Caching of Network Properties in ReactionSystems

using Pkg
Pkg.activate(; temp = true) # Creates a temporary environment, which is deleted when the Julia session ends.
Pkg.add("Catalyst")

When calling many of the network API functions, Catalyst calculates and caches in rn a variety of information. For example the first call to

rcs,B = reactioncomplexes(rn)

calculates, caches, and returns the reaction complexes, rcs, and the incidence matrix, B, of rn. Subsequent calls simply return rcs and B from the cache.

Similarly, the first call to

N = netstoichmat(rn)

calculates, caches and returns the net stoichiometry matrix. Subsequent calls then simply return the cached value of N. Caching such information means users do not need to manually know which subsets of network properties are needed for a given calculation (like the deficiency). Generally only

rcs,B = reactioncomplexes(rn)    # must be called once to cache rcs and B
any_other_network_property(rn)

should work to calculate a desired network property, with the API doc strings indicating when reactioncomplexes(rn) must be called at least once before a given function is used.

Because of the caching of network properties, subsequent calls to most API functions will be fast, simply returning the previously calculated and cached values. In some cases it may be desirable to reset the cache and recalculate these properties. This can be done by calling

Catalyst.reset_networkproperties!(rn)

Network property functions will then recalculate their associated properties and cache the new values the next time they are called.