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Added support for CRN graph plotting with Graphviz #21

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merged 11 commits into from
Apr 22, 2024
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Hooks into Catalyst's Graphviz interface to allow for plotting CRN graphs directly from SpeciesData/RxData CRNs.

This required a bit of a rewrite of Catalyst's main graphing function, as it doesn't support working with ReactionSystems based on Symbolics.jl's 'arrays of symbolic expressions' (see here for more details) due to missing name fields for species symbols.

This also adds onto the functionality present in Catalyst by allowing for passing Graphviz attributes through to the plotter, enabling greater customisability and, very importantly, a choice of layout engine since Catalyst's default for directed graphs (dot) scales very poorly to large CRNs.

@joegilkes joegilkes merged commit 438c123 into main Apr 22, 2024
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@joegilkes joegilkes deleted the crn-graphs branch April 22, 2024 21:06
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