CHANGES.txt

VERSION 1.2


Crucial edit to setup.py file

Adding PyFBA.model package to list.



VERSION 1.1


Updated all the code to work with Python 3.

However, this breaks compatibility with Python 2 because of the "errors"
keyword in open.

The main changes include relative imports, a new class in the tests/
package to allow deep assertions,
and using this type of construct with the open command to ignore unicode
errors in ModelData:

    with open(ssfile, 'r', errors='replace') as sin:

Added function to obtain Model SEED complexes from a set of roles

-   PyFBA/filters/roles_and_complexes.py

Added gap-fill step to add reactions based on existent EC numbers

-   PyFBA/gapfill/ecnumbers.py

Optimized and fixed bugs during gap-fill reaction minimization process

-   PyFBA/gapfill/reaction_minimization.py

New Model class objects

Model object contains functionality to make common processes easier to
facilitate.

-   Generate model from RAST annotations
-   Save model to hard disk location
-   Load model from hard disk location
-   Run FBA
-   Run FBA and obtain flux values
-   Run FBA and obtain flux values according to SEED subsystems
-   Run gap-fill
-   Remember which reactions were gap-filled reactions and which media

New iPython Notebooks

-   Find a metabolite.ipynb
-   PATRIC to FBA.ipynb
-   Gap-fill_a_model.ipynb
-   Saving_and_loading_a_model.ipynb



VERSION 1.0


Added a CITATION.md

Please cite us if you use PyFBA

Added the iPython Notebook directory

Example code showing:

importing an SBML file and running FBA

-   iPythonNotebooks/Using_an_SBML_model.ipynb

how to build your model from functional roles and how to gap-fill that
model on a media

-   iPythonNotebook/From_functional_roles_to_gap-filling.ipynb

Added minimization by accuracy

Removed PyFBA/gapfill/minimize_additional_reactions.py and created
reaction_minimization.py

Example gap-fill pipeline

-   example_code/gapfill_from_reactions_multiple_conditions.py



VERSION 0.951


Removed the author tag

It is superflous, that is what versioning is for.



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