Update Planckton to use HOOMD 3

[gwenwhite]

This is a work in progress and is NOT ready to be merged. Just creating the pull request so discussions/questions can be added along the way.

[chrisjonesBSU]

Some things left to do:

1. Fix e-factor implementation
2. Update wall time check using hoomd3's wall time API
3. Update versions in environment files

[codecov[bot]]

Codecov Report

Merging #94 (8a25f20) into master (555067d) will decrease coverage by 0.50%. The diff coverage is 95.38%.

:exclamation: Current head 8a25f20 differs from pull request most recent head 144e8b0. Consider uploading reports for the commit 144e8b0 to get more accurate results

Additional details and impacted files

[](https://codecov.io/gh/cmelab/planckton/pull/94?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) ```diff @@ Coverage Diff @@ ## master #94 +/- ## ========================================== - Coverage 98.07% 97.58% -0.50% ========================================== Files 6 5 -1 Lines 208 207 -1 ========================================== - Hits 204 202 -2 - Misses 4 5 +1 ``` | [Impacted Files](https://codecov.io/gh/cmelab/planckton/pull/94?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) | Coverage Δ | | |---|---|---| | [planckton/sim.py](https://codecov.io/gh/cmelab/planckton/pull/94?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab#diff-cGxhbmNrdG9uL3NpbS5weQ==) | `95.60% <95.38%> (-0.91%)` | :arrow_down: |