gnu: python-numpy-bootstrap, python-numpy: Fix build.

* gnu/packages/python.scm (python-numpy-bootstrap): Correct inputs, use
  modify-phases, add dummy newlines character to string to make emacs happy,
  set PYTHONPATH prior to running tests. (python-numpy): propagate inputs, set
  PYTHONPATH prior to building docs.

gnu: python-fonttools: Remove intervening directory in site-packges.

* gnu/packages/python.scm (python-fonttools): Add phase patch-setuppy.

gnu: python2-pysnptools: Correct inputs.

dateutil, pytz, and six do not occur in the code.

Remove python-dateutil, python-pytz, python-six from inputs;
Move python-cython to native-inputs; move python-pandas to
propagated-inputs.

gnu: python-zope-testing: Remove needless input.

* gnu/packages.python.scm (python-zope-testing): Remove
  python-zope-interface from native-imports.

gnu: python-zope-schema: Add missing inputs.

* gnu/packages.python.scm (python-zope-schema): Add python-coverage and
  python-nose to native-inputs.

gnu: python-pytest-flakes: Fix build.

* python.scm (python-pytest-flakes): Set PYTHONPATH prior to running tests.

gnu: python-pillow: Fix build.

* gnu/packages/python.scm (python-pillow)[check-installed]: Add
  installed site-package to PYTHONPATH.

gnu: python-singledispatch: correct inputs.

python-six is only required for conversion, not at run-time

* gnu/packages/python.scm (python-singledispatch, python2-singledispatch):
  [inputs] Move python-six to [native-inputs].

gnu: python-pbr: Rework bootstrapping.

For breaking the cyclic build, formerly a separate (older) version was used
for bootstrapping.  Now we use the same version just without tests and without
test dependencies.

* gnu/packages/python.scm (python-pbr-0.11, python2-pbr-0.11):
  replace by … (python-pbr-minimal, python2-pbr-minimal).
  (python-pbr) inherit from python-pbr-minimal, adding the requirements for
  testing and building the documentation.
  (python-fixtures) [native-inputs] Use python-pbr-minimal here.
  (python-testrepository): [native-inputs] Add it here, it was a missing
  dependency.

gnu: python-testrepositoryfixture: Correct inputs.

python-fixtures is required only for building.

* gnu/packages/python.scm (python-testrepository) [propagated-inputs] move
  python-fixtures to [native-inputs].

gnu: python-fixture: Enable tests.

* gnu/packages/python.scm (python-fixtures) [arguments] remove
  keyword `#:tests?`.

gnu: python-fixture: Correct inputs.

python-pbr is required only for building.

* gnu/packages/python.scm (python-fixtures) [propagated-inputs] move
  python-pbr-0.11 to [native-inputs].

gnu: python-hdf5: Correct inputs.

According to setup.py python-six is requried at run-time, thus has to be a
propagated input.

* gnu/packages/python.scm (python-hdf5) [inputs]: Move `python-six` to
  [propagated-inputs].

gnu: python-h5py: Remove needless "python2-variant" property.

* gnu/packages/python.scm (python-h5py) [python2-variant]: Remove
  property. (python2-h5py): Don't strip property "strip-python2-variant".

gnu: python-ccm: Update synopsis and description.

* gnu/packages/python.scm (python-ccm): Update synopsis and description.

gnu: python-ccm: Add missing input python-psutil.

* gnu/packages/python.scm (python-ccm) [propagated-inouts]: Add
  python-psutil.

gnu: python-sphinx-rtd-theme: Remove inputs.

This package is a plugin for python-sphinx, it does not require python-sphinx
nor docutils, but is an add-on for python-sphinx and should not be installed
by it's own.

* gnu/packages/python/.scm (python-sphinx-rtd-theme)[inputs]: Remove.

gnu: python-pytest-cov: Use upstream options for testing.

* gnu/packages/python.scm (python-pytest-cov): Replace phase "check"
  by one passing the options found in upstream's tox.ini-file
  to "python setup.py check".

gnu: scons: Do not use setuptools for building.

* gnu/packages/python.scm (scons): Set "#:use-setuptools" to #f.

gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.

* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
  [native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.