Some ruff formatting

Author: pgleeson

Diff for: omv/engines/getjnml.py

@@ -8,7 +8,6 @@
 
 
 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)

Diff for: 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

Diff for: omv/engines/getxpp.py

@@ -4,20 +4,19 @@
 from omv.engines.utils.wdir import working_dir
 from sysconfig import get_paths
 import sys
-        
-import fileinput
 
+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')
+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')
+    xpphomepath = os.path.join(xppinstallpath, "xppaut")
 
     inform(
         "Installing XPP to: %s" % (xpphomepath),
@@ -27,56 +26,27 @@ def install_xpp(version='latest'):
     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"
-                ]
-            )
-        )
+        print(check_output(["git", "clone", "https://github.com/NeuroML/xppaut"]))
 
     with working_dir(xpphomepath):
-        print(
-            check_output(
-                [
-                    "ls",
-                    "-alth"
-                ]
-            )
-        )
+        print(check_output(["ls", "-alth"]))
 
-        makefile = os.path.join(xpphomepath, 'Makefile')
-                
-        print(' - Replacing text in %s'%makefile)
-        with open(makefile, 'r') as file:
+        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)
+        filedata = filedata.replace("/usr/local/", "%s/" % xpphomepath)
 
         # Write the file out again
-        with open(makefile, 'w') as file:
+        with open(makefile, "w") as file:
             file.write(filedata)
 
-        print(
-            check_output(
-                [
-                    "make", "-j4"
-                ]
-            )
-        )
-        print(
-            check_output(
-                [
-                    "make", "install"
-                ]
-            )
-        )
-
+        print(check_output(["make", "-j4"]))
+        print(check_output(["make", "install"]))
 
 
 if __name__ == "__main__":

Diff for: omv/engines/jneuromlmoose.py

@@ -8,7 +8,6 @@
 
 
 class JNeuroMLMooseEngine(JNeuroMLEngine):
-
     name = "jNeuroML_Moose"
 
     @staticmethod
@@ -22,7 +21,6 @@ def is_installed():
 
     @staticmethod
     def install(version):
-
         if not JNeuroMLEngine.is_installed():
             JNeuroMLEngine.install(None)
         if not MooseEngine.is_installed():
@@ -34,7 +32,6 @@ 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:

Diff for: omv/engines/jneuromlvalidate.py

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

Diff for: omv/engines/jneuromlxpp.py

@@ -26,7 +26,6 @@ def install(xpp_version):
         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 @@ def run(self):
                 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),
             )
 

Diff for: omv/engines/moose_.py

@@ -10,7 +10,6 @@
 class MooseEngine(OMVEngine):
     name = "Moose"
 
-
     @staticmethod
     def is_installed():
         ret = True

Diff for: omv/engines/pyneuroml_.py

@@ -42,7 +42,6 @@ def install(version):
             inform("Failure to install, exiting", indent=1)
             exit(1)
 
-
     def run(self):
         try:
             inform(

Diff for: omv/engines/pyneuromlvalidatesbml.py

@@ -3,21 +3,24 @@
 
 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.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 @@ def is_installed():
 
     @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 @@ def run(self):
                 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 @@ def run(self):
             )
             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
-

Diff for: omv/engines/pyneuromlxpp.py

@@ -3,44 +3,40 @@
 
 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.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: 
+        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 +49,3 @@ def run(self):
             self.returncode = err.returncode
             self.stdout = err.output
             raise EngineExecutionError
-

Diff for: omv/engines/pyneuron.py

@@ -72,9 +72,7 @@ def run(self):
             )
             cmd = """\
             %s
-            """ % (
-                "\n".join(self.extra_pars)
-            )
+            """ % ("\n".join(self.extra_pars))
             if sys.version_info[0] == 3:
                 c = dedent(cmd).encode()
             else:

Diff for: omv/engines/xpp.py

@@ -12,7 +12,6 @@ class XppEngine(OMVEngine):
 
     @staticmethod
     def get_xpp_environment():
-
         # Default, if it was installed by omv...
         xpppath = os.path.join(os.environ["HOME"], "xppaut/bin")
 
@@ -36,7 +35,7 @@ def is_installed():
                 [environment_vars["XPP_HOME"] + "/xppaut", "-version"], verbosity=2
             )
             if "Problem" in r:
-                ret = 'v???'
+                ret = "v???"
 
             else:
                 ret = "%s" % r.split()[2]
@@ -68,7 +67,11 @@ def run(self):
                 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

Diff for: omv/omv_util.py

@@ -22,6 +22,7 @@
     --ignore-non-py3  If Python 3, ignore tests on non Py3 compatible engines [default: False]
     -y                Auto-select default options (non-interactive mode)
 """
+
 from docopt import docopt
 from omv.find_tests import test_all, test_one
 from omv.validation import validate_mep
@@ -351,7 +352,6 @@ def _install_engine(eng):
             install_genesis()
 
         elif eng.lower() == "Moose".lower():
-
             from omv.engines.moose_ import MooseEngine as ee
 
             if ee.is_installed():
@@ -367,7 +367,6 @@ def _install_engine(eng):
             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