hotfix from branch issue167.

Squashed commit of the following:

commit ee24065
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 14:04:27 2017 +0530

    Decreased rtol to 1e-5 in numpy.allclose .

commit 138906a
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 13:50:30 2017 +0530

    When test failes print the value of tuple.

commit 963de3a
Merge: ff64f41 8a6346d
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 13:47:36 2017 +0530

    Merge branch 'chamcham' into issue167

commit ff64f41
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 13:39:45 2017 +0530

    use matplotlib.use before importing matplotlib.

commit 1af2819
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 13:19:37 2017 +0530

    Fixes to travis related issue in test file.
    matplotlib.use('Agg') to make sure test passes when ssh is used without
    -X.

commit b20ad43
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 12:29:54 2017 +0530

    colname -> columnName .

commit 88b12b3
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 12:22:55 2017 +0530

    Fixes to neuroml test failure with python3.

commit 1297ac5
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 11:56:09 2017 +0530

    Relative to file import in test_kkit.py model.

commit e526fca
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 11:52:56 2017 +0530

    Enabled kkit test in cmake.

commit 1830f59
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 11:48:04 2017 +0530

    Added a kkit test scripts.

commit 33606b0
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 11:00:04 2017 +0530

    Build fixes after make clean.

commit f5258a5
Author: Dilawar Singh <[email protected]>
Date:   Thu Jan 5 10:41:14 2017 +0530

    Fixes to issue #167.

commit 3f077c1
Merge: 9b175c8 f0d4c02
Author: bhalla <[email protected]>
Date:   Thu Jan 5 09:48:44 2017 +0530

    Resolved merge conflict with Table.h

commit 9b175c8
Author: bhalla <[email protected]>
Date:   Thu Jan 5 09:35:53 2017 +0530

    Major bugfix for Table and derived class Streamer, to fix error introduced
    by duplicating the 'name' field which is already defined for Neutral.
    Minor bugfix for melement.cpp

commit f0d4c02
Author: Dilawar Singh <[email protected]>
Date:   Tue Jan 3 09:57:49 2017 +0530

    Update INSTALL.md

    Updated instructions.

commit 2737220
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 21:33:22 2017 +0530

    Fixes to issue165 (#166)

commit a934676
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 20:47:01 2017 +0530

    Update .travis.yml

commit 601d06a
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 13:19:31 2017 +0530

    Fixes to PYTHON3 build failure on travis.

commit 9d9d925
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 12:46:07 2017 +0530

    Tested locally for linux. The scripts seems to be fine on openSUSE-42.2

commit 93bbd4f
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 12:31:57 2017 +0530

    By default travis pick up /opt/bin/python when `which python` is used. Do not
    use this construct in script.
    Moved travis related scripts to a hidden folder .travis.

commit c0d3871
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 12:21:32 2017 +0530

    If python3 exists (installed on travis), then check for the compatibility
    otherwise don't.

commit 65a85da
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 12:14:15 2017 +0530

    Almost there. Calling script from top of directory.

commit 0db2016
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 12:05:10 2017 +0530

    Make trusty default build environment. python3-matplotlib is not available by
    default.

commit d8c1c6a
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 11:54:12 2017 +0530

    setuid to root for linux script.

commit 4c90f04
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 11:49:05 2017 +0530

    Some more fixes in travis script.

commit 429420b
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 11:45:40 2017 +0530

    Cleanup, osx related travis macros.

commit e287118
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 11:42:08 2017 +0530

    Disable OSX build here on master brach.
    Created issue #165 to build and test for MacOSX.

commit 87aeb1a
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 11:33:24 2017 +0530

    Travis build scripts for macosx and linux are in ./scripts folder.

commit 24643bc
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 09:58:54 2017 +0530

    Some more fixes to travis build failure on OSX.

commit a05826e
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 09:25:22 2017 +0530

    Fixing brew taps and build dependencies.

commit ea0ede1
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 09:19:00 2017 +0530

    This commit is just to test the OSX build on travis. Unfortunately there is no
    way to test it offline.

commit 1b6f42a
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 09:02:28 2017 +0530

    Fixes to travis scripts.

commit b0baaab
Author: Dilawar Singh <[email protected]>
Date:   Mon Jan 2 08:48:07 2017 +0530

    Excluded linux and osx build from config file.

commit 626fd30
Author: Dilawar Singh <[email protected]>
Date:   Sun Jan 1 19:28:32 2017 +0530

    Testing with OsX support on travis. xcode-8.1. Most likely to break

commit ab933ad
Author: Dilawar Singh <[email protected]>
Date:   Sun Jan 1 19:18:54 2017 +0530

    Fixes to recent travis build failure.
    make all python files python3 compatible in addition to #164.

commit 72afc02
Author: Dilawar Singh <[email protected]>
Date:   Sun Jan 1 19:02:31 2017 +0530

    Enabled macosx build on travis. Though allowing failure for now.

commit bedb51e
Author: Dilawar Singh <[email protected]>
Date:   Sun Jan 1 18:04:08 2017 +0530

    Fixes for issue #164. Also hotfix for branch chamcham.

Author: Dilawar Singh

INSTALL.md

@@ -1,16 +1,25 @@
 # Pre-built packages
 
+## Linux
+
 Use our repositories hosted at [Open Build Service](http://build.opensuse.org).
 We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL,
 Scientific Linux.  Visit the following page for instructions.
 
 https://software.opensuse.org/download.html?project=home:moose&package=moose
 
+## MacOSX
+
+MOOSE is available via [homebrew](http://brew.sh).
+
+    $ brew install homebrew/science/moose 
+
+
 # Building MOOSE from source
 
 To build `MOOSE` from source, you can either use `cmake` (recommended) or GNU `make` based flow.
 
-Download the latest source code of moose from github or sourceforge.
+Download the latest source code of moose from github.
 
     $ git clone -b master https://github.com/BhallaLab/moose-core
 
@@ -29,6 +38,10 @@ On Ubuntu-12.04 or higher, these can be installed with:
 
 __NOTE__ : On Ubuntu 12.04, gsl version is 1.15. You should skip `libgsl0-dev` install gsl-1.16 or higher manually.
 
+SBML support is enabled by installing [python-libsbml](http://sbml.org/Software/libSBML/docs/python-api/libsbml-installation.html). Alternatively, it can be installed by using `python-pip`
+
+    $ sudo pip install python-libsbml
+
 ## Use `cmake` to build moose:
 
     $ cd /path/to/moose-core 

MooseTests.cmake

@@ -115,3 +115,13 @@ ADD_TEST( NAME pymoose-test-streaming_in_tables
 set_tests_properties(pymoose-test-streaming_in_tables
     PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
     )
+
+# Test kkit support.
+ADD_TEST( NAME pymoose-test-kkit 
+    COMMAND ${TEST_COMMAND} 
+    ${PROJECT_SOURCE_DIR}/tests/python/test_kkit.py
+    )
+set_tests_properties(pymoose-test-kkit
+    PROPERTIES ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/python"
+    )
+

builtins/Streamer.cpp

@@ -292,8 +292,8 @@ void Streamer::addTable( Id table )
 
     // NOTE: If user can make sure that names are unique in table, using name is
     // better than using the full path.
-    if( t->getName().size() > 0 )
-        columns_.push_back( t->getName( ) );
+    if( t->getColumnName().size() > 0 )
+        columns_.push_back( t->getColumnName( ) );
     else
         columns_.push_back( moose::moosePathToUserPath( table.path() ) );
 }

builtins/Table.cpp

@@ -74,11 +74,13 @@ const Cinfo* Table::initCinfo()
         , &Table::getFormat
     );
 
-    static ValueFinfo< Table, string > name(
-        "name"
-        , "Name of the table."
-        , &Table::setName
-        , &Table::getName
+    // relevant for Streamer class.  When data is written to a datafile, this is
+    // used to create column name.
+    static ValueFinfo< Table, string > columnName(
+        "columnName"
+        , "Name of the table written in header of data file."
+        , &Table::setColumnName
+        , &Table::getColumnName
     );
 
     //////////////////////////////////////////////////////////////
@@ -126,7 +128,7 @@ const Cinfo* Table::initCinfo()
     {
         &threshold,		// Value
         &format,                // Value
-        &name,                  // Value
+        &columnName,            // Value
         &outfile,               // Value 
         &useStreamer,           // Value
         handleInput(),		// DestFinfo
@@ -347,15 +349,15 @@ string Table::getFormat( void ) const
     return format_;
 }
 
-/*  User defined name  */
-string Table::getName( void ) const
+/*  User defined column name for streamer  */
+string Table::getColumnName( void ) const
 {
-    return tableName_;
+    return tableColumnName_;
 }
 
-void Table::setName( const string name )
+void Table::setColumnName( const string colname )
 {
-    tableName_ = name ;
+    tableColumnName_ = colname ;
 }
 
 /* Enable/disable streamer support. */

builtins/Table.h

@@ -37,8 +37,8 @@ class Table: public TableBase
     void setFormat ( const string format );
     string getFormat( ) const;
 
-    void setName ( const string name );
-    string getName( ) const;
+    void setColumnName( const string colname );
+    string getColumnName( ) const;
 
     void setUseStreamer ( bool status );
     bool getUseStreamer ( void ) const;
@@ -84,7 +84,12 @@ class Table: public TableBase
     vector<string> columns_;                    /* Store the name of tables */
 
     string tablePath_;
-    string tableName_;
+
+
+    /**
+     * @brief Column name of this table. Use it when writing data to a datafile.
+     */
+    string tableColumnName_;
 
     /**
      * @brief If stream is set to true, then stream to outfile_. Default value
@@ -108,7 +113,7 @@ class Table: public TableBase
     bool outfileIsSet_;
 
     /**
-     * @brief format of data. Currently fixed to csv.
+     * @brief format of data. Default to csv.
      */
     string format_;
 

pymoose/melement.cpp

@@ -180,7 +180,7 @@ int moose_ObjId_init_from_path(_ObjId * self, PyObject * args,
     ostringstream err;
     // First see if there is an existing object with at path
     self->oid_ = ObjId(path);
-    PyTypeObject * basetype = getBaseClass((PyObject*)self);
+    PyTypeObject* basetype = getBaseClass((PyObject*)self);
     string basetype_str;
     if (type == NULL){
         if (basetype == NULL){
@@ -210,15 +210,26 @@ int moose_ObjId_init_from_path(_ObjId * self, PyObject * args,
     } else { // this is a non-root existing element
         // If the current class is a subclass of some predefined
         // moose class, do nothing.
+        string className = self->oid_.element()->cinfo()->name();
+        map <string, PyTypeObject * >::iterator ii = 
+        	get_moose_classes().find( className );
+        PyTypeObject * basetype = 0;
+        if ( ii != get_moose_classes().end() ) {
+    	    basetype = ii->second;
+            basetype_str = string(basetype->tp_name).substr(6); // remove `moose.` prefix from type name
+        } else {
+            err << "Unknown class: " << className << endl;
+            basetype = getBaseClass((PyObject*)self);
+        }
         if ((basetype != NULL) && PyType_IsSubtype(mytype, basetype)){
             return 0;
         }
         // element exists at this path, but it does not inherit from any moose class.
         // throw an error
         err << "cannot convert "
-            << Field<string>::get(self->oid_, "className")
+			<< className 
             << " to "
-            << basetype_str
+            << mytypename
             << ". To get the existing object use `moose.element(obj)` instead.";
         PyErr_SetString(PyExc_TypeError, err.str().c_str());
         return -1;

python/moose/add_Delete_ChemicalSolver.py

@@ -2,8 +2,8 @@
 
 
 def moosedeleteChemSolver(modelRoot):
-    """
-            Delete solvers from Chemical Compartment
+    """Delete solvers from Chemical Compartment
+
     """
     compts = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
     for compt in compts:
@@ -13,7 +13,7 @@ def moosedeleteChemSolver(modelRoot):
             moose.delete(st)
             if moose.exists((st_ksolve).path):
                 moose.delete(st_ksolve)
-                print("Solver is deleted for modelpath ", modelRoot)
+                print("Solver is deleted for modelpath %s " % modelRoot)
 
 
 def mooseaddChemSolver(modelRoot, solver):
@@ -79,4 +79,4 @@ def setCompartmentSolver(modelRoot, solver):
 
     for i in stoichList:
         i.filterXreacs()
-    print(" Solver is added to model path ", modelRoot)
+    print( " Solver is added to model path %s" % modelRoot )

python/moose/moose.py

@@ -21,10 +21,9 @@
 sbmlSupport_, genesisSupport_ = True, True
 try:
     import SBML.readSBML
-    import SBML.writeSBML
+    import SBML.writeSBML 
 except Exception as e:
-    print('MOOSE could not load SBML support')
-    print('\tError was %s' % e)
+    print( 'MOOSE could not load SBML support due to %s' % e )
     sbmlSupport_ = False
 
 try:
@@ -79,7 +78,7 @@ def mooseReadSBML(filepath, loadpath, solver='ee'):
     if not os.path.isfile(filepath):
         raise UserWarning('File %s not found' % filepath)
 
-    return SBML.readSBML.mooseReadSBML(filepath, loadpath, solver)
+    return SBML.readSBML.mooseReadSBML( filepath, loadpath, solver )
 
 
 def mooseWriteSBML(modelpath, filenpath, sceneitems={}):

python/moose/neuroml/MorphML.py

@@ -632,7 +632,7 @@ def set_compartment_param(self, compartment, name, value, mechanismname):
                     moose.connect(channel,'channel',compartment,'channel')
             ## if mechanism is present in compartment, just wrap it
             else:
-                neutralObj = moose.Neutral(compartment.path+'/'+mechanismname)
+                neutralObj = moose.element(compartment.path+'/'+mechanismname)
                 if 'CaConc' == neutralObj.className: # Ion concentration pool
                     caconc = moose.CaConc(compartment.path+'/'+mechanismname) # wraps existing channel
                     channel = None