Merge pull request #134 from OpenSourceBrain/test_jnml

To v0.3.6 & ruff formatting

Author: pgleeson

.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__":