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follow up on incorporating pyGSM into workflow #51

@joshkamm

Description

@joshkamm

Follow up things that didn't get addressed in #45 and #54:

  • See if github actions has a UGE setup action to test with UGE job queue
  • Clean up tests/test_gsm.py which is serving basically the same purpose as examples/suzuki.py. Actually I might end up using test_conf_gsm.py as the basis for suzuki.py in which case this will change.
  • Conformer generation / ensemble optimizer test (try setting environment variables which are accessed at import time pytest-dev/pytest#10027 (comment))
  • Deal with "HARDCODED TO SPECIFIC TEST MOLECULE" in gsm.py
  • Deal with "I think this should check if any of the conformers have DFT energies but this is only checking the last one" in main.py
  • Combine single and double ended methods in gsm.py
  • Merge tests / CI branch into pyGSM
  • pyGSM issue for the write_std_multixyz seemingly using an incorrect unit conversion assuming starting from kJ/mol when it's actually kcal/mol. It would seem to make more sense for a write function to use whatever units it is given
  • Improve the pyGSM error message when the fragments aren't contiguous
  • Streamline pyGSM installation including fixing why I have to append the pygsm folder to the python sys.path
  • Can you edit issues with gh desktop?
  • Clean up scratch files from pyGSM in personal directory
  • Update documentation
  • Update tests
  • Look through pull request changes
  • Clean up code and retest
  • Increment version number

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