Check for loops & disconnected species.

[ismael-lajaaiti]

Answer #76.

When creating a FoodWeb with a structural model (e.g. niche model), we check that the generated FoodWeb:

1. does not have cycle
2. does not have disconnected species
3. has a number of links in $[L - \Delta L; L + \Delta L]$ where $L$ is the value given by the user and $\Delta L$ is the tolerance controlled by the tol keyword argument (the same applies if the user provides a connectance instead of a number of links)

For point 1. and 2. I used functions from Graphs.jl as these operations are not trivial (see also #77).

For now, the checks for cycle(s) and disconnected species are only if the user use a structural model. However if the user build the FoodWeb with another method, for instance by providing directly an adjacency matrix, I don't check for cycle(s) and disconnected species. Should I add these checks and throw a warning if they do not pass? (Throwing an error would be too rough IMO, an informed user might want to model a food web with cycles).

[andbeck]

I think yes to the warning for users delivering non-niche model networks.

[iago-lito]

Here is your review! That's a good job again, and I find that the quality of your code is improving PR after PR :)

I see no major concern with your implementation, and my comments only points to possible minor ameliorations.

I agree that it would make sense that the error thrown in case of a cyclic/disconnected structural model be downgraded to a simple warning because a user inputting A or a graph directly possibly knows what they are doing. For instance, I would be glad to "paralellize" the simulation of two small systems by merging them into a single disconnected network.

I hear you are crafting a new commit to add the warning rn. Let's see this when it's ready :)

[ismael-lajaaiti]

Here is the commit to throw a warning if the food web has cycle(s) or disconnected species, when not using structural models. Note that the warning can be silent with the quiet kwarg. For instance :

FoodWeb([0 0; 0 0]) # throw a warning, because sp. are disconnected
FoodWeb([0 0; 0 0], quiet = true) # do not throw a warning thanks to 'quiet'

[ismael-lajaaiti]

@iago-lito here is the commit integrating your suggestions, everything should be in there (hope I missed nothing). ✨

[iago-lito]

Great! Let's land this now. Congratulations :)