[MNT] clean up and comment dep sets in pyproject.toml, remove unused graph dep set from CI

[fkiraly]

Cleans up dependency management without making changes to existing dep sets.

• create new dep set all_extras containing all used soft dependencies
• reorder dep sets in pyproject.toml and and comments about their usage
• remove unused graph dep set from installations in CI - the contained networkx package is never imported within the code base

[codecov-commenter]

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.20%. Comparing base (81aee66) to head (c099bf0).

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Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1650   +/-   ##
=======================================
  Coverage   90.20%   90.20%           
=======================================
  Files          32       32           
  Lines        4729     4729           
=======================================
  Hits         4266     4266           
  Misses        463      463           

Flag	Coverage Δ
cpu	90.20% <ø> (ø)
pytest	90.20% <ø> (ø)

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