Documentation improvements

[jchodera]

I wanted to start a thread to discuss what additions/changes to the excellent documentation Kyle has started [http://pymbar.readthedocs.org] we might want now or in the future.

Some quick things:

• I think I'll need to update the version available via the PyPI, last updated 11 Aug 2013: https://pypi.python.org/pypi/pymbar/2.0.1-beta Any thoughts on what sort of numbering/naming/revision scheme we should be using, since each version on PyPI must be a unique version number?
• I think we can mention on the Getting Started page that easy_install pymbar should also work.
• We should add some tutorials illustrating the application to the example systems we have in pymbar-examples that will eventually form the foundation for what we've been colloquially referring to as the "MBAR for Dummies" page.
  @mrshirts : What do you think we should focus on first, and how should the tutorials be structured? @kyleabeauchamp : Do you want to be the lead author on that paper, since this would also be a nice way for you to get credit for what you've done here? The notes for that paper are here in the old svn: https://simtk.org/websvn/wsvn/pymbar/manuscripts/#_manuscripts_
• Rework main README.md to also include reference to the online documentation or potentially just direct the user there (to remove redundancy).

[rmcgibbo]

Version numbering: http://semver.org/

Sent from my iPhone

On Sep 11, 2013, at 4:31 AM, John Chodera notifications@github.com wrote:

I wanted to start a thread to discuss what additions/changes to the excellent documentation Kyle has started [http://pymbar.readthedocs.org] we might want now or in the future.

Some quick things:

I think I'll need to update the version available via the PyPI, last updated 11 Aug 2013: https://pypi.python.org/pypi/pymbar/2.0.1-beta Any thoughts on what sort of numbering/naming/revision scheme we should be using, since each version on PyPI must be a unique version number? I think we can mention on the Getting Started page that easy_install pymbar should also work. We should add some tutorials illustrating the application to the example systems we have in pymbar-examples that will eventually form the foundation for what we've been colloquially referring to as the "MBAR for Dummies" page. @mrshirts : What do you think we should focus on first, and how should the tutorials be structured? @kyleabeauchamp : Do you want to be the lead author on that paper, since this would also be a nice way for you to get credit for what you've done here? The notes for that paper are here in the old svn: https://simtk.org/websvn/wsvn/pymbar/manuscripts/#_manuscripts_ — Reply to this email directly or view it on GitHub.

[jchodera]

Awesome, thanks @rmcgibbo !

[kyleabeauchamp]

Per discussion, we have decided:

1. For 2.0, we make minimal changes necessary to have useful docs (probably readthedocs.org)
2. For 3.0, we make more full-featured docs in the style of MDTraj with Notebooks.

[jchodera]

Was this addressed by #69?

[kyleabeauchamp]

No, we still need to figure out how we want to divide things between:

1. readthedocs
2. README.md
3. Example python scripts