gnu: miso: Update to 0.5.4-1.b714021.

* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.

gnu: Add samtools-1.2.

* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.

gnu: Add htslib-for-samtools-1.2.

* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.

gnu: python2-scipy: Override native inputs.

* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override;
replace gfortran with gfortran-7; add gcc-7.

gnu: python2-matplotlib: Fix mpl_toolkits module.

* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase
'create-init-file; restore 'sanity-check phase.

gnu: Add gfortran-7.

* gnu/packages/gcc.scm (gfortran-7): New variable.

gnu: python-slepc4py: Update to 3.16.1.

This is a followup 5b4d1e57b6d4931f6ee2a50abf84222fe015d045.

* gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to...
[propagated-inputs]: ... here.
(python-slepc4py): Update to 3.16.1.

gnu: python-petsc4py: Update to 3.16.1.

This is a followup to 07ac13a26a0d7c8319afb42c55fc2116ec44668f.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.

gnu: geeqie: Fix X11 error at startup.

Fixes <https://issues.guix.gnu.org/52089>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.
Patch provided by John Kehayias <john.kehayias@protonmail.com>.

* gnu/packages/patches/geeqie-clutter.patch: New file.
* gnu/packages/image-viewers.scm (geeqie)[sources]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.

gnu: mumps: Allow compilation with GCC 10.

Following the suggestion at
<https://community.freefem.org/t/compline-on-macos-10-15-6/543>.

* gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add
'-fallow-argument-mismatch' to 'OPTF'.

maint: Don't require unsupported packages such as GNOME on i686-linux.

* etc/release-manifest.scm (%system-manifest): Filter out PACKAGE when
it doesn't pass 'supported-package?'.

services: %desktop-services: Use SDDM rather than GDM on non-x86_64.

This works around the fact that Rust is currently unavailable in Guix on
platforms other than x86_64-linux:

  https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00197.html

* gnu/services/desktop.scm (desktop-services-for-system): New
procedure.
(%desktop-services): Turn into a macro.

system: Mark 'services' field as thunked.

This allows us to make services dependent on (%current-system), for
example.

* gnu/system.scm (<operating-system>)[services]: Mark as thunked.

gnu: idutils: Fix build with glibc 2.33.

* gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets'
from "lib/stdio.in.h".

gnu: libtorrent-rasterbar: Build with default cmake.

* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove
cmake flag.

gnu: tadbit: Update to 1.0.1-1.5c4c1dd.

* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd.
[arguments]: Remove trailing #T from build phases; pass -fcommon to test
binaries; run tests conditionally.

gnu: python2-sphinx: Remove websupport test.

* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test
file.

gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2.

* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to
1.1.2.
[arguments]: Override; delete 'sanity-check phase.
[propagated-inputs]: Override and add python2-six.
(python-sphinxcontrib-websupport)[properties]: Record python2-variant.

gnu: python2-jinja2: Downgrade to 2.11.3

* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version
supporting Python 2.
(python-jinja2)[properties]: Record python2-variant.

gnu: python2-markupsafe: Downgrade to 1.1.1.

* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1,
because that's the last version to support Python 2.