Add engine PyNeuroMLXppEngine

Author: pgleeson

.github/workflows/ci.yml

@@ -50,6 +50,7 @@ jobs:
           - Py_neuroConstruct
           - pyNeuroML
           - pyNeuroML_validate_sbml
+          - pyNEURON_XPP_LEMS
           - jNeuroML_Moose
           - MOOSE:3.1.5
           - XPP

.gitignore

@@ -124,3 +124,5 @@ report*.txt
 arm64
 /*ken.sh
 /utilities/tests/LEMS_NML2_Ex9_FN.ode
+/utilities/tests/LEMS_nca.xml
+/utilities/tests/nca.model.xml

omv/engines/__init__.py

@@ -44,6 +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/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
+

utilities/tests/.test.pynmlxpplems.omt

@@ -0,0 +1,17 @@
+target: nca.ode
+engine: pyNEURON_XPP_LEMS
+
+mep: .test.xpp.mep
+experiments:
+  spikes:
+    observables:
+      spike times:
+        file: 
+          path: output.dat
+          columns: [0,1]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.00
+