Update .gitignore to ignore PyCharm related folder.
README.rst
Create __init__.py
First implementation of the MILP model.

This is a first implementation of the MILP formulation for training boolean
signalling networks according to experimental data.
Update access to midas inhibitor information.

Information about inhibitors is no longer encoded with a trailing ":i"
after the name of the species.
Equation comments to LaTeX format.

Constraint and objective function expressions are expressed mathematically
before the code that implements them. Now, the mathematical expressions are
written in LaTeX.
Refactor code to simplify model building and bugfix in the formulation.

Before reactions where inferred from the pkn graph structure.
Now, reactions are read directly from the pkn.reactions attribute.

A bug in the formulation of one of the constraints has been fixed. There
was a "-1" being added outside pulp.lpSum(). Now it is included inside
pulp.lpSum(), correctly matching the mathematical formulation.

The name of the variables has been changed to better match the one in the
mathematical formulation.
Method for easily retrieving the solution.

The new method returns a dictionary with the reaction of the network as
keys and a 1 or a 0 as value depending on if the reaction is part of the
solution or not.
Create __init__.py
Tests for the MILP model.

Add some basic tests for the MILP model code.
Add docstrings.

Add docstrings documenting what the class does and the purpose of each
method.
Updata .gitignore to skip files generated by PuLP.

*-pulp.mps files are generated by PuLP when solving a linear programming
problem.
Reset model before training.

The program crashed before if train was called two times in a row.
Now, the constraint dictionary is cleared before building the model.
Update attributes if the pkn or the midas are changed by the user.

The class MILPTrain has some attributes that are used to build the
optimization model that are calculated from the pkn and midas information.
If one of those or both are changed, those attributes should be updated
to make sure that the problem formulation is correct.
Name the constraints.

The constraints in the model are now named to facilitate their
identification. The namce starts with 'Cx_', where 'C' stands for
constraint and x is a number (the number of the equation representing the
constraint in the paper Mitsos et al. 2009). After 'Cx_', the corresponding
i, j or k values are appended, separated by an underscore ('_'). Note that
some values of i, j or k may have underscores in their names. The order in
which this i, j or k values appear is the same in which their are written
in the equations of the paper.
Remove __author__.

Authorship is already tracked by version control.
Merge pull request #40 from ltobalina/feature/milp

Feature/milp