mapped-devices/luks: Support extra options.

Allow passing extra options to the 'cryptsetup open' command.

* gnu/system/mapped-devices.scm (luks-device-mapping-with-options):
[#:extra-options]: New argument.
(open-luks-device): Use it.
(check-luks-device): Validate it.
* doc/guix.texi (Mapped Devices): Document it.
* gnu/tests/install.scm (%test-encrypted-root-extra-options-os): New
test for it, as well as the previously untested #:allow-discards?
option.
(%encrypted-root-extra-options-os): New os declaration for the test.

Change-Id: I265a431efb0c81ed7cfc984344c6b8a4cc2f1624
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: uxn11: Enable tests.

* gnu/packages/emulators (uxn11)[arguments]
<#:tests?>: Remove.
<#:test-target>: Set to “test”.
<#:phases>: Delete ‘build’.  Move ‘check’ after ‘install’.
Add ‘fix-cc’ and ‘pre-check’.

Closes: guix/guix#3228
Change-Id: I27789bd36ecd6b66684403b0043ad75972ca0ced
Signed-off-by: 宋文武 <iyzsong@member.fsf.org>

gnu: python-louvain-igraph: Fix tests.

* gnu/packages/graph.scm (python-louvain-igraph)[native-inputs]:
Remove python-wheel; add python-pytest.

Change-Id: Iee027d8b6e838dd2deb6c02bc26aa55ff7fd3396

gnu: python-gffutils: Fix tests.

* gnu/packages/bioinformatics.scm (python-gffutils)[arguments]
<test-flags>: Ignore one not compatible test file.

Change-Id: I30c6abc726ba58a3ce3a08ad36cd48a6573efc29

gnu: python-episcanpy: Fix sanity check.

* gnu/packages/bioinformatics.scm (python-episcanpy):
[propagated-inputs]: Remove python-anndata; add python-anndata-0.11.

Change-Id: I8f6889b3fcce6c5c9f1eac27d45f49a81e815dcf

gnu: Add python-anndata-0.11.

* gnu/packages/python-science.scm (python-anndata-0.11): New variable.

Change-Id: I49d804d4434dfde618cfe7da76cae1d8db9444af

gnu: python-cyvcf2: Update to 0.31.2.

* gnu/packages/bioinformatics.scm (python-cyvcf2): Update to 0.31.2.
[native-inputs]: Remove python-wheel.

Change-Id: Ieba07d46864472b2c7d6a3f7936f1d225c174825

gnu: python-cgatcore: Update to 0.6.16.

* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.16.
[arguments] <test-flags>: Ignore not compatible test file.
[native-inputs]: Remove python-wheel.

Change-Id: Iec565987285443ea7303c44fe7eb0c8c967a5852

gnu: python-bx-python: Update to 0.14.0.

* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.14.0.
[propagated-inputs]: Add python-pyparsing.
[native-inputs]: Remove python-wheel.

Change-Id: I790eff97d37ea82220d7643d415c1213ff010411

gnu: packages/build-tools: Sort modules.

* gnu/packages/build-tools.scm: Group use-modules semantically and sort
alphabetically.

Change-Id: I3709f96c9484b311a89d73349074efbe9909877a

gnu: hyprland-protocols: Update to 0.7.0.

* gnu/packages/freedesktop.scm (hyprland-protocols): Update to 0.7.0.

Change-Id: Id57c9e2257b13d36da115080f9d04db14ccdb33a
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: hyprlock: Update to 0.9.2.

* gnu/packages/xdisorg.scm (hyprlock): Update to 0.9.2.

Change-Id: I8db39736e7404274fc26883393e905dfba4459eb
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: hyprsunset: Update to 0.3.3.

* gnu/packages/xdisorg.scm (hyprsunset): Update to 0.3.3.

Change-Id: I87a5a8d7e9a0d766253bca28d6af8fcf430eea5c
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: aquamarine: Update to 0.9.5.

* gnu/packages/xdisorg.scm (aquamarine): Update to 0.9.5.

Change-Id: I740152a5d5303447a785b350eeddc52ea63c86a8
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: hyprutils: Update to 0.10.0.

* gnu/packages/cpp.scm (hyprutils): Update to 0.10.0.

Change-Id: I47cf7881625f9487db29d06209fddbf470a03037
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: hyprgraphics: Update to 0.2.0.

Note: we use librsvg-for-system but for non-Rust systems the current version
is too old for this package to build there.

* gnu/packages/cpp.scm (hyprgraphics): Update to 0.2.0.
[inputs]: Add librsvg-for-system, pango.

Change-Id: I2437fa12278ee33de098a25fdb3e5a52f17ce6b1
Signed-off-by: John Kehayias <john@guixotic.coop>
Modified-by: John Kehayias <john@guixotic.coop>

gnu: hyprland: Update to 0.51.1.

* gnu/packages/wm.scm (hyprland): Update to 0.51.1.

Change-Id: Ia8fdf2d3f9a318202e5b1070d2efac6e819e061e
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: Remove wayland-protocols-next.

* gnu/packages/freedesktop.scm (wayland-protocols-next): Delete variable.
* gnu/packages/wm.scm (hyprland)[inputs]: Change wayland-protocols-next
to wayland-protocols.

This was a temporary package expected to be removed once the mesa-updates
branch was merged, it was only in use by hyprland.
See 7c1a30f3f91bd2e173d43ef110ed471abfcbb17e.

Change-Id: I9bf2f986815344ec79f013c0446cffbfdbdd76d7
Signed-off-by: John Kehayias <john@guixotic.coop>

gnu: python-cwlformat: Fix tests.

* gnu/packages/bioinformatics.scm (python-cwlformat)[arguments]
<test-flags>: Skip one test.
[native-inputs]: Remove python-wheel; add python-pytest.

Change-Id: Ic72c23fbe9a456d45e140c47ed06685ca5457b4b

gnu: python-prov: Update to 2.1.1.

* gnu/packages/python-xyz.scm (python-prov): Update to 2.1.1.
[source] <origin>: Switch to git-fetch.
[arguments] <#:phases>: Remove 'check phase, add 'disable-tests phase.
<#:test-backend>: Use unittest.
<#:test-flags>: Move flags from old 'check phase here.
[propagated-inputs]: Remove python-rdflib-6; add python-pydot, graphviz,
and python-rdflib.
[native-inputs]: Remove graphviz, python-pydot, and python-wheel.

Change-Id: I1dedb6b6f4394cdf14cdd496aa74e3390e48727d
Co-authored-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>