More api consistency

[hejung]

• asyncmd.utils methods now all require a MDEngine (class) to dispatch to the correct engine submodule
• take care of some pylint warnings

[codecov]

Codecov Report

❌ Patch coverage is 87.50000% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.08%. Comparing base (233d847) to head (4b06d58).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
src/asyncmd/gromacs/utils.py	40.00%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
+ Coverage   79.02%   79.08%   +0.05%     
==========================================
  Files          23       23              
  Lines        2455     2462       +7     
  Branches      316      318       +2     
==========================================
+ Hits         1940     1947       +7     
  Misses        421      421              
  Partials       94       94              

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