Merge pull request #118 from OpenSourceBrain/test_moose

Improved install of Moose

Author: pgleeson

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
           - pyNeuroML
           - pyNeuroML_validate_sbml
           - jNeuroML_Moose
-          - MOOSE
+          - MOOSE:3.1.5
 
     steps:
     - uses: actions/checkout@v4

omv/engines/brian2_.py

@@ -17,7 +17,7 @@ def is_installed():
             inform(
                 "Brian2 version %s is correctly installed..." % brian2.__version__,
                 indent=2,
-                verbosity=2,
+                verbosity=1,
             )
 
             ret = "v%s" % brian2.__version__

omv/engines/jneuromlmoose.py

@@ -8,6 +8,7 @@
 
 
 class JNeuroMLMooseEngine(JNeuroMLEngine):
+
     name = "jNeuroML_Moose"
 
     @staticmethod
@@ -21,6 +22,7 @@ def is_installed():
 
     @staticmethod
     def install(version):
+
         if not JNeuroMLEngine.is_installed():
             JNeuroMLEngine.install(None)
         if not MooseEngine.is_installed():
@@ -32,6 +34,7 @@ def install(version):
         JNeuroMLMooseEngine.environment_vars.update(MooseEngine.environment_vars)
         inform("PATH: " + JNeuroMLMooseEngine.path)
         inform("Env vars: %s" % JNeuroMLMooseEngine.environment_vars)
+        
 
     def run(self):
         try:

omv/engines/moose_.py

@@ -10,44 +10,24 @@
 class MooseEngine(OMVEngine):
     name = "Moose"
 
+
     @staticmethod
     def is_installed():
-        if is_verbose():
-            inform(
-                "Checking whether the engine %s has been installed correctly..."
-                % MooseEngine.name,
-                indent=1,
-            )
-
         ret = True
         try:
-            ret_str = sp.check_output(
-                ['python -c "import moose; print(moose.__version__)"'],
-                shell=True,
-                stderr=sp.STDOUT,
-            )
-            ret = len(ret_str) > 0
+            import moose
 
-            if isinstance(ret_str, bytes):
-                ret_str = ret_str.decode("utf-8").strip()
+            inform(
+                "Moose version %s is correctly installed..." % moose.__version__,
+                indent=2,
+                verbosity=1,
+            )
 
-            if ret and is_verbose():
-                inform(
-                    "%s is correctly installed (%s)..." % (MooseEngine.name, ret_str),
-                    indent=2,
-                )
-            if ret:
-                # import moose
-                ret = "v%s" % ret_str
+            ret = "v%s" % moose.__version__
 
         except Exception as err:
-            if is_verbose():
-                inform("Couldn't import moose into Python: ", err, indent=1)
+            inform("Couldn't import Moose into Python: ", err, indent=1, verbosity=1)
             ret = False
-        if not ret or not PyNeuroMLEngine.is_installed():
-            ret = False
-
-        inform("Moose is_installed(): %s" % ret, "", indent=1, verbosity=2)
         return ret
 
     @staticmethod

omv/omv_util.py

@@ -339,30 +339,43 @@ def _install_engine(eng):
             from omv.engines.getgenesis import install_genesis
 
             install_genesis()
+
         elif eng.lower() == "Moose".lower():
-            if engine_version is not None:
-                raise Exception(
-                    "Currently, cannot install a specific version of engine %s" % eng
-                )
-            from omv.engines.getmoose import install_moose
 
-            install_moose(engine_version)
+            from omv.engines.moose_ import MooseEngine as ee
+
+            if ee.is_installed():
+                already_installed = True
+            else:
+                from omv.engines.getmoose import install_moose
+
+                install_moose(engine_version)
+
         elif eng.lower() == "NetPyNE".lower():
             from omv.engines.getnetpyne import install_netpyne
 
             install_netpyne(engine_version)
+
         elif eng.lower() == "Brian".lower():
+
             if engine_version is not None:
                 raise Exception(
                     "Currently, cannot install a specific version of engine %s" % eng
                 )
             from omv.engines.getbrian1 import install_brian
 
             install_brian()
+
         elif eng.lower() == "Brian2".lower():
-            from omv.engines.getbrian2 import install_brian2
+            from omv.engines.brian2_ import Brian2Engine as ee
+
+            if ee.is_installed():
+                already_installed = True
+            else:
+                from omv.engines.getbrian2 import install_brian2
+
+                install_brian2(engine_version)
 
-            install_brian2(engine_version)
         elif eng.lower() == "NEST".lower():
             from omv.engines.nestsli import NestEngine as ee
 
@@ -372,6 +385,7 @@ def _install_engine(eng):
                 from omv.engines.getnest import install_nest
 
                 install_nest(engine_version)
+
         elif eng.lower() == "PyNEST".lower():
             from omv.engines.pynest import PyNestEngine as ee
 
@@ -403,6 +417,14 @@ def _install_engine(eng):
             else:
                 ee.install(engine_version)
 
+        elif eng.lower() == "jNeuroML_Moose".lower():
+            from omv.engines.jneuromlmoose import JNeuroMLMooseEngine as ee
+
+            if ee.is_installed():
+                already_installed = True
+            else:
+                ee.install(engine_version)
+
         elif eng.lower() == "jNeuroML_NEURON".lower():
             from omv.engines.jneuromlnrn import JNeuroMLNRNEngine as ee
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.2.18
+version = 0.2.19
 author = Boris Marin, Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/OpenSourceBrain/osb-model-validation