Maintenance and fixes and additions on vis::Graphs and its users

[jurgenvinju]

• improvements to the general graph framework
• do not overwrite dagre defaults with our own
• cleanup

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 46%. Comparing base (8ae6ced) to head (022df26).

Additional details and impacted files

@@           Coverage Diff           @@
##              main   #2769   +/-   ##
=======================================
- Coverage       46%     46%   -1%     
  Complexity    6726    6726           
=======================================
  Files          794     794           
  Lines        65936   65936           
  Branches      9888    9888           
=======================================
- Hits         30856   30852    -4     
- Misses       32690   32700   +10     
+ Partials      2390    2384    -6     

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[DavyLandman]

Looks good, my main concern is the inclusion of the cytoscape-dagre.js file in the repo.

[DavyLandman]

Why do we now ship the cytoscape file? It's a bit suprising to me that a fix PR changes how we run cytoscape.

I mean, I would not mind if we don't have this online dependency in our graph code, but then there are some cleaner ways to package this (like part of a maven phase that automatically downloads dependencies from npm).

Also, what is the license of this external file?

Looks like this PR should wait for cytoscape/cytoscape.js-dagre#163 to get merged and released? (which could be soon it looks like it)

[jurgenvinju]

1. I expect the merge to take several weeks.
2. I had issues running this code without a network. The online dependency sucks, however that also goes for the entire cytoscape.js library. I wasn't ready to make that decision yet, but this cytoscape-dagre.js code is now more lines of us than the original so I felt safe to copy it in.
3. I don't know what the wise decision is here. It's a trade-of. But for now we can include it and test it locally. When cytoscape.js-dagre is released we have a choice to make.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud