Fixes as suggested by PyLint. Added a target pylint in cmake file.

.travis.yml

@@ -20,22 +20,17 @@ addons:
       update: true
 
 before_script:
-- echo "OSX related"
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
 
 
 before_script:
-- echo "OSX related"
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh;
-  fi
-script:
+- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
 
-- python2 -m compileall -q . || echo "Python2 not found"
-- if type python3 > /dev/null; then python3 -m compileall -q . ; fi
+script:
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi
 

.travis/run_pylint.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash 
+set -e
+python3 -m pip install pylint --user 
+PYLINT="python3 -m pylint -E \
+    --disable=no-member --disable=no-name-in-module \
+    --disable=invalid-unary-operand-type \
+    --disable=import-error \
+    "
+function do_pylint() {
+    echo "Checking $1"
+    DIR=$(dirname $1)
+    SNAME=$(basename $1)
+    ( 
+        cd $DIR
+        $PYLINT $@ $SNAME
+    )
+}
+
+FILES=$(find . -type f -name "*.py" | shuf)
+N=4
+i=0
+for f in $FILES; do 
+    #i=$((i+1))
+    #if [ $i -eq $N ]; then
+    #    i=0
+    #    wait;
+    #fi
+    # do_pylint "$f"
+    echo "Checking $f"
+    DIR=$(dirname $f)
+    SNAME=$(basename $f)
+    ( 
+        cd $DIR
+        $PYLINT $@ $SNAME
+    )
+done

.travis/travis_build_osx.sh

@@ -23,12 +23,18 @@ set -e
 # NOTE: On travis, don't enable -j`nproc` option. It may not compile properly.
 
 (
-
     # Make sure not to pick up python from /opt.
-    PATH=/usr/bin:/usr/local/bin:$PATH
+    PATH=/usr/local/bin:/usr/bin:$PATH
+
+    # Get pylint
+    python -m pip install pylint --user
+    python -m pip install python-libsbml --user
+    python -m pip install pyneuroml --user
+
     mkdir -p _GSL_BUILD && cd _GSL_BUILD \
         && cmake -DDEBUG=ON \
         -DPYTHON_EXECUTABLE=`which python` ..
+    make pylint -j3
     make && ctest --output-on-failure
 
     cd .. # Now with boost.

.travis/travis_prepare_linux.sh

@@ -26,6 +26,7 @@ apt-get install -qq python-numpy python-matplotlib python-networkx python-pip
 apt-get install -qq python3-lxml python-lxml
 apt-get install -qq python3-numpy python3-matplotlib python3-dev
 apt-get install -qq python-pip python3-pip
+apt-get install -qq python-tk python3-tk
 apt-get install -qq libgraphviz-dev
 
 # Gsl
@@ -42,3 +43,4 @@ apt-get install -qq python-setuptools python3-setuptools
 apt-get install -qq python-tornado python3-tornado
 python2 -m pip install pyNeuroML libNeuroML
 python3 -m pip install pyNeuroML libNeuroML
+

CMakeLists.txt

@@ -518,5 +518,27 @@ foreach( _test_script ${PY_TEST_SCRIPTS} )
         )
 endforeach( )
 
+# add pylint target.
+set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python )
+file(GLOB_RECURSE PY_SCRIPTS  "python/*.py")
+add_custom_target( pylint )
+foreach( _py_script ${PY_SCRIPTS} )
+    get_filename_component( _py_name ${_py_script} NAME_WE)
+    file( READ ${_py_script} pytext)
+    string(MD5 _md5 "${pytext}")
+    set(TGT_NAME "${_py_name}-${_md5}" )
+    set(PYLINT_OPTIONS --disable=no-member --disable=no-name-in-module 
+            --disable=invalid-unary-operand-type 
+            --disable=import-error
+            --disable=no-method-argument
+        )
+    add_custom_target( ${TGT_NAME}
+        COMMAND ${PYTHON_EXECUTABLE} -m pylint -E ${PYLINT_OPTIONS} ${_py_script}
+        COMMENT "Running pylint on ${_py_script}"
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        )
+    add_dependencies(pylint ${TGT_NAME} )
+endforeach( )
+
 ############################ CPACK ######################################
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake_moose_cpack.cmake)

CheckCXXCompiler.cmake

@@ -15,6 +15,8 @@ add_definitions(-Wall
     )
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     add_definitions( -Wno-unused-local-typedefs )
+elseif(("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang") OR ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"))
+    add_definitions( -Wno-unused-local-typedef )
 endif()
 
 

python/moose/OrderedDict.py

@@ -14,7 +14,6 @@
 except ImportError:
     pass
 
-
 class OrderedDict(dict):
     'Dictionary that remembers insertion order'
     # An inherited dict maps keys to values.

python/moose/SBML/validation.py

@@ -112,5 +112,6 @@ def validateModel(sbmlDoc):
     # consistencyMessages)
 
 if __name__ == '__main__':
+    import libsbml
     sbmlDoc = libsbml.readSBML('00001-sbml-l3v1.xml')
     validateModel(sbmlDoc)

python/moose/SBML/writeSBML.py

@@ -32,17 +32,12 @@
 '''
 import sys
 import re
+import os
 import moose
 from moose.SBML.validation import validateModel
 from moose.chemUtil.chemConnectUtil import *
 from moose.chemUtil.graphUtils import *
 
-
-# ToDo:
-#   Table should be written
-# boundary condition for buffer pool having assignment statment constant
-# shd be false
-
 foundLibSBML_ = False
 try:
     from libsbml import *
@@ -171,9 +166,10 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
     else:
         return False, "Atleast one compartment should exist to write SBML"
 
-def calPrime(x):
-    prime = int((20 * (float(x - cmin) / float(cmax - cmin))) - 10)
-    return prime
+# This function does not make sense. Where is cmin, cmax?
+#def calPrime(x):
+#    prime = int((20 * (float(x - cmin) / float(cmax - cmin))) - 10)
+#    return prime
 
 def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
     for enz in moose.wildcardFind(modelpath + '/##[ISA=EnzBase]'):
@@ -1060,11 +1056,12 @@ def writeSimulationAnnotation(modelpath):
         modelAnno = modelAnno + "</moose:ModelAnnotation>"
     return modelAnno
 
-def xyPosition(objInfo,xory):
-    try:
-        return(float(moose.element(objInfo).getField(xory)))
-    except ValueError:
-        return (float(0))
+## Already defined in chemConnectUtil from which this module is importing *
+#def xyPosition(objInfo,xory):
+#    try:
+#        return(float(moose.element(objInfo).getField(xory)))
+#    except ValueError:
+#        return (float(0))
 
 def recalculatecoordinates(modelpath, mObjlist,xcord,ycord):
     positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \

python/moose/__init__.py

@@ -1,8 +1,13 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import, division, print_function
 
-# Bring moose.py functions into global namespace.
-
+# Bring everything from moose.py to global namespace.
 from moose.moose import *
 
-__version__ = version( )
+# Bring everything from c++ module to global namespace. Not everything is
+# imported by the pervios import statement.
+from moose._moose import *
+
+# create a shorthand for version() call here.
+__version__ = version()
+

python/moose/chemMerge/merge.py

@@ -714,17 +714,7 @@ def checkexist(spList,objB,objA):
 
     return allexist
 
-def findCompartment(element):
-    while not mooseIsInstance(element,["CubeMesh","CyclMesh"]):
-        element = element.parent
-    return element
-
-def mooseIsInstance(element, classNames):
-    return moose.element(element).__class__.__name__ in classNames
-
-
 if __name__ == "__main__":
-
     try:
         sys.argv[1]
     except IndexError:

python/moose/chemUtil/chemConnectUtil.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
 """ ChemconnectUtil.py Some of the command function are written """
 
-#Created : Friday May 27 12:19:00 2016(+0530)
-
 __author__           = "Harsha Rani"
 __copyright__        = "Copyright 2017, Harsha Rani and NCBS Bangalore"
 __credits__          = ["NCBS Bangalore"]
@@ -13,16 +11,14 @@
 __status__           = "Development"
 __updated__          = "Aug 8 2017"
 
-#Aug 8 : added findCompartment function here
-
 import moose
 import numpy as np
 
 def xyPosition(objInfo,xory):
     try:
-        return(float(moose.element(objInfo).getField(xory)))
-    except ValueError:
-        return (float(0))
+        return float(moose.element(objInfo).getField(xory))
+    except ValueError as e:
+        return float(0)
 
 def setupMeshObj(modelRoot):
     ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
@@ -94,9 +90,6 @@ def setupMeshObj(modelRoot):
                 ymax = max(ycord)
     return meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,listOfitems
 
-def sizeHint(self):
-    return QtCore.QSize(800,400)
-
 def getxyCord(xcord,ycord,list1,listOfitems):
     for item in list1:
         # if isinstance(item,Function):