gnu: linkchecker: Do not set PYTHONPATH.

* gnu/packages/web.scm (linkchecker): Remove trailing #t.
[phases]: Do not reorder the check phase after the install phase.
{check}: Do not set PYTHONPATH.

gnu: python-cffi: Do not set PYTHONPATH.

* gnu/packages/libffi.scm (python-cffi): Remove trailing #t.
[phases]{check}: Do not set PYTHONPATH.

gnu: python-xmlschema: Do not set PYTHONPATH.

* gnu/packages/xml.scm (python-xmlschema): Remove trailing #t.
[phases]{check}: Do not set PYTHONPATH.

gnu: python-loompy: Do not set PYTHONPATH.

* gnu/packages/bioinformatics.scm (python-loompy)
[phases]{check}: Do not set PYTHONPATH.

gnu: python-scanpy: Do not set PYTHONPATH.

* gnu/packages/bioinformatics.scm (python-scanpy)[phases]
{check}: Do not set PYTHONPATH.

gnu: python-screed: Adjust following Python build system changes.

* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no
longer necessary.

gnu: bamm: Update following changes to the Python build system.

* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t.
[phases]{check}: Override rather than delete phase.  Remove trailing #t.
{post-install-check}: Delete phase.
{wrap-executable}: Also wrap with the new GUIX_PYTHONPATH.

gnu: python-pysam: Adjust following Python build system changes.

* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the
'#:modules' argument.
[phases]: Remove trailing #t.
{check}: Do not manually set PYTHONPATH.

gnu: python-pybedtools: Streamline following Python build system changes.

* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.

gnu: intel-xed: Adjust build phase.

* gnu/packages/assembly.scm (intel-xed)
[phases]: Delete trailing #t.
{build}: Do not read PYTHONPATH from environment.

gnu: solaar: Do not read PYTHONPATH from environment.

* gnu/packages/admin.scm (solaar)
[phases]{setenv-PATH}: Do not read PYTHONPATH from environment.

gnu: python2-virtualenv: Fix build.

* gnu/packages/python-xyz.scm (python2-virtualenv)[arguments]{phases}: Remove
argument.

gnu: python2-packaging-bootstrap: Add missing dependency

* gnu/packages/python-xyz.scm (python2-packaging-bootstrap)
[propagated-inputs]: Add python2-six-bootstrap.

gnu: python-traceback2: Add missing dependency.

* gnu/packages/python-xyz.scm (python-traceback2)[propagated-inputs]:
Add python-six.

gnu: python-packaging-bootstrap: Remove dependency.

* gnu/packages/python-xyz.scm (python-packaging-bootstrap) [arguments]:
Remove dependency from setup.py, which we do not provide for this
variant.

gnu: python-automat: Remove broken console script.

* gnu/packages/python-xyz.scm (python-automat) [arguments]: Patch
setup.py.

gnu: python-twisted: Remove broken console scripts.

* gnu/packages/python-xyz.scm (python-twisted) [arguments]: Patch
setup.py.

gnu: python-idna-ssl: Add missing input.

* gnu/packages/python-xyz.scm (python-idna-ssl)[propagated-inputs]: Add
python-idna.

gnu: python-traitlets: Add missing input.

* gnu/packages/python-xyz.scm (python-traitlets)[propagated-inputs]:
Add python-six.

gnu: python-black: Remove blackd.

* gnu/packages/python-xyz.scm (python-black) [arguments]: Add new phase
to prevent installation of blackd.