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SciML / Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
https://docs.sciml.ai/Catalyst/stable/
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Drop Graphviz and requires #512

Open isaacsas opened 2 years ago

isaacsas commented 2 years ago

We need to find an actively maintained / developed graph plotting library to switch to though. GraphMakie.jl seems active, but that would pull in Makie (unless we split out the graph functionality to a sub-library like CatalystGraphs).

ChrisRackauckas commented 2 years ago

A graph viz sub package isn't a bad idea.

isaacsas commented 2 years ago

Looks like GraphViz may be fixed now too: https://github.com/JuliaPackaging/Yggdrasil/issues/1428, if so we can drop requires for it.

isaacsas commented 2 years ago

This will have to wait on https://github.com/JuliaPackaging/Yggdrasil/issues/4961 as I can't play with using the jll currently.

longemen3000 commented 1 year ago

https://github.com/JuliaPackaging/Yggdrasil/issues/4961 is fixed, what about moving the __init__ function into an extension?

isaacsas commented 1 year ago

Last I checked, on some platforms the Graphviz artifact is fine but on others it still has issues (i.e. last time I looked it wasn't working via artifacts on macs). Do you have any issues the current approach is causing?

Honestly though, I'd prefer to just completely drop Graphviz entirely and switch to a native-Julia plotting approach if/when there are reasonably maintained libraries. When we set this up there didn't seem to be anything, but perhaps that has changed in the last year.