OSBModelValidation 0.3.5__tar.gz → 0.3.8__tar.gz

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8/OSBModelValidation.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: OSBModelValidation
-Version: 0.3.5
+Version: 0.3.8
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -10,21 +10,21 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.7
-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: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.lesser
 Requires-Dist: PyYAML
-Requires-Dist: numpy<2.0.0
+Requires-Dist: numpy
 Requires-Dist: pyrx
 Requires-Dist: pathlib; python_version < "3.4"
 Requires-Dist: docopt
 Requires-Dist: importlib-metadata; python_version < "3.8"
+Dynamic: license-file
 
 [![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/)
@@ -185,3 +185,4 @@ Since you can run the validation with different [engines](https://github.com/Ope
 ### Running tests automatically on GitHub Actions
 
 To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml and place it in the required repository.
+

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/OSBModelValidation.egg-info/requires.txt

@@ -1,5 +1,5 @@
 PyYAML
-numpy<2.0.0
+numpy
 pyrx
 docopt
 

{osbmodelvalidation-0.3.5/OSBModelValidation.egg-info → osbmodelvalidation-0.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: OSBModelValidation
-Version: 0.3.5
+Version: 0.3.8
 Summary: Open Source Brain Model validation
 Home-page: https://github.com/OpenSourceBrain/osb-model-validation
 Author: Boris Marin, Padraig Gleeson
@@ -10,21 +10,21 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.7
-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: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Description-Content-Type: text/markdown
 License-File: LICENSE.lesser
 Requires-Dist: PyYAML
-Requires-Dist: numpy<2.0.0
+Requires-Dist: numpy
 Requires-Dist: pyrx
 Requires-Dist: pathlib; python_version < "3.4"
 Requires-Dist: docopt
 Requires-Dist: importlib-metadata; python_version < "3.8"
+Dynamic: license-file
 
 [![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/)
@@ -185,3 +185,4 @@ Since you can run the validation with different [engines](https://github.com/Ope
 ### Running tests automatically on GitHub Actions
 
 To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml and place it in the required repository.
+

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/README.md

@@ -157,3 +157,4 @@ Since you can run the validation with different [engines](https://github.com/Ope
 ### Running tests automatically on GitHub Actions
 
 To use OMV with GHA, copy an existing configuration file, e.g. https://github.com/OpenSourceBrain/ACnet2/blob/master/.github/workflows/omv-ci.yml and place it in the required repository.
+

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/autogen.py

@@ -27,7 +27,7 @@ def read_option(options, default=0):
     opt = None
     while opt is None:
         try:
-            sel = int(raw_input("Select option number [default: %s]: " % default))
+            sel = int(input("Select option number [default: %s]: " % default))
             opt = options[sel]
         except IndexError:
             print("invalid index!")

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/common/inout.py

@@ -103,7 +103,7 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
     if env:
         joint_env.update(env)
     for k in os.environ:
-        if not k in joint_env:
+        if k not in joint_env:
             joint_env[k] = os.environ[k]
 
     try:

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/engine.py

@@ -1,6 +1,5 @@
 from os.path import realpath
 from os import environ
-import sys
 from omv.common.inout import inform
 import platform
 
@@ -78,8 +77,8 @@ class OMVEngine(object):
     def set_environment(self):
         if self.environment_vars:
             for name, val in self.environment_vars.items():
-                if name in environ and not "HOME" in name:
-                    if not ":%s:" % val in environ[name]:
+                if name in environ and "HOME" not in name:
+                    if ":%s:" % val not in environ[name]:
                         environ[name] = "%s:%s" % (environ[name], val)
                 else:
                     environ[name] = val

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getarbor.py

@@ -8,7 +8,7 @@ def install_arbor(version=None):
         pip_install("arbor==%s" % version)
         import arbor
 
-        m = "Successfully installed Arbor..."
+        m = "Successfully installed Arbor %s..."%arbor.__version__
     except Exception as e:
         m = "ERROR installing Arbor: " + str(e)
     finally:

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getbrian1.py

@@ -1,5 +1,4 @@
 import os
-import pip
 from omv.common.inout import inform, check_output
 from omv.engines.utils.wdir import working_dir
 

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getbrian2.py

@@ -5,12 +5,12 @@ from omv.engines.getbrian1 import check_scipy_dev
 
 def install_brian2(version):
     if not version:
-        version = "2.5.3"
+        version = "2.7.1"
     try:
         pip_install("brian2", version)
         import brian2
 
-        m = "Successfully installed Brian2..."
+        m = "Successfully installed Brian2 %s..."%brian2.__version__
     except Exception as e:
         m = "ERROR installing Brian2: " + str(e)
     finally:

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getjnml.py

@@ -8,7 +8,6 @@ from omv.common.inout import inform
 
 
 def install_jnml(version):
-
     if not version:
         version = "v0.14.0"
 
@@ -45,4 +44,4 @@ def install_jnml(version):
         )
         check_output(["unzip", "jNeuroML.zip"])
 
-    inform("Successfully installed jNeuroML "+version, indent=1)
+    inform("Successfully installed jNeuroML " + version, indent=1)

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getmoose.py

@@ -3,7 +3,7 @@ from omv.common.inout import pip_install
 
 def install_moose(version):
     if not version:
-        version = "4.0.0"
+        version = "4.0.0.dev20240411"
     try:
         pip_install("pymoose", version)
         import moose

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getnrn.py

@@ -10,7 +10,7 @@ from omv.engines.utils.wdir import working_dir
 def install_neuron(version):
     if not version:
         if sys.version_info.major == 3:
-            version = "8.2.6"  # for pynn 0.11.0
+            version = "8.2.7"  # for pynn 0.11.0
         else:
             version = "7.6"
 

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/getpynn.py

@@ -15,7 +15,8 @@ def install_pynn(version=None):
 
         pip_install("pynn", version)
         import pyNN
-        '''
+
+        """
         install_root = os.environ["HOME"]
 
         pyNN_src = "PyNN_src"
@@ -36,7 +37,7 @@ def install_pynn(version=None):
             print(check_output(["pwd"]))
             print("Finished attempting to install PyNN")
         # import pyNN
-        '''
+        """
         m = "Successfully installed pyNN..."
     except Exception as e:
         m = "ERROR during install_pynn: %s" % e

osbmodelvalidation-0.3.8/omv/engines/getxpp.py

@@ -0,0 +1,51 @@
+import os
+from omv.common.inout import inform, check_output
+
+from omv.engines.utils.wdir import working_dir
+from sysconfig import get_paths
+
+
+
+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-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/jneuroml.py

@@ -24,7 +24,7 @@ class JNeuroMLEngine(OMVEngine):
                     jnmlhome = os.path.join(
                         os.environ["XDG_DATA_HOME"], "jnml/jNeuroMLJar"
                     )
-                except KeyError as e:
+                except KeyError:
                     localsharepath = os.path.join(os.environ["HOME"], ".local/share")
                     if os.path.isdir(localsharepath):
                         jnmlhome = os.path.join(

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/jneuromlmoose.py

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

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/jneuromlvalidate.py

@@ -6,6 +6,7 @@ from omv.common.inout import inform, check_output
 from omv.engines.engine import PATH_DELIMITER
 from omv.engines.utils import resolve_paths
 
+
 class JNeuroMLValidateEngine(JNeuroMLEngine):
     name = "jNeuroML_validate"
 

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/jneuromlxpp.py

@@ -26,7 +26,6 @@ class JNeuroMLXppEngine(JNeuroMLEngine):
         if not XppEngine.is_installed():
             XppEngine.install(xpp_version)
 
-
     def run(self):
         self.environment_vars = XppEngine.get_xpp_environment()
         self.set_environment()
@@ -44,9 +43,13 @@ class JNeuroMLXppEngine(JNeuroMLEngine):
                 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'],
+                [
+                    self.environment_vars["XPP_HOME"] + "/xppaut",
+                    self.modelpath.replace(".xml", ".ode"),
+                    "-silent",
+                ],
                 cwd=os.path.dirname(self.modelpath),
             )
 

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/moose_.py

@@ -3,14 +3,13 @@ import subprocess as sp
 
 from omv.engines.pyneuroml_ import PyNeuroMLEngine
 
-from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.common.inout import inform, trim_path, check_output
 from omv.engines.engine import OMVEngine, EngineExecutionError
 
 
 class MooseEngine(OMVEngine):
     name = "Moose"
 
-
     @staticmethod
     def is_installed():
         ret = True

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/nestsli.py

@@ -42,7 +42,7 @@ class NestEngine(OMVEngine):
             if "-" in ret:
                 ret = "v%s" % ret.split("-")[-1]
 
-            if not "v" in ret:
+            if "v" not in ret:
                 ret = "v%s" % ret
 
             inform("NEST %s is correctly installed..." % ret, indent=2, verbosity=1)

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/neuron_.py

@@ -42,7 +42,7 @@ class NeuronEngine(OMVEngine):
 
         environment_vars = {"PYTHONPATH": pp}
 
-        if not "NEURON_HOME" in os.environ:
+        if "NEURON_HOME" not in os.environ:
             pip_install_dir1 = "/usr/local"
             pip_install_nrniv1 = os.path.join(pip_install_dir1, "bin", "nrniv")
             scripts_bin = get_paths()["scripts"]
@@ -85,6 +85,7 @@ class NeuronEngine(OMVEngine):
             inform("Checking whether %s is installed..." % NeuronEngine.name, indent=1)
         try:
             output = check_output(["nrniv", "--version"], verbosity=2)
+            output = output[output.index('NEURON'):]
             if is_verbose():
                 inform(
                     "%s is installed; env: %s"

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pylems.py

@@ -1,6 +1,5 @@
 import os
 import subprocess as sp
-import sys
 
 from omv.common.inout import inform, trim_path, check_output, is_verbose
 from omv.engines.engine import OMVEngine, EngineExecutionError

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pyneuroml_.py

@@ -1,7 +1,7 @@
 import os
 import subprocess as sp
 
-from omv.common.inout import inform, trim_path, is_verbose, check_output
+from omv.common.inout import inform, trim_path, check_output
 from omv.engines.engine import OMVEngine, EngineExecutionError
 
 
@@ -42,7 +42,6 @@ class PyNeuroMLEngine(OMVEngine):
             inform("Failure to install, exiting", indent=1)
             exit(1)
 
-
     def run(self):
         try:
             inform(

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pyneuromlvalidatesbml.py

@@ -1,23 +1,26 @@
 import os
 import subprocess as sp
 
-from omv.common.inout import inform, trim_path, check_output
+from omv.common.inout import inform, check_output
 from omv.engines.engine import EngineExecutionError
-from omv.engines.pyneuroml_ import PyNeuroMLEngine 
+from omv.engines.pyneuroml_ import PyNeuroMLEngine
 from omv.engines.engine import PATH_DELIMITER
 from omv.engines.utils import resolve_paths
 
+
 class PyNeuroMLValidateSBMLEngine(PyNeuroMLEngine):
     name = "pyNeuroML_validate_sbml"
 
     @staticmethod
     def is_installed():
-        if not PyNeuroMLEngine.is_installed(): return False
+        if not PyNeuroMLEngine.is_installed():
+            return False
 
         ret = True
         try:
             inform(
-                "Checking whether %s is installed..." % PyNeuroMLValidateSBMLEngine.name,
+                "Checking whether %s is installed..."
+                % PyNeuroMLValidateSBMLEngine.name,
                 indent=1,
                 verbosity=2,
             )
@@ -37,7 +40,8 @@ class PyNeuroMLValidateSBMLEngine(PyNeuroMLEngine):
 
     @staticmethod
     def install(version):
-        if not PyNeuroMLEngine.is_installed(): PyNeuroMLEngine.install(None)
+        if not PyNeuroMLEngine.is_installed():
+            PyNeuroMLEngine.install(None)
 
         from omv.engines.getlibsbml import install_libsbml
 
@@ -54,19 +58,20 @@ class PyNeuroMLValidateSBMLEngine(PyNeuroMLEngine):
                 verbosity=1,
             )
 
-            #pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
+            # pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
             cmds = ["pynml", "-validate-sbml"]
             for p in path_s:
                 cmds.append(p)
 
             inform(
-                "Running with %s, using: %s..." % (PyNeuroMLValidateSBMLEngine.name, cmds),
+                "Running with %s, using: %s..."
+                % (PyNeuroMLValidateSBMLEngine.name, cmds),
                 indent=1,
             )
             self.stdout = check_output(
                 cmds,
-                cwd=os.path.dirname(self.modelpath.split(PATH_DELIMITER)[0])
-                #env=PyNeuroMLEngine.get_environment(),
+                cwd=os.path.dirname(self.modelpath.split(PATH_DELIMITER)[0]),
+                # env=PyNeuroMLEngine.get_environment(),
             )
             inform(
                 "Success with running ",
@@ -76,8 +81,9 @@ class PyNeuroMLValidateSBMLEngine(PyNeuroMLEngine):
             )
             self.returncode = 0
         except sp.CalledProcessError as err:
-            inform("Error with ", PyNeuroMLValidateSBMLEngine.name, indent=1, verbosity=1)
+            inform(
+                "Error with ", PyNeuroMLValidateSBMLEngine.name, indent=1, verbosity=1
+            )
             self.returncode = err.returncode
             self.stdout = err.output
             raise EngineExecutionError
-

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pyneuromlxpp.py

@@ -1,11 +1,10 @@
 import os
 import subprocess as sp
 
-from omv.common.inout import inform, trim_path, check_output
+from omv.common.inout import inform, 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
+from omv.engines.pyneuroml_ import PyNeuroMLEngine
+
 
 class PyNeuroMLXppEngine(PyNeuroMLEngine):
     name = "pyNEURON_XPP_LEMS"
@@ -13,34 +12,29 @@ class PyNeuroMLXppEngine(PyNeuroMLEngine):
     @staticmethod
     def is_installed():
         pynml_ver = PyNeuroMLEngine.is_installed()
-        if not pynml_ver: 
+        if not pynml_ver:
             return False
         else:
             return pynml_ver
 
-
     @staticmethod
     def install(version):
-        if not PyNeuroMLEngine.is_installed(): PyNeuroMLEngine.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
+            # 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')
+            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)
-            )
+            self.stdout = check_output(cmds, cwd=os.path.dirname(self.modelpath))
             inform(
                 "Success with running ",
                 PyNeuroMLXppEngine.name,
@@ -53,4 +47,3 @@ class PyNeuroMLXppEngine(PyNeuroMLEngine):
             self.returncode = err.returncode
             self.stdout = err.output
             raise EngineExecutionError
-

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pyneuron.py

@@ -6,7 +6,7 @@ import sys
 
 from omv.engines.neuron_ import NeuronEngine
 
-from omv.common.inout import inform, is_verbose, check_output
+from omv.common.inout import inform, is_verbose
 from omv.engines.engine import EngineExecutionError
 
 
@@ -72,9 +72,7 @@ class PyNRNEngine(NeuronEngine):
             )
             cmd = """\
             %s
-            """ % (
-                "\n".join(self.extra_pars)
-            )
+            """ % ("\n".join(self.extra_pars))
             if sys.version_info[0] == 3:
                 c = dedent(cmd).encode()
             else:

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/pynn.py

@@ -1,7 +1,7 @@
 import os
 import subprocess as sp
 
-from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.common.inout import inform, trim_path, check_output
 from omv.engines.engine import OMVEngine, EngineExecutionError
 
 

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/utils/__init__.py

@@ -1,21 +1,21 @@
 from omv.engines.engine import PATH_DELIMITER
 
+
 def resolve_paths(path_s):
-    '''
+    """
     Make explicit list from: '*.nml myfile.xml' etc.
-    '''
+    """
 
     if "*" in path_s:
         import glob
 
         if PATH_DELIMITER in path_s:
-            all = []
+            all_paths = []
             for p in path_s.split(PATH_DELIMITER):
                 for g in glob.glob(p):
-                    all.append(g)
-            path_s = all
+                    all_paths.append(g)
+            path_s = all_paths
         else:
             path_s = glob.glob(path_s)
 
     return path_s
-

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/engines/xpp.py

@@ -1,5 +1,4 @@
 import os
-import sys
 
 import subprocess as sp
 
@@ -12,7 +11,6 @@ class XppEngine(OMVEngine):
 
     @staticmethod
     def get_xpp_environment():
-
         # Default, if it was installed by omv...
         xpppath = os.path.join(os.environ["HOME"], "xppaut/bin")
 
@@ -36,11 +34,11 @@ class XppEngine(OMVEngine):
                 [environment_vars["XPP_HOME"] + "/xppaut", "-version"], verbosity=2
             )
             if "Problem" in r:
-                ret = 'v???'
+                ret = "v???"
 
             else:
                 ret = "%s" % r.split()[2]
-                if not "v" in ret:
+                if "v" not in ret:
                     ret = "v%s" % ret
 
             inform("XPP %s is correctly installed..." % ret, indent=2, verbosity=1)
@@ -68,7 +66,11 @@ class XppEngine(OMVEngine):
                 indent=1,
             )
             self.stdout = check_output(
-                [self.environment_vars["XPP_HOME"] + "/xppaut", self.modelpath, '-silent'],
+                [
+                    self.environment_vars["XPP_HOME"] + "/xppaut",
+                    self.modelpath,
+                    "-silent",
+                ],
                 cwd=os.path.dirname(self.modelpath),
             )
             self.returncode = 0

{osbmodelvalidation-0.3.5 → osbmodelvalidation-0.3.8}/omv/find_tests.py

@@ -93,7 +93,7 @@ def test_all(
         engs = {}
         tot_tests = 0
         for t in tallies:
-            if not t.engine in engs:
+            if t.engine not in engs:
                 engs[t.engine] = 0
             engs[t.engine] += 1
             tot_tests += 1