[cctbxbb] Tidy up CCTBX

[Marcin Wojdyr]

Hi Graeme,

> Turns out that the assert that libtbx has no dependencies is not strictly true:
>

>   if (not libtbx.env.has_module(name="phenix")):
>     print "phenix module not available: skipping advanced tests"
>     return

This is optional dependency (cctbx optionally uses Phenix for testing
in various places) and doesn't cause problems.
If you'd like to do disentangling, dxtbx-iotbx would be a good
starting point as it really causes problems.