gnu: xorg-server: Update to 21.1.11 [security fixes].

Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886,
CVE-2024-0409, and CVE-2024-0408.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2024-January/061525.html> for more
information.

Copyright line updated as followup to commits
3080abba40c819933d1857abe4abaaa3cf65baab and
158502e40d800407f1bd697dd5dd0437086730bf.

* gnu/packages/xorg.scm (xorg-server): Update to 21.1.11.

Change-Id: I07cb273e2a504f94f8f26624d26ad79c6e92f109
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>

gnu: gnutls: Update to 3.8.3 [security-fixes].

Fixes CVE-2024-0553 and CVE-2024-0567.

gnu/packages/tls.scm (gnutls-3.8.2): Rename to ...
(gnutls/fixed): ... this.  Update to 3.8.3.
(gnutls): Rename replacement to gnutls/fixed.

Change-Id: Ic44b3b0481ffd51cdc42a2d71a598f001b43c6f7
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Co-authored-by: John Kehayias <john.kehayias@protonmail.com>

gnu: Add python-manimpango.

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

Co-authored-by: Troy Figiel <troy@troyfigiel.com>
Change-Id: I80effb2412e7c35ddf69c0d3ff6e2f052f282840
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: r-org-hs-eg-db: Update to 3.18.0.

* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.18.0.

Change-Id: Iaba83a413858a95e81b6488a2f8cde648f0bdeed

gnu: Add r-methylclockdata.

* gnu/packages/bioconductor.scm (r-methylclockdata): New variable.

Change-Id: Id76373a9aec8276dcfd1ec3428d2ce9c81cc51d2

gnu: Add r-experimenthubdata.

* gnu/packages/bioconductor.scm (r-experimenthubdata): New variable.

Change-Id: I5faf26f483898b162bc1f863a4aceb6f46c52c18

gnu: Add r-jaspar2016.

* gnu/packages/bioconductor.scm (r-jaspar2016): New variable.

Change-Id: Ib2970791207b426c39bd0226e01107a35fec0bb2

gnu: Add r-genomicstate.

* gnu/packages/bioconductor.scm (r-genomicstate): New variable.

Change-Id: I1b86c8e849af7b69b5fa9ea2a0e43b4e3e1850b2

gnu: Add r-shinymeta.

* gnu/packages/cran.scm (r-shinymeta): New variable.

Change-Id: I35e1c032283cdc010e4551c0d33f9d4202d9deee

gnu: Add r-ensdb-hsapiens-v79.

* gnu/packages/bioconductor.scm (r-ensdb-hsapiens-v79): New variable.

Change-Id: I773615df66194ddb195f013f7000d175ac07d095

gnu: Add rust-rustc-demangle-capi-0.1.

* gnu/packages/crates-io.scm (rust-rustc-demangle-capi-0.1): New variable.

Change-Id: I98afb19ed4bdbcb9107a1ab30af49b055802b8b0

Reviewed-by: Efraim Flashner <efraim@flashner.co.il>
Change-Id: Ifeaefa5a377600320c3fd2a637aefaf29707e3b7

gnu: guile-hall: Update to 0.4.1-1.7558ba9.

* gnu/packages/guile-xyz.scm (guile-hall): Update to 0.4.1-1.7558ba9.
[arguments] <modules>: Remove (ice-9 match) and (ice-9 ftw) modules.
Add (guix build guile-build-system).
<phases>: Use gexps.  Streamline hall-wrap-binaries phase.
[native-inputs]: Add guile-3.0 and gettext-minimal.
[propagated-inputs]: Delete field, moving guile-config to...
[inputs]: ... here.  Add bash-minimal and guile-lib.

Change-Id: Idef796dc3ba9ca3fa4df8114efe91af7c5cf7be0

gnu: reuse: Update to 3.0.1.

* gnu/packages/license.scm (reuse): Update to 3.0.1.
[arguments]: New field.

Change-Id: Ibbc5ae8cfa0e0e62b6c64bd90387022e88f9c933

gnu: symengine: Update to 0.11.2.

* gnu/packages/algebra.scm (symengine): Update to 0.11.2.

Change-Id: I34c24dd8591e306a7740f0a3d51077aceec67fab

gnu: python-metpy: Update to 1.6.1.

* gnu/packages/geo.scm (python-metpy): Update to 1.6.1.

Change-Id: Id8d8d6db3e31307242e56c494b6dee7c2ffab8f1

gnu: python-deepxde: Update to 1.10.1.

* gnu/packages/machine-learning.scm (python-deepxde): Update to 1.10.1.

Change-Id: If3515735d4adee8a2f1e9460d6ccb72c6ce26321

gnu: python-mapie: Update to 0.8.2.

* gnu/packages/statistics.scm (python-mapie): Update to 0.8.2.

Change-Id: I82098caa8ed5d3bf68eec9f374f600d203d6b178

gnu: libngspice: Update to 42.

* gnu/packages/engineering.scm (libngspice, ngspice): Update to 42.

Change-Id: Ib7b72724f8f46ce376bd6517cb2652c870edcb0d

gnu: darktable: Update to 4.6.0.

* gnu/packages/photo.scm (darktable): Update to 4.6.0.

Change-Id: Ic64b02e8d191ba91fde1b95b9bcb4321a471dcba

gnu: darktable: Enable more optional features.

* gnu/packages/photo.scm (darktable)[inputs]: Add libjxl, portmidi.

Change-Id: I7747dfc2e88379a13182590f87514951bdd70e0c