Initial commit
Version 0.01 - August 2013

1. First commit.  The networkx directory is included with graph algorithms and
manipulation.

2. Functions added to open pipeline configuration file and build graph.

3. Task and data nodes identified and task nodes are tagged with tool information.
Version 0.02 - August 2013

1. Added extra functionality for handling tool configuration files and
adding data to nodes.
Branch graph, version 0.01 - August 2013

1. Started a new branch for integrating networkx graph architecture into gkno.
Configuration file formats are changed with this new branch.
Branch graph, version 0.02 - August 2013

1. Modified functions in command line for determining the mode of operation.
This gets rid of dependence on the tl and pl objects which no longer exist.
These objects have been replaced by objects defined in the configurationClass
library.
Branch graph, version 0.03 - August 2013

1. Continual development.
Version 0.01 - August 2013

1. Moved pythin files into src directory.

2. Modified name of function.
Version 0.03 - August 2013

1. Moved python files into src directory.

2. Modified name of function.
Merge remote-tracking branch 'origin/master'
Merge github.com:AlistairNWard/configurationClass into graph
Branch graph, Version 0.03 - August 2013

1. Read in data from tool configuration files and populated data structures.
Branch graph, Version 0.04 - August 2013

1. Completed graph construction.  All nodes are added and tagged as
required as necessary.  The existence of all tool edges are checked.
Branch graph, Version 0.04 - August 2013

1. Modified the helpClass to handle the graph for generating help messages.
Branch graph, Version 0.06 - August 2013

1. Committed minor changes in order to switch to main branch.
Branch graph, Version 0.07 - August 2013

1. Modified general flow to account for modified data structures in the
configuration class.
Branch graph, Version 0.08 - August 2013

1. Modified errors file to gknoErrors to avoid conflict with configurationClass
errors.
Branch graph, Version 0.08 - August 2013

1. Parsed command line and populated data structures.

2. If the user accesses tool arguments using the --tool [arguments] syntax, arguments
can be accessed for which no node exists.  The node built for holding the tool information
is now inserted into the graph and connected up.
Branch graph, Version 0.09 - September 2013

1. Made more modifications for graph compatibility.

2. In the event that a flag command line argument is given for a task in
a pipeline (e.g. --align [-a]) and there are consequently no spaces inside
the square brackets, an unhandled error would occur.  This isn't an error
and is now fixed.
Branch graph, Version 0.10 - September 2013

1. Modified gkno to handle updated configurationClass.
Branch graph, Version 0.11 - September 2013

1. Fixed a bug with specific pipeline help.