gnu: gnome-session: Restore elogind support.

* gnu/packages/patches/gnome-session-support-elogind.patch: New file.
* gnu/local.mk: Add it.
* gnu/packages/gnome.scm (gnome-session)[source]: Use it.
[arguments]: Add "-Delogind=true" to #:configure-flags; remove
phases that patch in old-style elogind support.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>

gnu: genimage: Update to 14-1.11bb044.

Update to commit 11bb04455 to integrate fixes related to new genext2fs and
e2fsprogs versions.

* gnu/packages/genimage.scm (genimage): Update to 14-1.11bb044.
[arguments]{fix-failing-tests}: Update it.
* gnu/packages/patches/genimage-mke2fs-test.patch: Update it.

gnu: python-scanpy: Set PYTHONPATH variable.

This is a follow-up to commit 664721422cd17c151df00b9ecab268d1aa18e3b3.

* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Set PYTHONPATH
variable during the build as GUIX_PYTHONPATH does not have the intended
effect.

gnu: python-scanpy: Update to 1.8.2.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.

gnu: xfce-weather-plugin: Fix build by depending on libsoup2.

* gnu/packages/xfce.scm (xfce-weather-plugin)[inputs]: Replace libsoup with
libsoup-minimal-2.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: python-libvirt: Update to 7.9.0.

* gnu/packages/virtualization.scm (python-libvirt): Update to 7.9.0.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: python-seaborn: Update to 0.11.2.

* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.11.2.

gnu: emacs-elpy: More aggressively trim nondeterministic tests.

More failing tests keep appearing sparingly, a few at a time.  With the
following change, the build succeeded 20 rounds.

* gnu/packages/emacs-xyz.scm (emacs-elpy)
[phases]{disable-broken-tests}: Disable whole tests families affected by
nondeterministic failures rather than individual tests.

gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH.

* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.

gnu: python-scanpy: Use GUIX_PYTHONPATH.

* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.

gnu: python-numpy: Alias to python-numpy-1.20.

Numpy 1.20 is required by numba and umap-learn.  Attempts to rename numpy 1.20
to allow it to coexist with numpy 1.21 in the same environment have not been
successful.

* gnu/packages/python-xyz.scm (python-numpy): Rename to...
(python-numpy-next): ...this variable.
(python2-numpy): Use python-numpy-next package as parent.
(python-numpy-1.20): Inherit from python-numpy-next.
(python-numpy): New variable pointing to python-numpy-1.20.
(python-numba)[propagated-inputs]: Replace python-numpy-1.20 with
python-numpy.

gnu: multiqc: Remove sanity check.

* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.

gnu: multiqc: Use GUIX_PYTHONPATH.

* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.

gnu: libmp4v2: Build with '-std=c++03'.

* gnu/packages/video.scm (libmp4v2)[arguments]: Add #:configure-flags.

gnu: python-qtconsole: Add dependency on python-pyqt.

* gnu/packages/python-xyz.scm (python-qtconsole)[propagated-inputs]: Add
PYTHON-PYQT.

vm: <virtual-machine> defaults to using 'qemu-minimal'.

'qemu-minimal' is enough for system tests, which is the main (only?) use
of <virtual-machine>.

* gnu/system/vm.scm (<virtual-machine>)[qemu]: Default to QEMU-MINIMAL.

gnu: tcp-wrappers: Allow compilation with glibc 2.33.

* gnu/packages/networking.scm (tcp-wrappers)[source]: Add 'snippet'.

gnu: grafx2: Build with '-fcommon'.

* gnu/packages/game-development.scm (grafx2)[arguments]: Add '-fcommon'
to #:make-flags.

gnu: grafx2: Add 'file-name' field to source.

Without a file name ending in ".tgz" (or similar), the 'unpack' phase
wouldn't extract it (as implemented in commit
cfcead2e515c0dae02127e5a76496463898be6b6).

* gnu/packages/game-development.scm (grafx2)[source]: Add 'file-name'
field.

gnu: ledger: Remove failing test output.

* gnu/packages/finance.scm (ledger)[source]: Add snippet to remove a failing
  test.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>