Bring multistate samplers into openmmtools

[jchodera]

This PR brings multistate samplers and the FIRE minimizer from YANK into openmmtools.

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

[jchodera]

I've enabled sphinx builds for this branch, but it looks like they are failing:
https://readthedocs.org/projects/openmmtools/builds/8453444/

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/openmmtools/conda/multistate/lib/python3.7/site-packages/sphinx/registry.py", line 472, in load_extension
    mod = __import__(extname, None, None, ['setup'])
ModuleNotFoundError: No module named 'sphinxcontrib.bibtex'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/openmmtools/conda/multistate/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/openmmtools/conda/multistate/lib/python3.7/site-packages/sphinx/application.py", line 228, in __init__
    self.setup_extension(extension)
  File "/home/docs/checkouts/readthedocs.org/user_builds/openmmtools/conda/multistate/lib/python3.7/site-packages/sphinx/application.py", line 449, in setup_extension
    self.registry.load_extension(self, extname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/openmmtools/conda/multistate/lib/python3.7/site-packages/sphinx/registry.py", line 475, in load_extension
    raise ExtensionError(__('Could not import extension %s') % extname, err)
sphinx.errors.ExtensionError: Could not import extension sphinxcontrib.bibtex (exception: No module named 'sphinxcontrib.bibtex')

Extension error:
Could not import extension sphinxcontrib.bibtex (exception: No module named 'sphinxcontrib.bibtex')

Looks like we need to add sphinxcontrib-bibtex to docs/environment.yml.

[hannahbrucemacdonald]

Will add that now, missed it because there's no docs/environment.yaml in yank

[hannahbrucemacdonald]

Will try figure out why the python 3.7 travis build is seg faulting, but I can't reproduce it locally

[andrrizzi]

That may be a known problem, see #192 . I've never been able to figure out a work-around (beside restarting the Travis tests). It seems more of a Travis+SWIG+nosetests problem than a real issue.

[jchodera]

You don't think switching to pytest would help, would it?

[hannahbrucemacdonald]

You don't think switching to pytest would help, would it?

Happy to try switching over. I think the tests that use yield will need to be updated

[andrrizzi]

You don't think switching to pytest would help, would it?

Possibly, I'm not sure. I'm still getting familiar with pytest's features so I can't really give an estimate about how much time the conversion will take.

[jchodera]

Maybe we can do that switch as part of a larger overhaul to conform to the latest cookiecutter structure, after @andrrizzi has more time to get familiar with it?

[jchodera]

Multistate sampler docs are being built and pushed to this branch of readthedocs. You can see the API docs here.

[jchodera]

This is almost ready to be merged, @andrrizzi. I'm just solving some problems with SAMS tests that use the currently-unsupported non-global jumps, but I might just change that to global jump only and punt the rest of the local jump to later.

[jchodera]

Correction: The failing tests are with SAMS and global jump, and started when we upgraded the NetCDF libraries to a version that uses masked arrays by default. However, I think this may have revealed a bug in the old SAMS analysis implementation. Will be important to see if we can fix this.

[jchodera]

I think I've sorted this. If tests pass, this should be ready to merge.

[jchodera]

Yay! Travis tests pass now.

Windows tests fail because drand48() doesn't exist in windows, and this causes the cython compile of _mix_replicas to fail. We can later fix this by instead using the C++11 standard library, but we aren't supporting windows now.

[jchodera]

The docs build on readthedocs now!
The travis failure is the stochastic barostat segfault, so I'll merge this now.