Cythonized files now deleted after setup. (closes #667 / #629)

[mnmelo]

Default behavior now depends on release or dev status. When in dev mode
default is to use Cython and delete cythonized files. When in release
mode default is to skip Cython but keep existing cythonized files.

setup.py now reads the version string directly from version.py.

Environment variable handling in setup.py enhanced to recognize strings
with boolean meaning.

I tried to keep the burden on the release manager to a minimum:

• The version string now only needs to be set in version.py;
• For a release build, generating the cythonized files for shipping is as easy as issuing:

MDA_USE_CYTHON=1 python setup.py build

• For a development build cythonized files are generated by default, and deleted after compilation. To keep them just run:

MDA_KEEP_CYTHONIZED=1 python setup.py build

[richardjgowers]

Does this always work even when the package is installed in weird ways? Ie is MDAnalysis/version.py always there? Or would it be better to use resource_filename like we do with the test files?

[mnmelo]

After I submitted I realized that this is relatively fragile (the tests' setup.py can't do the same, for instance). It was mostly a convenience so that you'd only need to change the version string in one place. It's not even directly related to the issue at hand.
I'll revert it.

[richardjgowers]

If we're removing the pyx->c files from develop, doesn't that need to be done in this PR?

[jbarnoud]

@richardjgowers It would make sense indeed.

[mnmelo]

Duh... git add no longer adds deletions by default and I didn't pay attention to the warning notice.

One important aspect:
From what I could gather, the release process that @richardjgowers follows involves updating version strings and documentation on develop and then merging into master. This means that there are brief points in develop history with non-dev version strings (see tag release-0.13.0, for instance).

Any work branched from one of these release points carries the non-dev version string. Since this PR changes behavior based on those strings, devs might run into non-obvious inconsistencies.
I don't know if this is a showstopper to my changes, or if we should become more consistent about the version strings (perhaps by only updating them in master, after merging develop).

[richardjgowers]

@mnmelo so that's correct, but I only ever push a dev suffixed version to develop, so you'd have to put effort in to branch from there.

No worries about the version number, 2 places is ok

[mnmelo]

Ok, with that out of the way this should be done (I didn't add anything to CHANGELOG, as this is a dev-side change. Let me know if you think I should).

[jbarnoud]

There something to do with the travis build. It make no sense anymore to have a no-cython build. Having two build continue to make sense, though, to have a full and a minimal dependency builds.