gnu: python-pre-commit: Move deprecated variable next to replacement.

This fixes a module import dependency cycle, which was introduced in
831baaf81e57ce9d9053ba6f9e0653a2d27298c4 ("gnu: python-pre-commit: Replace
with pre-commit.").  The rule of thumb to avoid these is that the deprecated
package should live next to the replacement package (in the same module).

* gnu/packages/python-xyz.scm (python-pre-commit): Move to...
* gnu/packages/version-control.scm (python-pre-commit): ... here.

gnu: git: Fix missing native-inputs after commit ccb62d8feb.

* gnu/packages/version-control.scm (git)[native-inputs]: Restore
native-inputs to what they were prior to the merge commit ccb62d8feb.

Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: gnulib: Depend on git-minimal/pinned.

* gnu/packages/build-tools.scm (gnulib)[native-inputs]: Change git to
git-minimal/pinned.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

Merge remote-tracking branch 'origin/master' into core-updates

gnu: openjdk10: Apply patch again.

This partially reverts commit 7636c49b45adb9870cf416c64bde032ec858a820
where the patch was dropped.

* gnu/packages/java.scm (openjdk10)[source]: Apply patch.

Merge remote-tracking branch 'origin/master' into core-updates

gnu: Add r-annotationhubdata.

* gnu/packages/bioconductor.scm (r-annotationhubdata): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

gnu: Add r-affylmgui.

* gnu/packages/bioconductor.scm (r-affylmgui): New variable.

gnu: Add r-tkrplot.

* gnu/packages/cran.scm (r-tkrplot): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.

gnu: Add r-affyplm.

* gnu/packages/bioconductor.scm (r-affyplm): New variable.

gnu: Add r-affyilm.

* gnu/packages/bioconductor.scm (r-affyilm): New variable.

gnu: python-google-api-client: Update to 1.12.8.

* gnu/packages/python-web.scm (python-google-api-client): Update to
1.12.8.
[arguments]: Remove custom phase to adjust setup.py.
[native-inputs]: Remove python-oauth2client, python-uritemplate. Move
python-httplib2, python-six ...
[propagated-inputs]: ... here. Add python-google-api-core-1,
python-google-auth-1, python-google-auth-httplib2, python-uritemplate-3.

gnu: python-googleapis-common-protos: Update to 1.56.4.

* gnu/packages/python-web.scm (python-googleapis-common-protos): Update
to 1.56.4.
[arguments]: Enable test suite.

gnu: Add python-google-api-core-1.

* gnu/packages/python-web.scm (python-google-api-core-1): New variable.

gnu: Add python-google-auth-1.

* gnu/packages/python-web.scm (python-google-auth-1): New variable.

gnu: Add python-google-auth-httplib2.

* gnu/packages/python-web.scm (python-google-auth-httplib2): New
variable.

gnu: Add python-uritemplate-3.

* gnu/packages/python-web.scm (python-uritemplate-3): New variable.

gnu: python-httplib2: Update to 0.15.0.

* gnu/packages/python-web.scm (python-httplib2): Update to 0.15.0.
[source]: Download using git.
[arguments]: Add a phase to adjust the test package version
requirements.
[native-inputs]: Add python-flake8, python-future, python-mock,
python-pytest, python-pytest-cov, python-pytest-forked,
python-pytest-randomly, python-pytest-timeout, python-pytest-xdist,
python-six.
[home-page]: Switch to new upstream homepage.

gnu: zig: Increase max-silent-time.

* gnu/packages/zig.scm (zig-0.10)[properties]: Set max-silent-time to 3
hours.

gnu: Add transanno.

* gnu/packages/bioinformatics.scm (transanno): New variable.