gnu: corefreq: Update to 1.96.5.

* gnu/packages/linux.scm (corefreq): Update to 1.96.5.

gnu: r-pando: Fix hash.

* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.

gnu: bismark: Update to 0.24.1.

* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.

installer: Restore LatGrkCyr-8x16 console font depending on language.

Partially-Fixes: <https://issues.guix.gnu.org/64006>

* gnu/installer/services.scm (system-services->configuration): When the
LANGUAGE environment variable matches a known native console font, wrap the
base services with modify-services, configuring console-font-service-type to
set the native console font on every tty instead of the default console font.

Signed-off-by: Florian Pelz <pelzflorian@pelzflorian.de>

gnu: linux-libre 5.15: Update to 5.15.20.

* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.20.
(linux-libre-5.15-pristine-source): Update hash.

gnu: linux-libre 6.1: Update to 6.1.38.

* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.38.
(linux-libre-6.1-pristine-source): Update hash.

gnu: linux-libre: Update to 6.3.12.

* gnu/packages/linux.scm (linux-libre-6.3-version): Update to 6.3.12.
(linux-libre-6.3-pristine-source): Update hash.

gnu: l3afpad: Update to 0.8.18.1.11-0.16f2222.

* gnu/packages/text-editors.scm (l3afpad): Update to 0.8.18.1.11-0.16f2222.
[arguments]: Install the README and the man page.

gnu: python-pikepdf: Update to 7.2.0.

* gnu/packages/python-xyz.scm (python-pikepdf): Update to 7.2.0.
[native-inputs]: Remove PYTHON-SETUPTOOLS, PYTHON-SETUPTOOLS-SCM,
PYTHON-SETUPTOOLS-SCM-GIT-ARCHIVE, PYTHON-TOML, PYTHON-WHEEL.  Add
PYTHON-ATTRS, PYTHON-COVERAGE, PYTHON-HYPOTHESIS, PYTHON-PSUTIL,
PYTHON-PYTEST, PYTHON-PYTEST-COV, PYTHON-PYTEST-TIMEOUT, PYTHON-PYTEST-XDIST,
PYTHON-DATEUTIL, PYTHON-TOMLI.
[propagated-inputs]: Remove PYTHON-LXML.  Add PYTHON-DEPRECATION,
PYTHON-PACKAGING, PYTHON-PILLOW.

gnu: Add passwdqc.

* gnu/packages/password-utils.scm (passwdqc): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: guile-jsonld: Improve package style.

* gnu/packages/guile-xyz.scm (guile-jsonld): Improve overall indentation.
[propagated-inputs]: Remove labels.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: guile-jsonld: Fix build.

* gnu/packages/guile-xyz.scm (guile-jsonld)[propagated-inputs]: Replace GNUTLS
with GUILE-GNUTLS.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-vertico: Remove an unused argument in a phase.

* gnu/packages/emacs-xyz.scm (emacs-vertico)[arguments]<#:phases>: Remove OUTPUTS argument.

gnu: emacs-vertico: Update to 1.4.

* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 1.4.

gnu: emacs-tempel: Update to 0.8.

* gnu/packages/emacs-xyz.scm (emacs-tempel): Update to 0.8.

gnu: emacs-osm: Update to 0.13.

* gnu/packages/emacs-xyz.scm (emacs-osm): Update to 0.13.

gnu: emacs-marginalia: Remove an unused argument in a phase.

* gnu/packages/emacs-xyz.scm (emacs-marginalia)[arguments]<#:phases>: Remove OUTPUTS argument.

gnu: emacs-marginalia: Update to 1.3.

* gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 1.3.

gnu: emacs-corfu: Remove an unused argument in a phase.

* gnu/packages/emacs-xyz.scm (emacs-corfu)[arguments]<#:phases>: Remove OUTPUTS argument.

gnu: emacs-corfu: Update to 0.37.

* gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.37.