Add sampling-driven dFBA and make optional deps robust.

[Mohit-Lakra]

    ## Summary
    - add DynamicFBA helper and result container with sampling-based tie-breaking
    - document usage and cite Mahadevan/DFBAlab/COMETS references
    - guard cobra/sparseqr/volestipy/matplotlib imports so the CLI stays usable without optional deps
    - add regression test that exercises biomass/media updates

    ## Testing
    - python -m pytest tests/test_dfba.py

[vissarion]

@hariszaf could you have time to help us reviewing here?

[hariszaf]

Hi!

@Mohit-Lakra thanks for your interest on dingo and for your effort on this issue.

In your attempt, you miss updating the medium after each step;
you need to calculate how much of each compound is being consumed in each step and how much is being produced, and then update the medium based on those calculations.

By not doing so, you end up with what your test on README suggests now:

>>> result.biomass
array([0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
       0.1, 0.1, 0.1, 0.1, 0.1, 0.1])
>>> result.concentrations["EX_glc__D_e"]
array([5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
       5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
       5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
       5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
       5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.,
       5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5., 5.])

That means that you don't have a dynamic scenario but rather a fixed one where the concentration of glucose is always 5 and your biomass is 0.1.

You may have a look here for a simple example of what I'm trying to say, or here for a more concrete approach.