Basic documentation for readthedocs

[jchodera]

This PR creates basic sphinx documentation for readthedocs.

Note that this required removing an earlier aborted attempt (which contained nothing useful).

Since so many files have changed, please just review the rendered docs and the updated README.

[jchodera]

And here's the rendered product!

http://openmmtools.readthedocs.io/

[kyleabeauchamp]

Points to wrong repo here?

[jchodera]

Whoops, thanks!

[jchodera]

What's the best way to include a list of authors/contributors? Is there some way to pull this in from github?

[jchodera]

This should be ready to merge now.

The docstrings can probably use a lot of cleanup in a separate PR.
We'll especially have to figure out how signatures for subclasses that just use *args, **kwargs to pass arguments up to base classes could provide more informative signatures.

[andrrizzi]

The docs look great!

I'm not very familiar with Sphinx so I can't comment on the scripts, but the documentation looks good!

[bas-rustenburg]

One ` too many

[bas-rustenburg]

Might need to edit the highlighted section (not sure where in the files this occurs).

[bas-rustenburg]

http://openmmtools.readthedocs.io/en/latest/api/generated/openmmtools.testsystems.HostGuestImplicitHCT.html#openmmtools.testsystems.HostGuestImplicitHCT

Once you go into an API page, there doesn't seem to be a link to click back into another part of the page. The user can press the back button in the browser but could be convenient to have the table of content link there like on the other, regular pages.

Minor point, and not sure if this is easy to achieve.

[bas-rustenburg]

Minor points only. Looks like the structure is there. We can refine the content as we go. Should be helpful.

[jchodera]

Might need to edit the highlighted section (not sure where in the files this occurs).

These are docstring issues. The docstrings need some major cleanup, but that's beyond the scope of this PR.

Minor points only. Looks like the structure is there. We can refine the content as we go. Should be helpful.

That's exactly my hope.

Once you go into an API page, there doesn't seem to be a link to click back into another part of the page. The user can press the back button in the browser but could be convenient to have the table of content link there like on the other, regular pages.

I have no idea how to do this with sphinx, but if you can figure it out, that would make a great other PR.

[jchodera]

Merging this since I'm having trouble fixing the typos by pushing to this branch.