Initial commit after project creation using modern-package-template with minimal info added during the set up script.
Basic Structure and code begins
Packaging: Doc Stuff
Refactoring of project setup
followup
Removed gfunc/parsers/parsers.py since its contents had been split into better places
added gfunc/xpermutations.py
src/gfunc/data_classes.py:
- removed registry class shells
- added class Bunch()
- capitalized GFuncX class names
- removed internal object tracking since we will have node/edge_dict
- finished prototyping GFuncNode, GFuncEdge
/src/gfunc/graphTools.py:
- empty class GraphBuilder()
src/gfunc/parsers/Cufflinks.py:
- finished prototyping class CDiffFpkmTrackerParser()
src/gfunc/parsers/ETE.py:
- finished prototyping class PhyloXMLParser()
src/gfunc/parsers/MAST.py:
- empty file with doc str
added files:
- analysis_classes.py
- maths.py
- parsers/base.py
- parsers/JASPAR.py
- scripts/Cq_Ag.conf
- scripts/Cq_Ag_ecrTeam.conf
- scripts/find_motifs.py
-  scripts/gfunc_build.py
-  scripts/gfunc_sort.py
-  scripts/__init__.py
src/gfunc/data_classes.py:
ADDED:
- bunchify()
- Bunch() 
- GFuncNode.get_copy()
- GFuncNode.total_votes()
- GFuncNode.get_sub_scores()

CHANGED:
- GFuncNode.__init__()
- GFuncNode.__repr__()
- GFuncEdge.__init__()
- GFuncEdge.__repr__()


REMOVED:
- GFuncNode.get_neighbors()
- GFuncNode.poll_neighbors()
- to ADD back:
-"""
-####################
-data_classes.py
-####################
-Code defining container classes for supported data types.
-"""
src/gfunc/fileIO.py:
ADDED:
- tableFile2namedTuple()

CHANGED:

REMOVED:
src/gfunc/graphTools.py:
ADDED:
- import Bunch
- import GFuncEdge
- import GFuncNode
- class GraphBuilder()
- class GraphHandler()

CHANGED:

REMOVED:
src/gfunc/parsers/Cufflinks.py:
ADDED:
- import defaultdict,numpy,GFuncParserBase,GFuncNode,Bunch,tableFile2namedTuple
- CDiffFpkmTrackerParser._sum_transcripts()
 - transfer_nearestRefgeneSymbol_from_isoform_to_gene_tracking()


CHANGED:
- CDiffFpkmTrackerParser inherits from GFuncParserBase
- CDiffFpkmTrackerParser.__init()
- CDiffFpkmTrackerParser._setup_expn_vector()
- CDiffFpkmTrackerParser.register_nodes()

REMOVED:
src/gfunc/parsers/ETE.py:
ADDED:
- import cPickle,GFuncParserBase

CHANGED:
- load_phyloXMLs()
- PhyloXMLParser(GFuncParserBase)
- PhyloXMLParser.__init__() [started to add pickle ability]
- PhyloXMLParser.resgister_nodes_and_edges()

REMOVED:
src/gfunc/parsers/__init__.py
ADDED:
__all__ = ['base','Cufflinks','ETE','JASPAR','MAST']

CHANGED:

REMOVED:
src/gfunc/analysis_classes.py:
- added  PhyloExpnCorrelationIndex(Metric)