added logos both for light/dark modes, and updated the notebooks

[Atilaac]

Added logos based on the discussion in #196 . I have two versions of the logo, one normal for light backgrounds and the other inverted for dark backgrounds. I tested it locally, and it works.

I also updated the notebooks in docs to reflect the changes and enable interactive Plotly plots.

I can select one reviewer thus I am adding you here in the text of the PR @Gitdowski

[github-actions]

[ltalirz]

Moved it to the sidebar

P.S. The night-mode effect with the white network is pretty cool...

[Atilaac]

this looks amazing, thanks @ltalirz

[ltalirz]

I have two nitpicks

• If you zoom into the structure, the circles and lines are not actually circles and lines. This was not the case for the first version of the logo, which did look like it was a png generated from an SVG. Did you get the later SVGs by tracing the PNG? I wonder whether there is a way to get the actual geometrical forms in the SVG (would also make the SVG itself much less complicated).

• In the screenshot above there is a small version of the logo next to the amorphouspy text in the blue top bar, but it's not recognizable. We can make it a bit larger by removing the text (and I think we should have such a version of the logo for favicons), but it will still be very small and the wrong color, i.e. we could drop it from there.

[Atilaac]

1. the svg is generate by tracing a png. The only way I am aware of is to recreate the logo by adding lines and circles manually.

2. I did not see it until you mentioned it.

[ltalirz]

Where did you get this version of the logo from?

[ltalirz]

It looks like whatever generated it has an SVG representation of it

[Atilaac]

I use a prompt for gemini to make it.

[Atilaac]

What about this! I have an avg image of this and Python code that we can modify? the colors need to change but look at the shape only

[Atilaac]

here is a newer version with slightly curved bond

[ltalirz]

Thanks @Atilaac - I liked the "brain"-like outline of the first logo (it works better together with the tagline), and also the somewhat "open" structure towards the outside (symbolizing that this is just part of a network)

If you can recreate this + the colors from the first logo in python easily, let's see it
(in python we of course have the advantage that we can reduce the complexity of the network relatively easily)

But let's not spend too much time on it now. If you are ok with an update to the logo later (e.g. before the JOSS publication), we can also go with what we have so far

[Atilaac]

I am fine with an update later. Anyway, I need to finish my slides so I can share them with you on time.

I can recreate the first one later on in Inkscape, no need for Python code; it will take some time, but it is doable.

Thanks again for the comments and input.

[ltalirz]

Cheers, then feel free to merge