Update everything to match MolSSI cookiecutter

[jchodera]

This PR overhauls the testing infrastructure to match the current MolSSI cookiecutter.

logsumexp has been moved form scipy.misc to scipy.special.

cc: choderalab/yank#1162

• Implement feature / fix bug
• Add tests
• Update documentation as needed
• Update changelog

[jchodera]

The one deviation (I know of) is that I'm still using nosetests here since it would take considerable effort to convert all the test generators over to pytest right now.

[jaimergp]

I haven't tried, but pytest should be able to run nosetests just fine.

[andrrizzi]

The main problem for the conversions will be the many nose generators using yield. As far as I understand, pytest's support for those is shaky.

[andrrizzi]

Looks great, thanks so much! The tests are currently failing but it looks just a missing dependency so far.

[andrrizzi]

I think we'll have to add also nose-timer here to get the --with-timer option working.

[jchodera]

@andrrizzi : Interestingly, we're now seeing segfaults in a different place!

Test method AlchemicalState.apply_to_context. ... python(2864,0x7fff8a436340) malloc: *** error for object 0x7fb943705c38: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug