Sam Isaacson
Sam Isaacson
- https://docs.sciml.ai/Catalyst/dev/catalyst_functionality/parametric_stoichiometry/ Once https://github.com/SciML/ModelingToolkit.jl/issues/2296 is fixed we need to add a test for ensuring mixed parameter types are preserved going forward.
Which means they are not usable programmatically within code. For example ```julia @variables t @species A(t) B(t) a = A @compound AB a B # errors @compound AB $a B...
To aid users who may not know what can be done in such environments.
Explain about using absolute values of rates, but that this doesn't guarantee the solution stays positive.
Once https://github.com/domluna/JuliaFormatter.jl/issues/741 is settled and a new style is released we need to reformat the repo. It will likely impact almost every file. As that PR points out the most...
In https://github.com/SciML/Catalyst.jl/pull/609 I had to disable Latexify tests as `Latexify.@generate_test` doesn't seem to generate tests that pass anymore. We should investigate this and if there is a fix at some...
@TorkelE pointed out that on a multisite phosphorylation benchmark where species can have many phosphorylation states, we are starting to lose performance relative to network-free methods as the number of...
NRM and CoEvolve are often bottlenecked by the cost of updating next event times within their data structures. I suspect swapping out the indexed priority queue we use for another...
Adds Aqua test, seems to indicate that https://github.com/SciML/JumpProcesses.jl/issues/384 is fixed. @Vilin97 the Aqua test is giving a bunch of method ambiguities coming from the spatial mass action jump constructors. I...
Right now we only call `reset_aggregated_jumps!` when parameters are modified via `remake` or `jprob[:psymb]`. I don't think mutating `jprob.prob.p` directly will correctly lead to `MassActionJump`s getting updated.