Allow for creating models from Python strings

[willfurnass]

Following on from #67 I I think it would be a very good thing if MuMoT models could be created and referenced in Notebooks without using Notebook cell execution numbers. At present the example Notebooks contain cells like:

%%model
$
U -> A : g_A
U -> B : g_B
A -> U : a_A
B -> U : a_B 
A + U -> A + A : r_A
B + U -> B + B : r_B
A + B -> A + U : s
A + B -> B + U : s
$

then

model1 = mumot.parseModel(In[2])

This approach causes problems for the user if they want to re-run a given cell as then calls like mumot.parseModel(In[X}) in subsequent cells won't work without manual editing of the cell execution number.

I suggest that what's needed is a Python function to generate a model from a multi-line string:

model_1 = mumot.model_from_latex("""
U -> A : g_A
U -> B : g_B
A -> U : a_A
B -> U : a_B 
A + U -> A + A : r_A
B + U -> B + B : r_B
A + B -> A + U : s
A + B -> B + U : s
""")

This is almost as readable as the but should allow Notebooks to be run more flexibly and robustly. You'd loose the LaTeX rendering beneath the %%model magic cells but that seems redundant given that MuMoTmodel.show() produces a more attractive rendering of that information.

Another advantage of allowing models to be generated by parsing a Python string is that it would make it easier to create models for unit testing outside Notebooks.

[jarmarshall]

If this is necessary to close issue #157 I should be able to do something quick in a few days - the existing functionality is probably nicer for a user though - it separates describing the model from writing the function call to parse the model.

[willfurnass]

NB this can currently be done with e.g.

model1 = mumot.parseModel("""
U -> A : g_1
U -> B : g_2
A -> U : a_1
B -> U : a_2
A + U -> A + A : r_1
B + U -> B + B : r_2
A + B -> A + U : s
A + B -> B + U : s
""".replace('\n', '\\n'))

Some extra logic in parseModel would allow .replace('\n', '\\n') to be omitted in the above.

[jarmarshall]

You mean it already works as described @willfurnass (I'd be surprised unless you changed something) or it would be straightforward to make it work (I agree, was thinking the same, and could make the change quickly)?

[willfurnass]

The snipped of code in https://github.com/DiODeProject/MuMoT/issues/156#issuecomment-428546922 works for me. I tried something like this a while ago but think I was missing the .replace('\n', '\\n').

[jarmarshall]

Great, on reflection I can see why this would work - since this is a satisfactory workaround for testing purposes I can focus now on #158

[jarmarshall]

Feel free to add some pre-processing to the input string within the parseModel(...) method though, and close