replaced bondgraph with networkx

[chrisiacovella]

PR Summary:

Related to PR #1084

Basically, the bond graph is replaced with networkx.

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[chrisiacovella]

Tests for converting to gmso will fail until we can push a PR with updates to the gmso conversion functions, but all tests pass on my local machine (with updated gmso routines).

[codecov]

Codecov Report

Attention: Patch coverage is 81.25000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 89.37%. Comparing base (7092d58) to head (898c7a9).
Report is 96 commits behind head on main.

Files	Patch %	Lines
mbuild/lib/recipes/silica_interface.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1087      +/-   ##
==========================================
- Coverage   90.64%   89.37%   -1.27%     
==========================================
  Files          61       61              
  Lines        6240     6164      -76     
==========================================
- Hits         5656     5509     -147     
- Misses        584      655      +71     

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[daico007]

Did some digging and googling, I think the failing test probably memory related (known issue with networkx graph of complicated graph)

[daico007]

actions/runner-images#6680

[daico007]

LGTM!

[CalCraven]

Minor changes, and one major change if we deem it worthwhile to try to make the bondgraphs as fast as possible. If we want this connected_components change, I will open the PR in GMSO that will allow the 5 tests to pass in mBuild.

[CalCraven]

Okay, as soon as the CI get's figured out this is good to go. Can we make a change to mbuild/.github/workflows/CI.yaml, such as this line, to skip over that test?