Add linting

[mikemhenry]

trafficstars

Developers certificate of origin

• [x] I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[mikemhenry]

black 120 chars

[codecov[bot]]

Codecov Report

Attention: 205 lines in your changes are missing coverage. Please review.

Comparison is base (60a5eca) 93.73% compared to head (804a657) 91.89%.

Files	Patch %	Lines
openfe/utils/handle_trajectories.py	0.00%	36 Missing :warning:
...tests/protocols/test_openmm_equil_rfe_protocols.py	86.34%	31 Missing :warning:
...enfe/protocols/openmm_rfe/_rfe_utils/multistate.py	51.11%	22 Missing :warning:
openfe/analysis/plotting.py	50.00%	16 Missing :warning:
openfecli/commands/gather.py	65.11%	15 Missing :warning:
openfe/tests/protocols/test_openmm_afe_slow.py	26.31%	14 Missing :warning:
.../protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py	64.86%	13 Missing :warning:
openfe/protocols/openmm_rfe/equil_rfe_methods.py	88.09%	10 Missing :warning:
openfe/protocols/openmm_utils/omm_settings.py	82.75%	10 Missing :warning:
openfe/tests/protocols/conftest.py	79.48%	8 Missing :warning:
... and 16 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #723      +/-   ##
==========================================
- Coverage   93.73%   91.89%   -1.84%     
==========================================
  Files         133      133              
  Lines        9650     9645       -5     
==========================================
- Hits         9045     8863     -182     
- Misses        605      782     +177     

Flag	Coverage Δ
fast-tests	91.89% <89.79%> (?)
slow-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[mikemhenry]

using isort on openfe/setup/__init__.py gives me errors like

E   ImportError: cannot import name 'LomapAtomMapper' from partially initialized module 'openfe.setup' (most likely due to a circular import) (/home/mmh/Projects/openfe/openfe/setup/__init__.py)

[IAlibay]

From today's call: to be discussed in an upcoming power hour.

[mikemhenry]

I have the same PR on GUFE, so we can talk about linting-org wide on a power hour