
-            PyNNNRNEngine.install(None)
+            PyNNNRNEngine.install(version)
             inform(
                 "%s installed PyNN & NRN..." % JNeuroMLPyNNNRNEngine.name,
                 indent=2,

omv/engines/jneuromlvalidate.py

@@ -16,7 +16,7 @@ def is_installed():
     @staticmethod
     def install(version):
         if not JNeuroMLEngine.is_installed():
-            JNeuroMLEngine.install(None)
+            JNeuroMLEngine.install(version)
 
         JNeuroMLValidateEngine.path = JNeuroMLEngine.path
         JNeuroMLValidateEngine.environment_vars = {}

omv/engines/jneuromlvalidatev1.py

@@ -17,7 +17,7 @@ def is_installed():
     @staticmethod
     def install(version):
         if not JNeuroMLEngine.is_installed():
-            JNeuroMLEngine.install(None)
+            JNeuroMLEngine.install(version)
 
         JNeuroMLValidateV1Engine.path = JNeuroMLEngine.path
         JNeuroMLValidateV1Engine.environment_vars = {}

omv/engines/jneuromlxpp.py

@@ -0,0 +1,59 @@
+import os
+import subprocess as sp
+
+from omv.engines.jneuroml import JNeuroMLEngine
+from omv.engines.xpp import XppEngine
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import EngineExecutionError
+
+
+class JNeuroMLXppEngine(JNeuroMLEngine):
+    name = "jNeuroML_XPP"
+
+    @staticmethod
+    def is_installed():
+        if is_verbose():
+            inform(
+                "Checking whether %s is installed..." % JNeuroMLXppEngine.name,
+                indent=1,
+            )
+        return JNeuroMLEngine.is_installed() and XppEngine.is_installed()
+
+    @staticmethod
+    def install(xpp_version):
+        if not JNeuroMLEngine.is_installed():
+            JNeuroMLEngine.install(None)
+        if not XppEngine.is_installed():
+            XppEngine.install(xpp_version)
+
+
+    def run(self):
+        self.environment_vars = XppEngine.get_xpp_environment()
+        self.set_environment()
+        try:
+            inform(
+                "Running file %s with %s"
+                % (trim_path(self.modelpath), JNeuroMLXppEngine.name),
+                indent=1,
+            )
+            from omv.engines.jneuroml import JNeuroMLEngine
+
+            jnml = JNeuroMLEngine.get_executable()
+            self.stdout = check_output(
+                [jnml, self.modelpath, "-xpp"],
+                cwd=os.path.dirname(self.modelpath),
+                env=JNeuroMLEngine.get_environment(),
+            )
+
+            self.stdout = check_output(
+                [self.environment_vars["XPP_HOME"] + "/xppaut", self.modelpath.replace('.xml','.ode'), '-silent'],
+                cwd=os.path.dirname(self.modelpath),
+            )
+
+            inform("Success with running ", JNeuroMLXppEngine.name, indent=1)
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            inform("Error with ", JNeuroMLXppEngine.name, indent=1)
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError

omv/engines/netpyne_.py

@@ -73,7 +73,7 @@ def install(version):
 
         home = os.environ["HOME"]
         inform("Will fetch and install the latest NetPyNE..", indent=2)
-        install_netpyne()
+        install_netpyne(version)
         inform("Done, NetPyNE is correctly installed...", indent=2)
 
         NetPyNEEngine.path = PyNRNEngine.path

omv/engines/pylemsnml2.py

@@ -28,7 +28,7 @@ def is_installed():
 
     def install(self, version):
         if not PyLemsEngine.is_installed():
-            PyLemsEngine.install(None)
+            PyLemsEngine.install(version)
         if not os.path.isdir(default_nml2_dir):
             install_nml2()
 

omv/engines/pyneuromlxpp.py

@@ -0,0 +1,56 @@
+import os
+import subprocess as sp
+
+from omv.common.inout import inform, trim_path, check_output
+from omv.engines.engine import EngineExecutionError
+from omv.engines.pyneuroml_ import PyNeuroMLEngine 
+from omv.engines.engine import PATH_DELIMITER
+from omv.engines.utils import resolve_paths
+
+class PyNeuroMLXppEngine(PyNeuroMLEngine):
+    name = "pyNEURON_XPP_LEMS"
+
+    @staticmethod
+    def is_installed():
+        pynml_ver = PyNeuroMLEngine.is_installed()
+        if not pynml_ver: 
+            return False
+        else:
+            return pynml_ver
+
+
+    @staticmethod
+    def install(version):
+        if not PyNeuroMLEngine.is_installed(): PyNeuroMLEngine.install(version)
+
+
+    def run(self):
+        try:
+
+            #pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
+            cmds = ["pynml-xpp"]
+            cmds.append(self.modelpath)
+            cmds.append('-lems')
+            cmds.append('-run')
+
+            inform(
+                "Running with %s, using: %s..." % (PyNeuroMLXppEngine.name, cmds),
+                indent=1,
+            )
+            self.stdout = check_output(
+                cmds,
+                cwd=os.path.dirname(self.modelpath)
+            )
+            inform(
+                "Success with running ",
+                PyNeuroMLXppEngine.name,
+                indent=1,
+                verbosity=1,
+            )
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            inform("Error with ", PyNeuroMLXppEngine.name, indent=1, verbosity=1)
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError
+

omv/engines/pynnneuroml.py

@@ -22,7 +22,7 @@ def is_installed():
     @staticmethod
     def install(version):
         if not PyNeuroMLEngine.is_installed():
-            PyNeuroMLEngine.install(None)
+            PyNeuroMLEngine.install(version)
             inform(
                 "%s installed PyNeuroML..." % PyNNNeuroMLEngine.name,
                 indent=2,

omv/engines/pynnneuron.py

@@ -25,7 +25,7 @@ def is_installed():
     @staticmethod
     def install(version=None):
         if not NeuronEngine.is_installed():
-            NeuronEngine.install(None)
+            NeuronEngine.install(version)
             inform("%s installed NEURON..." % PyNNNRNEngine.name, indent=2, verbosity=1)
         if not PyNNEngine.is_installed():
             PyNNEngine.install(None)

utilities/tests/.test.ex9.jnmlxpp.omt

@@ -0,0 +1,26 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_NML2_Ex9_FN.xml 
+engine: jNeuroML_XPP
+mep: .test.ex9.mep
+experiments:
+  V:
+    observables:
+      spike times:
+        file: 
+          path: output.dat
+          columns: [0,1]
+          scaling: [1000, 1000]
+        spike detection: 
+          method: derivative
+        tolerance: 0.004098360655737705
+  W:
+    observables:
+      spike times:
+        file: 
+          path: output.dat
+          columns: [0,2]
+          scaling: [1000, 1]
+        spike detection: 
+          method: derivative
+        tolerance: 0.00033585982982530405

utilities/tests/.test.nca.pynmlxpplems.omt

@@ -0,0 +1,17 @@
+target: nca.ode
+engine: pyNEURON_XPP_LEMS
+
+mep: .test.nca.mep
+experiments:
+  spikes:
+    observables:
+      spike times:
+        file: 
+          path: output.dat
+          columns: [0,14]
+          scaling: [1000, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.009999966556292568
+

utilities/tests/.test.xpp.omt

@@ -1,7 +1,7 @@
 target: nca.ode
 engine: XPP
 
-mep: .test.xpp.mep
+mep: .test.nca.mep
 experiments:
   spikes:
     observables: