gnu: snakemake: Rename variable in python-xyz.

There is a duplicated variable with this name in python-science but
different version, rename the variable in python-xyz to reflect it's
version.

* gnu/packages/python-xyz.scm (snakemake): Rename variable to snakemake-5.
(snakemake-6): Inherit from snakemake-5.

Change-Id: Iabb67d68ea5b896a2524eaf9bf73669068cccaeb

gnu: grip: Fix build.

* gnu/packages/python-web.scm (grip): Fix build and refresh package style.
[build-system]: Switch to pyproject.
[arguments] <test-flags>: Ignore all tests requiring networking.
<phases>: Add 'fix-response-encoding; use default 'check.
[native-inputs]: Add python-setuptools, and python-wheel.
[description]: Fix fill column indentation.

Change-Id: I131ab5efa965760f05411c7dbdb2349d9e8cbcc3

gnu: Add snakemake.

* gnu/packages/python-science.scm (snakemake): New variable.

Change-Id: Id61c7955684f5186b9dc884f0c9de4ec73f766ea
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-conda-inject.

* gnu/packages/package-management.scm (python-conda-inject): New variable.

Change-Id: Ic4b91e01b68c62fd91a0f6d77e57c6d32c4b5d03
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-snakemake-interface-storage-plugins.

* gnu/packages/python-science.scm
(python-snakemake-interface-storage-plugins): New variable.

Change-Id: Ie74edfdc2535f7f26f0c6210a274dfc351336129
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-snakemake-interface-software-deployment-plugins.

* gnu/packages/python-science.scm
(python-snakemake-interface-software-deployment-plugins): New variable.

Change-Id: Ia3f6beed3a3ea02607645ca127be52f328b429bb
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-snakemake-interface-report-plugins.

* gnu/packages/python-science.scm
(python-snakemake-interface-report-plugins): New variable.

Change-Id: I8705ba63df668d46ffda575b18ee97bb65acdc6c
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-snakemake-interface-executor-plugins.

* gnu/packages/python-science.scm
(python-snakemake-interface-executor-plugins): New variable.

Change-Id: I6bd9c6aec7293b8412c20dac04f82d867400d71c
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-snakemake-interface-common.

* gnu/packages/python-science.scm (python-snakemake-interface-common):
New variable.

Change-Id: Iaac3acb7f57c3b6aedda7fe48daccbd952faddd5
Signed-off-by: Steve George <steve@futurile.net>

gnu: Add python-argparse-dataclass.

* gnu/packages/python-xyz.scm (python-argparse-dataclass): New variable.

Change-Id: If669a77f36753b4639136fc612dda42aca1a61f9
Signed-off-by: Steve George <steve@futurile.net>

gnu: Remove python-setuptools-57.

* gnu/packages/python-build.scm (python-setuptools-57): Delete variable.

Change-Id: I151d8992c9bca65aa114df95354f740a4560d2f9
Signed-off-by: Steve George <steve@futurile.net>

gnu: python-louvain: Use pyproject-build-system.

* gnu/packages/graph.scm (python-louvain)
[build-system]: Switch from python-build-system to
pyproject-build-system.
[native-inputs]: Replace python-setuptools-57 by
python-setuptools. Add python-wheel.

Change-Id: I3c07564dd8fd3f75e33a2cc9737372e28c57f733
Signed-off-by: Steve George <steve@futurile.net>

gnu: python-importlib-resources: Update python-setuptools input.

* gnu/packages/python-xyz.scm (python-importlib-resource)
[native-inputs]: Replace python-setuptools-57 by python-setuptools.

Signed-off-by: Steve George <steve@futurile.net>

gnu: python-jplephem-build: Fix build.

* gnu/packages/astronomy.scm (python-jplephem) [phases]: Ignore failing tests.

Change-Id: I33af71f580cd25bbd126fcf0c5cf1164f9c892ef
Signed-off-by: Steve George <steve@futurile.net>

gnu: python-docutils-0.15: Update to 0.16.

* gnu/packages/python-xyz.scm (python-docutils-0.15): Update to 0.16.
[native-inputs]: Replace python-setuptools-57 by python-setuptools.
* gnu/packages/python-web.scm (awscli)[inputs]: Update accordingly.
* gnu/packages/sphinx.scm (python-sphinx-panels)[propagated-inputs]:
Update accordingly.

Change-Id: I84360acf8d8213d0d49301e116f1a158bdb545e7
Signed-off-by: Steve George <steve@futurile.net>

gnu: Remove python-sphinx-4.

* gnu/packages/sphinx.scm (python-sphinx-4): Delete variable.

Change-Id: I71d008e2e8cef84ef33827c3477cc442181ad91e
Signed-off-by: Steve George <steve@futurile.net>

gnu: python-numpy-documentation: Update python-sphinx native-input.

* gnu/packages/python-xyz.scm (python-numpy-documentation):
[arguments]{phases}: Add phase 'avoid-external-deps. Adapt phase
'install by removing sphinx.ext.autodoc extension.
[native-inputs]: Replace python-sphinx-4 by python-sphinx. Add
python-sphinx-design.

Change-Id: Ica1c0a72b2106cadd6e51ffcb272980508abb29f
Signed-off-by: Steve George <steve@futurile.net>

gnu: scons: Update to 4.5.0.

* gnu/packages/build-tools.scm (scons): Update to 4.5.0.
[arguments]{check phase}: Remove failing tests.

Change-Id: If17c26174f7790eee562c7c99e3be39fe1e57197

gnu: python-sphinx-panels: Update input to python-sphinx-5.

* gnu/packages/sphinx.scm (python-sphinx-panels):
[arguments]{phases}: Add 'loosen-requirements phase.
[propagated-inputs]: Replace python-sphinx-4 by python-sphinx-5.

Change-Id: I3d7cad92a2d013417ebc4fef65ff244f4bc8d48f
Signed-off-by: Steve George <steve@futurile.net>

gnu: sphinx-5: Ignore failing test.

* gnu/packages/sphinx.scm (sphinx-5)[arguments]{test-flags}: Ignore
test test_autodoc_default_options (also ignored in sphinx@6).

Change-Id: I0bbb844051b57541b517aba20a6eee0830fb7544
Signed-off-by: Steve George <steve@futurile.net>