gnu: notmuch: Update to 0.38.2.

* gnu/packages/mail.scm (notmuch): Update to 0.38.2.
* gnu/packages/patches/notmuch-emacs-test-output.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Apply file deletion.

Change-Id: I60d0487f2258ed5ef8602de7a624686c5f012a4f

gnu: emacs-shx: Fix test failure.

* gnu/packages/patches/emacs-shx-byte-compilation-test.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/emacs-xyz.scm (emacs-shx): Apply it.

Change-Id: I6d8edd3b50f99f1c4cd495216caf9648dfee4ea3

gnu/local.mk: Sort Emacs patches and fix 2044 year in copyright notice.

* gnu/local.mk: Correct 2044 copyright year.
(dist_patch_DATA): Sort emacs patches.

Change-Id: Ib9669bb1d7fb2556d6d809d62624981fa66d27f3

gnu: u-boot: Update to 2024.01.

* gnu/packages/bootloaders.scm (u-boot): Update to 2024.01.
[source]: Remove patman patch, add build-without-libcrypto patch.
* gnu/packages/patches/u-boot-allow-disabling-openssl.patch: Remove
upstreamed diffs.
* gnu/packages/patches/u-boot-build-without-libcrypto.patch: Add file.
* gnu/packages/patches/u-boot-patman-change-id.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Add patch, remove patch.

Change-Id: I5a21d4cd645449ff669f17cdabe5313870bec46f
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>

gnu: python-pyls-black: Fix build.

* gnu/packages/patches/python-pyls-black-41.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python-xyz.scm (python-pyls-black)[source]: Add patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable one failing test.

Change-Id: I14b2982644e58c0b43d76838febc6dfceb220b15

gnu: python-scikit-bio: Update to 0.5.9.

* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7

gnu: openssh: Fix build on ppc64le.

* gnu/packages/ssh.scm (openssh)[source]:
Use 'openssh-gcc-13-ppc64le-fzero-call-used-regs.patch'.
* gnu/packages/patches/openssh-gcc-13-ppc64le-fzero-call-used-regs.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Reported-by: Marcel van der Boom <marcel@van-der-boom.nl>.

Change-Id: I41b1350b2cdd1487a8fd69b13b64f63c0dc166c9
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: unknown-horizons: Fix build and runtime errors.

Apply two upstream commits that allow building with Python 3.9 or newer and
running with Python 3.10.

* gnu/packages/patches/unknown-horizons-python-3.9.patch: New file.
* gnu/packages/patches/unknown-horizons-python-3.10.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/games.scm (unknown-horizons)[source]: Apply them.

Change-Id: Icbc8b698b913be01465b09ab26afb29e5fd62a87
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
Fixes: Unknown Horizons fails to start <https://bugs.gnu.org/54815>

gnu: fifengine: Fix runtime error when using Python 3.9 or newer.

* gnu/packages/patches/fifengine-python-3.9-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/games.scm (fifengine)[source]: Apply it.

Change-Id: I61001d6b87db00c71f1e2e6ca3bac8581e941451
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

Merge branch 'lisp-team'

Change-Id: I4ec6ad695392c76c389224255477819fa686eecb

gnu: sbcl: Fix riscv build.

* gnu/packages/patches/sbcl-fix-riscv-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/lisp.scm (sbcl)[source]: Use it.

Change-Id: I63f1b9a7a7b6f3a1961d0a0cb31189b74a60abc3

gnu: openjdk10: Fix time bomb in ‘GenerateCurrencyData.java’.

Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f4241c9beac0c82deae946bfdc70b49ff0.

* gnu/packages/java.scm (openjdk10)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb2.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: I42fc14d305883f672cd6764a0ee6462852e41a5b

gnu: Fix patch location.

This is a follow-up to commit db7488a7fbd829d25b0b5c5e53b1c680b67832b1.

* gnu/local.mk (dist_patch_DATA): Restore "packages/" prefix.

Change-Id: I1f8e420e75c3f4e1927dac935c2de337fd1306eb

gnu: openjdk9: Fix time bomb in ‘GenerateCurrencyData.java’.

Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f4241c9beac0c82deae946bfdc70b49ff0.

* gnu/packages/java.scm (openjdk9)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Change-Id: I45ca1fe5bad922307eba64d46a330a8f233c0f55

gnu: icedtea: Fix time bomb in ‘GenerateCurrencyData.java’.

Fixes <https://issues.guix.gnu.org/68333>.

* gnu/packages/java.scm (icedtea-7)[drop]: Add optional ‘patches’
parameter and honor it.
[native-inputs]: Add patch for “jdk-drop”.
(icedtea-8): Likewise.
* gnu/packages/patches/jdk-currency-time-bomb.patch,
gnu/packages/patches/jdk-currency-time-bomb2.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.

Change-Id: I3b4cf562ce4bedb87ce0e7c289e431fbb0dbb6f8

Merge branch 'master' into lisp-team

Change-Id: I6c2ce53e782a00861c3adf01c2505099daef7728

gnu: jami: Update to 20231222.2.

* gnu/packages/jami.scm (%jami-version): Rename to...
(%jami-nightly-version): ... this.  Update to 20231222.2.
(%jami-daemon-commit): New variable.
(%jami-sources): Delete variable.
(libjami) Adjust source to use %jami-nightly-version, %jami-daemon-commit.
[source]: Fetch from git.  Apply libjami-ac-config-files.patch.
[arguments] <make-flags>: Skip ut_media_player test.
<phases>: Add extend-scheduler-test-timeout and extend-scheduler-test-timeout
phases.
[inputs]: Replace dbus-c++ with sdbus-c++.
Add dhtnet.  Replace libgit2 with libgit2-1.6.
(jami): Set version to %jami-nightly-version.
[source]: Fetch from git.  Apply new jami-qml-tests-discovery.patch,
jami-skip-tests-requiring-internet.patch and jami-unbundle-dependencies.patch
patches.
[arguments] <configure-flags>: Add -DWITH_DAEMON_SUBMODULE=OFF.
<phases>: Delete change-directory/maybe.
Adjust check phase.  Add fake-x11-environment,
copy-3rdparty-source-dependencies and disable-problematic-tests phases.
[inputs]: Add md4c and tidy-html.
* gnu/packages/patches/jami-qml-tests-discovery.patch: New file.
* gnu/packages/patches/libjami-ac-config-files.patch: Likewise.
* gnu/packages/patches/jami-skip-tests-requiring-internet.patch: Likewise.
* gnu/packages/patches/jami-unbundle-dependencies.patch: Likewise.
* gnu/packages/patches/jami-libjami-headers-search.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/patches/jami-disable-integration-tests.patch: Adjust patch.

Series-changes: 2
 - Update Jami to latest nightly version (20231222.2)

Change-Id: If30f1178bdfa29c4ea3e54dbb7997e360788adae

gnu: ffmpeg-jami: Relocate to (gnu packages video).

To avoid Guile module dependency cycles, inherited packages must be defined in
the same module.  Use this opportunity to simplify the patches applying
mechanism, versioning custom patches the same as for other packages.

* gnu/packages/patches/ffmpeg-jami-change-RTCP-ratio.patch: New file.
* gnu/packages/patches/ffmpeg-jami-rtp_ext_abs_send_time.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusdec-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-reload-packet-loss-at-encode.patch:
Likewise.
* gnu/packages/patches/ffmpeg-jami-remove-mjpeg-log.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-screen-sharing-x11-fix.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Register them.
* gnu/packages/jami.scm (jami-apply-custom-patches): Delete procedure.
(%ffmpeg-default-configure-flags): Delete variable.
(ffmpeg-compose-configure-flags): Delete procedure.
(ffmpeg-jami): Move to...
* gnu/packages/video.scm (ffmpeg-jami): ... here.  Apply patches to origin and
repatriate configure flags.

Change-Id: Id374fae18240cd76b224915d80b61422635ccb77

gnu: Add python-pyreadstat.

* gnu/packages/patches/python-pyreadstat-link-libiconv.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (python-pyreadstat): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Change-Id: I361df91487412e4bfd26fb728a6999752e6343e5

gnu: sbcl: Fix build on powerpc64.

* gnu/packages/patches/sbcl-fix-ppc64-build.patch: New file.
* gnu/local.mk: Register it.
* gnu/packages/lisp.scm (sbcl)[source]: Use it.

Change-Id: If81321bc7e4075ac7ec63f7b8d623011b4b975d5