Fix logging across scilpy

[frheault]

Thanks to Laurent I realized that scil_search_keywords.py stopped working.
It was due to the fact that setting logging to INFO or DEBUG the way we did (everywhere in Scilpy) does not work anymore.

So it also meant that around 70% of our logging was not working properly (WARNING is fine, because it was the default for the root::logging).
So I fixed it everywhere.

I also added a pytest.ini to print warnings from other libraries only once and keep all warnings from Scilpy (even if many) reducing printed line from 1M to

PS: A few pep8 changes got in there while saving files, a few scripts didn't have permissions like everything else (777) so I changed it for uniformity.

[arnaudbore]

Build passed ! Good Job 🍻 !

[arnaudbore]

Build passed ! Good Job 🍻 !

[frheault]

Ok so now the pytest.ini is more explicit and ignore all major import except a few that will display once.

The idea is that we will never care about issues in scipy or numpy, but we might care about trimeshphy, commit or dipy, and we will always care about scilpy.

[arnaudbore]

Build passed ! Good Job 🍻 !

[frheault]

So the total output of tests on Travis is now less than 1000 (including the checkout, build, tests and warning)
= 368 passed, 76 warnings in 2029.82s (0:33:49) =

[arnaudbore]

Build passed ! Good Job 🍻 !

[AntoineTheb]

One comment but otherwise LGTM !

[AntoineTheb]

Why is lazy_streamlines_count no longer imported ? Was it unused before ?

[frheault]

I am setting up my new computer and my autopep8 settings had too much power I think.

[EmmaRenauld]

I tested the pytest locally and, man!! Nice! So much easier! Takes a lot less time, too.