Update inference of variables and default differential from @equations macro

[TorkelE]

Updates what we infer as variables from equations, and also when we detect that the default differential D is used. The new formula is a bit more liberal, which will make describing it a bit easier.

Inferring variables

The order of inference of species/variables/parameters is now:
(1) Every symbol explicitly declared using @species, @variables, and @parameters are assigned to the correct category.
(2) Every symbol used as a reaction reactant is inferred as a species.
(3) Every symbol not declared in (1) or (2) that occurs in an expression provided after @equations is inferred as a variable.
(4) Every symbol not declared in (1), (2), or (3) that occurs either as a reaction rate or stoichiometric coefficient is inferred to be a parameter.

E.g. in

@reaction_network begin
    @equations V1 + S ~ V2^2
    (p + S + V1), S --> 0
end

S is inferred as a species, V1 and V2 as variables, and p as a parameter.

The previous special cases for the @observables (if not declared as symbol/variable, becomes a variable without additional info), @compounds (counts as @species declarations), and @differentials (used to declare non-D differentials) still hold.

Finally, we also now have the @require_declaration options which can be used to remove any uncertainty in messy cases.

Inferring use of differential D

When determining whether the default differentials have been used within an @equations option. Now, if any expression D(...) is encountered (where ... can be anything), this is inferred as usage of the default differential D. E.g. in the following equations D is inferred as a differential with respect to the default independent variable:

@reaction_network begin
  @equations D(V) + V ~ 1
end
@reaction_network begin
  @equations D(D(V)) ~ 1
end

The code handling is getting a bit messier than it has to be. This will be better in the PR which finally fixes the mess that is the DSL file. Primarily we will probably just create lists for stuff declared using @species, @variables, and @parameters and then which is inferred. And then this can just be processed in an orderly manner. But for now, this does all the breaking changes, which we want with v15.

I have also added a couple of tests for good measure.

[TorkelE]

Update designated_syms with species_extracted so these are excluded from the next step.

[TorkelE]

I need to fix this thing. I have checked an re-checked and there is no actual difference (more than space removal). I think I put in, and then removed, a debug statement in this file (and the space removal happened). Hence changes appeared here.

[isaacsas]

I think you must have some VSCode setting enabled.

[isaacsas]

What happens if someone uses D in a reaction as an implicit species?

[isaacsas]

Aside from that question this is fine to merge I think.

[TorkelE]

Using D in any other context (e.g. as a species, variable or parameter) should disable inference of D as a differential. Will clarify this

[isaacsas]

I think you must have some VSCode setting enabled.

[TorkelE]

Turns out the docs have started failing, something in the oscillation parameter fitting example.