replaced bondgraph with networkx

chrisiacovella commented 1 year ago

PR Summary:

Related to PR #1084

Basically, the bond graph is replaced with networkx.

PR Checklist

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

chrisiacovella commented 1 year ago

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[bot] commented 1 year ago

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 :warning:

Additional details and impacted files

```diff @@ 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 commented 1 year ago

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

daico007 commented 1 year ago

https://github.com/actions/runner-images/issues/6680

CalCraven commented 1 year ago

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?

mosdef-hub / mbuild