OSBModelValidation 0.2.19__tar.gz → 0.2.21__tar.gz

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21/OSBModelValidation.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: OSBModelValidation
-Version: 0.2.19
+Version: 0.2.21
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.lesser
@@ -24,6 +25,7 @@ Requires-Dist: pyrx
 Requires-Dist: pathlib; python_version < "3.4"
 Requires-Dist: docopt
 Requires-Dist: importlib-metadata; python_version < "3.8"
+Requires-Dist: setuptools
 
 [![Continuous builds](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml)
 [![PyPI](https://img.shields.io/pypi/v/OSBModelValidation)](https://pypi.org/project/OSBModelValidation/)

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/OSBModelValidation.egg-info/SOURCES.txt

@@ -58,6 +58,7 @@ omv/engines/getoctave.py
 omv/engines/getpylems.py
 omv/engines/getpyneuroml.py
 omv/engines/getpynn.py
+omv/engines/getxpp.py
 omv/engines/jlems.py
 omv/engines/jneuroml.py
 omv/engines/jneuromlbrian.py
@@ -71,6 +72,7 @@ omv/engines/jneuromlnrn.py
 omv/engines/jneuromlpynnnrn.py
 omv/engines/jneuromlvalidate.py
 omv/engines/jneuromlvalidatev1.py
+omv/engines/jneuromlxpp.py
 omv/engines/moose_.py
 omv/engines/nestsli.py
 omv/engines/netpyne_.py
@@ -84,6 +86,7 @@ omv/engines/pynest.py
 omv/engines/pyneuroconstruct.py
 omv/engines/pyneuroml_.py
 omv/engines/pyneuromlvalidatesbml.py
+omv/engines/pyneuromlxpp.py
 omv/engines/pyneuron.py
 omv/engines/pynn.py
 omv/engines/pynnbrian1.py
@@ -91,6 +94,7 @@ omv/engines/pynnbrian2.py
 omv/engines/pynnnest.py
 omv/engines/pynnneuroml.py
 omv/engines/pynnneuron.py
+omv/engines/xpp.py
 omv/engines/utils/__init__.py
 omv/engines/utils/genesis_utils.g
 omv/engines/utils/wdir.py

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/OSBModelValidation.egg-info/requires.txt

@@ -2,6 +2,7 @@ PyYAML
 numpy
 pyrx
 docopt
+setuptools
 
 [:python_version < "3.4"]
 pathlib

{OSBModelValidation-0.2.19/OSBModelValidation.egg-info → osbmodelvalidation-0.2.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: OSBModelValidation
-Version: 0.2.19
+Version: 0.2.21
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.lesser
@@ -24,6 +25,7 @@ Requires-Dist: pyrx
 Requires-Dist: pathlib; python_version < "3.4"
 Requires-Dist: docopt
 Requires-Dist: importlib-metadata; python_version < "3.8"
+Requires-Dist: setuptools
 
 [![Continuous builds](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenSourceBrain/osb-model-validation/actions/workflows/ci.yml)
 [![PyPI](https://img.shields.io/pypi/v/OSBModelValidation)](https://pypi.org/project/OSBModelValidation/)

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/common/inout.py

@@ -121,8 +121,8 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
 
     except sp.CalledProcessError as err:
         inform(
-            "Error running commands: %s in %s (return code: %s)"
-            % (cmds, cwd, err.returncode),
+            "CalledProcessError running commands: %s in %s (return code: %s), output:\n%s"
+            % (cmds, cwd, err.returncode, err.output),
             indent=2,
             verbosity=verbosity,
         )

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/__init__.py

@@ -12,6 +12,7 @@ from omv.engines.jneuromlnetpyne_np2 import JNeuroMLNetPyNENP2Engine
 # 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
@@ -23,6 +24,7 @@ from omv.engines.genesis import GenesisEngine
 # from omv.engines.brian1 import Brian1Engine
 from omv.engines.brian2_ import Brian2Engine
 from omv.engines.arbor_ import ArborEngine
+from omv.engines.xpp import XppEngine
 from omv.engines.eden_ import EdenEngine
 from omv.engines.nestsli import NestEngine
 from omv.engines.pynest import PyNestEngine
@@ -42,6 +44,7 @@ from omv.engines.netpyne__np2 import NetPyNENP2Engine
 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 = {

osbmodelvalidation-0.2.21/omv/engines/getxpp.py

@@ -0,0 +1,83 @@
+import os
+from omv.common.inout import inform, check_output
+
+from omv.engines.utils.wdir import working_dir
+from sysconfig import get_paths
+import sys
+        
+import fileinput
+
+
+def install_xpp(version='latest'):
+
+    if version is None: 
+        version='latest'
+    elif not version=='latest':
+        raise Exception('Can currently only install the latest XPP version')
+
+    inform("Installing XPP", indent=2, verbosity=1)
+    xppinstallpath = os.path.join(os.environ["HOME"])
+    xpphomepath = os.path.join(xppinstallpath, 'xppaut')
+
+    inform(
+        "Installing XPP to: %s" % (xpphomepath),
+        indent=2,
+        verbosity=1,
+    )
+    pypaths = get_paths()
+    inform("Python lib info: %s" % (pypaths), indent=2, verbosity=1)
+
+
+    with working_dir(xppinstallpath):
+        print(
+            check_output(
+                [
+                    "git",
+                    "clone",
+                    "https://github.com/NeuroML/xppaut"
+                ]
+            )
+        )
+
+    with working_dir(xpphomepath):
+        print(
+            check_output(
+                [
+                    "ls",
+                    "-alth"
+                ]
+            )
+        )
+
+        makefile = os.path.join(xpphomepath, 'Makefile')
+                
+        print(' - Replacing text in %s'%makefile)
+        with open(makefile, 'r') as file:
+            filedata = file.read()
+
+        # Replace the target string
+        filedata = filedata.replace("/usr/local/", "%s/"%xpphomepath)
+
+        # Write the file out again
+        with open(makefile, 'w') as file:
+            file.write(filedata)
+
+        print(
+            check_output(
+                [
+                    "make", "-j4"
+                ]
+            )
+        )
+        print(
+            check_output(
+                [
+                    "make", "install"
+                ]
+            )
+        )
+
+
+
+if __name__ == "__main__":
+    install_nest()

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuroml.py

@@ -81,6 +81,10 @@ class JNeuroMLEngine(OMVEngine):
         inform("Will fetch and install jNeuroML jar", indent=2)
         install_jnml(version)
 
+        if not JNeuroMLEngine.is_installed():
+            inform("Failure to install, exiting", indent=1)
+            exit(1)
+
     def run(self):
         try:
             inform(

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuromlbrian.py

@@ -26,7 +26,7 @@ class JNeuroMLBrianEngine(JNeuroMLEngine):
         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 = {}

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuromlnetpyne.py

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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuromlpynnnrn.py

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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuromlvalidate.py

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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/jneuromlvalidatev1.py

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

osbmodelvalidation-0.2.21/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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/netpyne_.py

@@ -73,7 +73,7 @@ class NetPyNEEngine(OMVEngine):
 
         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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/pylemsnml2.py

@@ -28,7 +28,7 @@ class PyLemsNeuroML2Engine(OMVEngine):
 
     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()
 

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/pyneuroml_.py

@@ -38,6 +38,11 @@ class PyNeuroMLEngine(OMVEngine):
         inform("Will fetch and install the latest pyNeuroML", indent=2)
         install_pynml(version)
 
+        if not PyNeuroMLEngine.is_installed():
+            inform("Failure to install, exiting", indent=1)
+            exit(1)
+
+
     def run(self):
         try:
             inform(

osbmodelvalidation-0.2.21/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
+

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/pynnneuroml.py

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

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/engines/pynnneuron.py

@@ -25,7 +25,7 @@ class PyNNNRNEngine(PyNNEngine):
     @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)

osbmodelvalidation-0.2.21/omv/engines/xpp.py

@@ -0,0 +1,82 @@
+import os
+import sys
+
+import subprocess as sp
+
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import OMVEngine, EngineExecutionError
+
+
+class XppEngine(OMVEngine):
+    name = "XPP"
+
+    @staticmethod
+    def get_xpp_environment():
+
+        # Default, if it was installed by omv...
+        xpppath = os.path.join(os.environ["HOME"], "xppaut/bin")
+
+        if "XPP_HOME" in os.environ:
+            xpppath = os.environ["XPP_HOME"] + "/"
+
+        environment_vars = {
+            "XPP_HOME": xpppath,
+        }
+
+        return environment_vars
+
+    @staticmethod
+    def is_installed():
+        ret = True
+        environment_vars = XppEngine.get_xpp_environment()
+        try:
+            FNULL = open(os.devnull, "w")
+
+            r = check_output(
+                [environment_vars["XPP_HOME"] + "/xppaut", "-version"], verbosity=2
+            )
+            if "Problem" in r:
+                ret = 'v???'
+
+            else:
+                ret = "%s" % r.split()[2]
+                if not "v" in ret:
+                    ret = "v%s" % ret
+
+            inform("XPP %s is correctly installed..." % ret, indent=2, verbosity=1)
+
+        except OSError as err:
+            if is_verbose():
+                inform("Couldn't execute XPP: ", err, indent=1)
+            ret = False
+        return ret
+
+    @staticmethod
+    def install(version):
+        from omv.engines.getxpp import install_xpp
+
+        install_xpp(version)
+        inform("Done...", indent=2)
+
+    def run(self):
+        self.environment_vars = XppEngine.get_xpp_environment()
+        self.set_environment()
+
+        try:
+            inform(
+                "Running file %s with %s" % (trim_path(self.modelpath), self.name),
+                indent=1,
+            )
+            self.stdout = check_output(
+                [self.environment_vars["XPP_HOME"] + "/xppaut", self.modelpath, '-silent'],
+                cwd=os.path.dirname(self.modelpath),
+            )
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError
+        except Exception as err:
+            inform("Another error with running %s: " % self.name, err, indent=1)
+            self.returncode = -1
+            self.stdout = "???"

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/omv/omv_util.py

@@ -279,6 +279,16 @@ def _install_engine(eng):
 
                 install_arbor(engine_version)
 
+        elif eng.lower() == "XPP".lower():
+            from omv.engines.xpp import XppEngine as ee
+
+            if ee.is_installed():
+                already_installed = True
+            else:
+                from omv.engines.getxpp import install_xpp
+
+                install_xpp(engine_version)
+
         elif eng.lower() == "EDEN".lower():
             from omv.engines.eden_ import EdenEngine as ee
 

{OSBModelValidation-0.2.19 → osbmodelvalidation-0.2.21}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.2.19
+version = 0.2.21
 author = Boris Marin, Padraig Gleeson
 author_email = borismarin@gmail.com
 url = https://github.com/OpenSourceBrain/osb-model-validation
@@ -18,6 +18,7 @@ classifiers =
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Topic :: Scientific/Engineering
 
 [options]
@@ -28,6 +29,7 @@ install_requires =
 	pathlib; python_version<'3.4'
 	docopt
 	importlib-metadata; python_version<'3.8'
+	setuptools
 packages = find:
 
 [options.packages.find]