Version 0.95
============

Several changes to files:

Updated the subsystem functions and changed the name to a generic name. The date is handled by versioning!

-   PyFBA/Biochemistry/SEED/Subsystems/SS_functions.txt  
-   PyFBA/Biochemistry/SEED/Subsystems/SS_functions_Oct_2015.txt

Changing the version number

-   PyFBA/init.py

Adding reaction flux information that can be pulled after the sm has been solved

-   PyFBA/fba/init.py  
-   PyFBA/fba/fluxes.py

External reactions

Fixed an issue where we were over-incorporating reactions based on
things in the media

-   PyFBA/fba/bounds.py  
-   PyFBA/parse/model_seed.py

Adding verboseness

-   PyFBA/fba/run_fba.py  
-   PyFBA/gapfill/roles.py  
-   PyFBA/parse/read_media.py

Reduced complexity

We only test the right half of the reactions if the left half do not
grow, and once we have <10 reactions  
to search through we just iterate and knock out each reaction
sequentially. It is faster than the shuffle  
approach.

-   PyFBA/gapfill/minimize_additional_reactions.py

Changed the way we read roles

SEED has a notion of multifunctional roles, and we added splitting those
functions into roles

-   PyFBA/gapfill/subsystem.py

Gap generation code

Testing each of the individual reactions in a model

-   PyFBA/gapgeneration/test_reactions.py  
-   example_code/test_individual_reactions.py

Shifted the order of gapfilling

This order makes more logical sense!

-   example_code/gapfill_from_reactions.py

Updated the tests

With all these changes, the tests were not right

-   PyFBA/tests/reaction_list.txt  
-   PyFBA/tests/test_fba.py  
-   PyFBA/tests/test_suggestions.py

Version 0.9
===========

Refactored separating roles to functions. SEED has a concept of
multifunctional roles and this separates out our roles before we search
for them.

Version 0.8
===========

Version 0.7
===========

Version 0.6
===========

-   Removed installation dependencies from setup.py because they break
    installation! You need to install the dependencies manually  
-   Refactored the code to remove the os.environ dependencies

Version 0.5
===========

-   Initial release

