Catalyst.jl
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SciML
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
I briefly go through periodic events in ODEs as well (primarily as a baseline to compare to, but I think there is some general useful input on these as well....
I have gone through the network analysis file and added comments where appropriate. I am not super familiar with it, so I basically went through ti from start to finish,...
Adds a dedicated section on the network analysis page which goes through conservation laws and their various API functions. Also adds a short section about this in the ODE performance...
New doc page for events and callbacks. Goes through the various types, and how to declare and use them. Also describes some common pitfuls one can encounter while working with...
Again not sure what to call this one. This is basically a third introduction page. While the two previous ones are more or less parallel (i.e. have the same purpose,...
Not actually sure what to call this one, but this is the tutorial that goes through how to access stuff within a `ReactionSystem`. - For a starter, it goes through...
Imagine if we have a vector-valued species: ```julia using Catalyst t = default_t() @species X[1:100] ``` where each degrades at the same rate `d`, it would be neat to declare...
All broken tests in Catalyst should have corresponding issues (mostly outside of Catalyst). This issue tracks them all: ModelingToolkit/SciML issues: https://github.com/SciML/ModelingToolkit.jl/issues/1761 https://github.com/SciML/ModelingToolkit.jl/issues/2612 https://github.com/SciML/ModelingToolkit.jl/issues/2614 ~https://github.com/SciML/ModelingToolkit.jl/issues/2778~ https://github.com/SciML/ModelingToolkit.jl/issues/2779 ~https://github.com/SciML/SciMLBase.jl/issues/662~ https://github.com/SciML/SciMLBase.jl/issues/709 ~https://github.com/SciML/SciMLBase.jl/issues/710~ https://github.com/SciML/SciMLBase.jl/issues/711 ~https://github.com/SciML/JumpProcesses.jl/issues/417~...
Given they are not likely to support `PeriodicCallback`s any time soon due to https://github.com/SciML/JumpProcesses.jl/issues/417,
Right now we have a lot of places using `@set!` and such to generate new, modified `ReactionSystem`s. It might be easier to just create an internal `remake` type function, which...