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

Base: 90.64% // Head: 89.37% // Decreases project coverage by -1.27% ⚠️

Coverage data is based on head (898c7a9) compared to base (7092d58).
Patch coverage: 81.25% of modified lines in pull request are covered.

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     

Impacted Files	Coverage Δ
mbuild/lib/recipes/silica_interface.py	15.38% <0.00%> (-84.62%)	⬇️
mbuild/bond_graph.py	37.50% <100.00%> (-51.64%)	⬇️
mbuild/compound.py	96.77% <100.00%> (-0.10%)	⬇️
mbuild/lib/bulk_materials/amorphous_silica_bulk.py	42.85% <0.00%> (-57.15%)	⬇️

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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?