add automated testing of notebooks about an-introduction-to-applied-bioinformatics

[gregcaporaso]

Thanks for the links @ElBrogrammer. runipy does look pretty handy.

[jairideout]

I've started working on this using runipy and ran into a possible issue:

In programming-and-se/3-lists-and-loops.ipynb, there's a cell that intentionally raises an error to illustrate a concept. There isn't enough information to tell that this is an intentional failure and not a legitimate error in a notebook. @gregcaporaso is this notebook going to be removed in the near future? Do you foresee iab having more cases like this in the future?

[gregcaporaso]

All of the python programming notebooks are going to be removed, and that's not something that we'll need to support in the future. If it helps, I can remove them now (didn't want to before because we were still going through them in class, but I finished that section).

[jairideout]

Sure, that'd be great. If you don't have time, just let me know what ones can be removed and I'll delete them in my upcoming PR.

[gregcaporaso]

I can do it, I'm going to move them to a gist or another repo because they
are useful for teaching, but just outside the scope of this project (and I
don't care about CI testing for them, etc).

On Thu, Apr 10, 2014 at 1:37 PM, Jai Ram Rideout
[email protected]:

Sure, that'd be great. If you don't have time, just let me know what ones
can be removed and I'll delete them in my upcoming PR.

Reply to this email directly or view it on GitHubhttps://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/issues/20#issuecomment-40135032
.

[jairideout]

Cool, thanks!

[gregcaporaso]

Merged this change. (Still early enough in this project that I don't think strict review of all PRs is necessary - once it stabilizes I will switch to that model.)

[jairideout]

Thanks, and agree re: merging your own PRs this early on.