Documentation improvements and related changes

[mwaskom]

This is primarily an update of the docs, moving to a thumbnail-based example gallery (closing #69) and making a new, simpler example for using volume-based data more prominent in the set of examples. I also tweaked a number of the existing examples, primarily to improve the choices of colors (banishing the jet colormap once and for all from the example gallery). I also unified the license throughout the package, closing #67.

The one outstanding thing I'd like to have in the docs is a page on how the hell to use PySurfer on OSX (i.e. #68). I don't feel like I have a great solution to the problem, although "use Canopy and set the ETS_TOOLKIT environment variable sounds like the best option to recommend; I did all this development on Anaconda which works, sort of, with the hack Denis shared (although I have not had to build matplotlib from source).

I ran into an issue where io.Surface was being used (but not imported) in the utils module (for the label generation function). For some reason there is an issue with doing a relative import of the io module. I ended up moving the Surface class to utils, which sort of makes more sense anyway. I expect that we can deprecate io in 0.5 and probably remove it altogether in 0.6.

Since I didn't change anything that would make the docs not correspond to the 0.4 version, I'll probably push them to the main site soon, but I'm currently serving (and will continue to serve) a development version of the docs on my Stanford page

[agramfort]

looks great to me. Some remarks:

• I don't like having Surface in utils.py. How about surface.py ?
• the install.rst page should be extended as you suggest (Mac OS X how to etc.)

nice work !

[mwaskom]

I am not wild about Surface in utils.py either but splitting it off into surface.py (or leaving it in io.py, I think this was my problem yesterday, built-in names being a red herring) runs into circular import issues where Surface needs the _get_subjects_dir function from utils, but utils needs Surface to do things.

I cannot figure out a way to deal with the circular import, although I am pretty close to putting my head through a wall.

[agramfort]

feel free to merge and open an issue with what's left to be done.

I'll try to take a stab at moving surface from utils.py

[agramfort]

just one thing.

why the pysurfer_logo_small.eps ? it's 6.6 MB in the repo.

if you're ok I'll remove it before anybody pulls from upstream

[mwaskom]

oh yeah go ahead, I just dumped the whole logo_files directory I found on my old laptop into the repo. didn't think to check the sizes.

the logo_large files can actually be removed too probably, the "large" refers to the size of the lenses, not the image, and we decided to go with the small lenses for the logo.

On Sun, Nov 17, 2013 at 11:51 AM, Alexandre Gramfort < notifications@github.com> wrote:

just one thing.

why the pysurfer_logo_small.eps ? it's 6.6 MB in the repo.

if you're ok I'll remove it before anybody pulls from upstream

— Reply to this email directly or view it on GitHubhttps://github.com/nipy/PySurfer/pull/76#issuecomment-28662016 .

[agramfort]

ok I will do it now and force push (don't do this at home ...)

[agramfort]

done. You can do

git fetch upstream git checkout master git reset --hard upstream/master

let me know if it's ok

[mwaskom]

Looks OK I think, the history is a bit wonky but everything seems to be at the right state.