GraphMakie docs update

[vyudu]

Update docs and drop Graphviz dependency. Ran into an issue on my machine where ExpandTemplates was hanging for a really long time, so I changed some of the @example blocks to just ```julia, but it was still sort of hanging on the machine so not sure what's happening. In any case wanted to see how it did on the CI.

[isaacsas]

You need to also update all the places in the current docs where we show graphs to use the new code (preferably dynamically).

[isaacsas]

GLMakie tests are failing?

[vyudu]

seems something GLFW-related, happening in the docs build too. Will probably debug tomorrow

[isaacsas]

ok

[isaacsas]

Seems like somehow the plot from Makie is getting loaded now even in tutorials that don't use Makie for plotting?

[vyudu]

seems like it was because GLMakie is loaded in that @example block, added an explicit import to fix

[vyudu]

Let's see how these look. I need to think about how to reduce the amount of whitespace though. I think it should do a bit better with Stress() but it might not be good enough.

[vyudu]

Removed most of the GLMakie instances in the docs but there's still a GLMakie instance in the interactive Brusselator doc.

[isaacsas]

There shouldn't be in an @example block, that is just in a @julia block.

[isaacsas]

(I removed all GLMakie doc dependencies last week I thought.)

[vyudu]

Check the last two commits, I changed a couple instances there? But let me know if I did something wrong

[isaacsas]

@vyudu looks like there are some text tweaks needed for the new colors / removal of labels, then this should be good.

[isaacsas]

Looks like there is a bad link in one of the new doc files?

[isaacsas]

Oh, this needs to also remove this stuff in Catalyst.jl that loads the GraphViz.jll:

Catalyst.jl/src/Catalyst.jl

Lines 63 to 74 in b7d8c61

	# as used in Catlab
	const USE_GV_JLL = Ref(false)
	function __init__()
	@require Graphviz_jll="3c863552-8265-54e4-a6dc-903eb78fde85" begin
	USE_GV_JLL[] = true
	let cfg = joinpath(Graphviz_jll.artifact_dir, "lib", "graphviz", "config6")
	if !isfile(cfg)
	Graphviz_jll.dot(path -> run(`$path -c`))
	end
	end
	end
	end

[vyudu]

Hmm I can't find the new bad link, it's supposedly in api.md but I don't see a [``ReactionComplex\``](@ref) in api.md.

[isaacsas]

Is it linked via a docstring?

[vyudu]

Ah I see. But in that case I don't know why it's resolving to Main or CatalystGraphMakieExtension and not looking in Catalyst.

[isaacsas]

This worked completely fine before (for example, the current docs). Why would this be the underlying issue?

[vyudu]

Hm yeah this doesn't make sense. But I don't understand what could cause the error it raises otherwise, will keep looking.