Add test on jnml -xpp

Author: pgleeson

.github/workflows/ci.yml

@@ -46,6 +46,7 @@ jobs:
           - jNeuroML_PyNN_NEURON
           - jNeuroML_validate
           - jNeuroML_validatev1
+          - jNeuroML_XPP
           - Py_neuroConstruct
           - pyNeuroML
           - pyNeuroML_validate_sbml

.gitignore

@@ -123,3 +123,4 @@ report*.txt
 /utilities/tests/*_eden.py
 arm64
 /*ken.sh
+/utilities/tests/LEMS_NML2_Ex9_FN.ode

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

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

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