New ability to create a Jupyter/Ipython notebook instead of the analyze script

[Lnaden]

This does not auto-render, but it does auto generate based on the settings.

This commit includes:

• Template Jupyter Notebook used to construct new ones
• Example notebook fully rendered with real data (can be removed from repo once approval is done)
• Updated version to 0.15.1
• Automatically include the template ipython notebook in the installed repo
• Template is fully load even if YANK is installed as .egg

[andrrizzi]

So cool! I could only spot few typos in the template/example notebook (I can't point them in the diff):

• manditory -> mandatory
• therefor -> therefore
• yeild -> yield
• nubmer -> number

In the future, we could make it even cleaner by encapsulating some of the code in the notebook in functions in a separate report.py module.

[andrrizzi]

We could also pre-render the notebook if we let the user specify the mandatory settings through the CLI with something like this.

[Lnaden]

pre-rendering is something I wanted to have also, but figured it could wait until we further detailed what we wanted in this report. Besides the matplotlib-fu to get the pictures of what analyze is doing, are there other features you can think of that we want in the report on this initial commit?

[andrrizzi]

are there other features you can think of that we want in the report on this initial commit?

Not that I can think of.

[jchodera]

This is great!

I'd move as much of the analysis code to Yank/analysis.py as possible in order to have the notebook really focus on the data presentation rather than the data analysis.

[Lnaden]

I'm not quite sure I follow. All of the data crunching is handled by the analyze.py module. Unless you are referring to the last code cell where its running through a subset of commands the analyze() function does. I can refactor the analyze.py script to avoid some of that code duplicate if that is what you are referring to.

The rest of the code is matplitlib-fu and formatting.

[jchodera]

Plotting and formatting code can also be included into analyze.py (or even notebook.py) to minimize the code needed in the notebook, couldn't it?

[Lnaden]

That is a good point. I'll work to bring all that code into a .py file somewhere. to minimize what is in the notebook.

[Lnaden]

@jchodera I have split all of the notebook functions into a new module class which handles all the formatting. Is this more what you had in mind for the notebook?

I also think that we can make improvements on this from here if this initial report looks good.

[jchodera]

@jchodera I have split all of the notebook functions into a new module class which handles all the formatting. Is this more what you had in mind for the notebook?

This is perfect! It looks much cleaner now.

I also think that we can make improvements on this from here if this initial report looks good.

Agreed!

[Lnaden]

Great! I also got some input from the people here for improvements we can make with additional details. For now though, Merging!