Module for high-level API about overreact HOT 6 CLOSED

Projects and issues related to the degree of rate control were moved to milestone 1.2.

from overreact.

The ideas on rate control are still planned for 1.2, but all other suggestions are expected to be ready in 1.1.

from overreact.

This is important to have as we go public as we want to publish tutorials as Jupyter Notebooks (see #49).

from overreact.

There is a demand for an API in Python for thermochemistry; see patonlab/GoodVibes#35.

from overreact.

We could benefit from a high-level interface, defined as an interface that deals with logfile and model objects directly. All functions would be higher-level versions of internal procedures. This is related to the discussion in #28.

* [x]  As such, the user would be able to do something similar to:

The current status has improved the example above a lot. A draft of how we can currently accomplish the same thing now:

import numpy as np
import matplotlib.pyplot as plt

import overreact as rx

model = rx.parse_model("my-model.k")
for temperature in [200.0, 300.0, 400.0]:
    # already multiplies contains transmission coefficients
    k = rx.get_k(model.scheme, model.compounds)
    dydt = rx.get_dydt(model.scheme, k)

    y0 = [1.0, 0.0]
    y, r = simulate.get_y(dydt, y0)

    t = np.linspace(y.t_min, y.t_max)
    plt.plot(t, y(t)[1], label=f"P @{temperature}K")

plt.legend()
plt.xlabel("Time (s)")
plt.ylabel("Concentration (M)")
plt.show()

Furthermore, other related things are proposed:

* [ ]  Calculate the degree of rate control with a factory function that receives the free energies as first parameter and returns one reaction rate:

I'm postponing this for now as I currently don't prioritize this anymore. The example above is good though. As such, this is going to 1.2 again.

from overreact.

I'm postponing the development on the degree of rate control and sensitivity analysis in general. The rest of this issue is there already.

from overreact.