To v0.3.6 & ruff formatting

.github/workflows/ci.yml

@@ -65,6 +65,7 @@ jobs:
         pip install .
         pip install scipy sympy matplotlib cython pandas tables
         #sudo apt install octave
+        sudo apt-get install -y subversion # for neuroConstruct full install...
 
     - name: Run OMV tests on engine ${{ matrix.engine }}
       run: |

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!")

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:

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 @@ def build_query_string(self, name, cmd):
     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

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:

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
 

omv/engines/getbrian2.py

@@ -10,7 +10,7 @@ def install_brian2(version):
         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:

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)

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

omv/engines/getxpp.py

@@ -3,21 +3,18 @@
 
 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')
+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 +24,27 @@ 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")
 
-        makefile = os.path.join(xpphomepath, 'Makefile')
-
-        print(' - Replacing text in %s'%makefile)
-        with open(makefile, 'r') as file:
+        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__":

omv/engines/jneuroml.py

@@ -24,7 +24,7 @@ def get_environment():
                     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(

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:

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"
 

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),
             )
 

omv/engines/moose_.py

@@ -3,14 +3,13 @@
 
 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

omv/engines/nestsli.py

@@ -42,7 +42,7 @@ def is_installed():
             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)

omv/engines/neuron_.py

@@ -42,7 +42,7 @@ def get_nrn_environment():
 
         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"]

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

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

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 @@ 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
-