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Author SHA1 Message Date
Ricardo Wurmus
6c453e04b8
gnu: python-distributed: Disable breaking test. 
This test times out since the merge of the mesa-updates branch.

* gnu/packages/python-science.scm (python-distributed)[arguments]: Disable
test_tell_workers_when_peers_have_left.

Change-Id: Ib65b971a3a821ea13d36a4be60658ffc366ca6ac
 2024-01-10 20:35:28 +01:00
nafkhamdc
c1fda6cf61
gnu: Add r-jaspar2020. 
* gnu/packages/bioconductor.scm (r-jaspar2020): New variable.

Change-Id: I84f0fc2a7defc5d179ffc24aa1f30177cb3b3060
 2024-01-10 18:39:13 +01:00
nafkhamdc
feab3943c1
gnu: Add r-dsb. 
* gnu/packages/bioconductor.scm (r-dsb): New variable.

Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd
 2024-01-10 18:39:13 +01:00
nafkhamdc
db75afb4c5
gnu: r-signac: Update to 1.12.0-1.8ecdde2. 
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.12.0-1.8ecdde2.

Change-Id: Ib852f7a23768383fc62d60577f2aaa893c509317
 2024-01-10 18:39:13 +01:00
nafkhamdc
2ec29a8c11
gnu: Add r-escape. 
* gnu/packages/bioconductor.scm (r-escape): New variable.

Change-Id: Ia308f9c90fa81c3304f97daa4f56ae4cd722d5cc
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus
6688e9f4bd
gnu: Add python-telomerecat. 
* gnu/packages/bioinformatics.scm (python-telomerecat): New variable.

Change-Id: Ice4cd367cab677466630f44f6900fc38e3be350c
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus
16a277e0a9
gnu: Add python-parabam. 
* gnu/packages/bioinformatics.scm (python-parabam): New variable.

Change-Id: I66ccf5fd0647f908f1cefd38f0d92e589a81683b
 2024-01-10 18:39:13 +01:00
Ludovic Courtès
5c0f77f424
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
 2024-01-10 16:42:03 +01:00
Zheng Junjie
a126e8120d
gnu: mesa: Fix cross-compilation. 
* gnu/packages/gl.scm(mesa)[arguments]<#:phases>: When cross-compiling, force
the use of the cmake method to find llvm.

Change-Id: I27f6f4d9d71028c15588eeade48d3a918c042b9c
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-10 15:29:11 +01:00
Zheng Junjie
6401efb554
gnu: yaml-cpp: Update to 0.8.0. 
* gnu/packages/serialization.scm (yaml-cpp): Update to 0.8.0.

Change-Id: I927111f2d103dbb30ff336b64dd4ab90c22312a0
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-10 15:25:45 +01:00
Andre A. Gomes
537768018e
gnu: Add cl-stripe. 
* gnu/packages/lisp-xyz.scm (sbcl-stripe): New variable.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: Ideeff671b8577bcfceb241a86624ac26f1d077f7
 2024-01-10 10:53:01 +01:00
Andre A. Gomes
d34fe10018
gnu: nyxt: Update to 3.11.0. 
* gnu/packages/web-browsers.scm (nyxt): Update to 3.11.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
 2024-01-10 10:13:42 +01:00
Andre A. Gomes
d8ddf42712
gnu: cl-prompter: Update to 0.1.1-0.7890ed5. 
* gnu/packages/lisp-xyz.scm (sbcl-prompter): Update to 0.1.1-0.7890ed5.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
Change-Id: I65a7d23d4a889c1d7c4821e83b8ea3a56701a5c8
 2024-01-10 10:09:56 +01:00
Maxim Cournoyer
e541f9593f
Authorize Oleg (Sharlatan)'s key. 
* .guix-authorizations (sharlatan): Register PGP key fingerprint.

Change-Id: I0d20e50a37971237721964852a404c5cf136f0be
 2024-01-09 23:08:17 -05:00
Maxim Cournoyer
58ab25a2ce
tests: telephony: Fix typo. 
* gnu/tests/telephony.scm: Fix typo.

Series-to: 65371@debbugs.gnu.org
Series-postfix: telephony-team
Series-version: 2

Change-Id: I3eb048b8cdd1335c45ffb61b08425a18a2e7a4b2
 2024-01-09 22:10:14 -05:00
Wojtek Kosior
693a4785be
tests: telephony: Fix VPATH builds. 
* gnu/tests/telephony.scm (%jami-account-content-sexp): New variable.  Compute
its value with `read` instead of using `include`.
* gnu/tests/data/jami-dummy-account.dat (%jami-account-content-sexp): Remove
variable.  Make the file contain just the S-expression.

Change-Id: I8d37aaf7b739f5f39715bfb8a9b8c9536385fd09
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer
c5fb46685f
gnu: jami-docs: Update to 0.0.0-2.a48997d. 
* gnu/packages/jami.scm (jami-docs): Update to 0.0.0-2.a48997d.

Change-Id: I0c6ee456dec6251a66d1566c855069f3ecf2e44e
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer
8237f4e997
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
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer
d9c9b97e93
gnu: Add sortfilterproxymodel. 
* gnu/packages/jami.scm (sortfilterproxymodel): New variable.

Change-Id: I7c46fce26d5fcdc98e8646e65dd119155a8b9287
 2024-01-09 22:10:13 -05:00
Maxim Cournoyer
de002b93db
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
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
5a38120c67
gnu: ffmpeg-jami: Update configure flags. 
* gnu/packages/jami.scm (%ffmpeg-default-configure-flags): Add new flags.

Change-Id: I1bac70e7b0ec58c46348a7138f7260b40cdf79f8
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
202b16e31a
gnu: pjproject-jami: Update and relocate. 
* gnu/packages/jami.scm (pjproject-jami): Move to...
* gnu/packages/telephony.scm (pjproject-jami): ... here.  Update to latest
commit.
[arguments]: Use same configure flags as done in Jami/DhtNet projects.

Change-Id: I638364ebc94f17762ee072311b5fe439b7c6f837
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
88f294cc14
gnu: Add dhtnet. 
* gnu/packages/networking.scm (dhtnet): New variable.

Change-Id: I91cc3541f476c8614be35b1ae7cb1740690f685a
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
79bd3c685f
gnu: opendht: Update to 3.1.7. 
* gnu/packages/networking.scm (opendht): Update to 3.1.7.
[arguments]: Add a new relax-test-timeouts phase.

Change-Id: Ida7fe021599e9c469e49f6540a908e80b7264241
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
edb03ceb60
gnu: msgpack: Deprecate with msgpack-c. 
* gnu/packages/serialization.scm (msgpack-c): New variable.
(msgpack-cxx): New variable.
(msgpack): Rename to...
(msgpack-3): ... this, and inherit from msgpack-c.
* gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c
phase.
[inputs]: Replace msgpack with msgpack-c.
* gnu/packages/terminals.scm (tmate)
[inputs]: Replace msgpack with msgpack-3.
* gnu/packages/networking.scm (opendht)
[propagated-inputs]: Replace msgpack with msgpack-cxx.
* gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
504b46cd87
gnu: libnatpmp: Update to 20230423-0.6a850fd. 
* gnu/packages/networking.scm (libnatpmp): Update to 20230423-0.6a850fd.
[source]: Fetch from git.
[build-system]: Use cmake-build-system.
[arguments]: Add patch-build-system and fix-version phases.  Reinstate
configure and check phase, but set #:tests? to #f.  New #:configure-flags
argument.
[native-inputs]: Add which.
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer
0860b612f2
gnu: restinio: Update to 0.7.1. 
* gnu/packages/networking.scm (restinio): Update to 0.7.1.
[arguments] <configure-flags>: Remove RESTINIO_FIND_DEPS,
RESTINIO_USE_EXTERNAL_HTTP_PARSER and RESTINIO_USE_EXTERNAL_SOBJECTIZER
configure flags.  Add -DRESTINIO_DEP_LLHTTP=system, -DRESTINIO_DEP_FMT=system,
-DRESTINIO_DEP_EXPECTED_LITE=system and -DRESTINIO_WITH_SOBJECTIZER=OFF.
<phases>: Add use-system-catch2.
[native-inputs]: Remove clara.  Replace catch2 with catch2-3.
[propagated-inputs]: Replace http-parser with llhttp.
(restinio-0.6): New variable.
(opendht) [propagated-inputs]: Replace restinio with restinio-0.6.

Change-Id: Id69fde5e2c476d7e44b8dd6e065c489314707c31
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer
6f20c8df0e
gnu: Add xdiff. 
* gnu/packages/version-control.scm (xdiff): New variable.
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer
39bd088e75
gnu: Add llhttp. 
* gnu/packages/web.scm (llhttp): New variable.

Change-Id: I3c0475ff6d86a16f51d8870577808ce97ee66a92
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer
0ec349078f
gnu: Add expected-lite. 
* gnu/packages/cpp.scm (expected-lite): New variable.

Change-Id: I5a21dd631e1f2a3c97b920efcdca69f2537b42da
 2024-01-09 22:10:11 -05:00
Maxim Cournoyer
45d07a0b01
gnu: catch2-3: Update to 3.5.1. 
* gnu/packages/check.scm (catch2-3.3): Rename to...
(catch2-3): ... this.  Update to 3.5.1.
* gnu/packages/logging.scm (spdlog) [native-inputs]: Rename catch2-3.3 to
catch2-3.
* gnu/packages/potassco.scm (clingo) [inputs]: Likewise.

Change-Id: Ied7724597ff4c6371dc4fedc10452ae870d23933
 2024-01-09 22:10:10 -05:00
Maxim Cournoyer
1e35c18c86
gnu: asio: Update to 1.28.0. 
* gnu/packages/networking.scm (asio): Update to 1.28.0.

Change-Id: I517fb9c6c52c5b5e5c41c5760c06eca6750d3765
 2024-01-09 22:10:10 -05:00
Maxim Cournoyer
9e9e373751
gnu: libnatpmp: Update home page. 
* gnu/packages/networking.scm (libnatpmp) [home-page]: Update.
 2024-01-09 22:10:10 -05:00
Maxim Cournoyer
c235957534
gnu: libnatpmp: Use gexps and simplify. 
* gnu/packages/networking.scm (libnatpmp) [arguments]: Use gexps.  Use gexp
variables and cc-for-target in make flags.
 2024-01-09 22:10:10 -05:00
Nicolas Goaziou
8fefe1b345
gnu: emacs-repology: Update to 1.2.4. 
* gnu/packages/emacs-xyz.scm (emacs-repology): Update to 1.2.4.

Change-Id: I72b0801ba732a4f34a2891f04d3d1b62674a1bd3
 2024-01-09 22:44:37 +01:00
Wilko Meyer
6e76509d24
gnu: linux-libre 4.14: Update to 4.14.335. 
* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.335.
(linux-libre-4.14-pristine-source, deblob-scripts-4.14): Update hashes.

Change-Id: I071427a52f188d599f28703374f5b7c42314777c
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-09 13:31:10 -05:00
Wilko Meyer
11baa979ef
gnu: linux-libre 4.19: Update to 4.19.304. 
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.304.
(linux-libre-4.19-pristine-source, deblob-scripts-4.19): Update hashes.

Change-Id: I14f228aa3b4a57417d7f8c392dc647709f599fac
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-09 13:31:10 -05:00
Wilko Meyer
029dd48301
gnu: linux-libre 5.4: Update to 5.4.266. 
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.266.
(linux-libre-5.4-pristine-source, deblob-scripts-5.4): Update hashes.

Change-Id: Ia1578dc94d3172735e5765ee90c46f865412810a
Signed-off-by: Leo Famulari <leo@famulari.name>
 2024-01-09 13:31:06 -05:00
Oleg Pykhalov
8920cf302c
news: Add entry for the new '--max-layers=N' option. 
* etc/news.scm: Add entry.

Change-Id: I286c04fd2cef820007606d1092ab45be4466fb19
 2024-01-09 15:49:36 +03:00
Troy Figiel
a1a645337a
gnu: Add python-ripser. 
* gnu/packages/machine-learning.scm (python-ripser): New variable.

Change-Id: I21b42e555a5017e68cf43a6eaa19d991db36723d
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:44 +01:00
Troy Figiel
7d25add8dd
gnu: Add python-persim. 
* gnu/packages/machine-learning.scm (python-persim): New variable.

Change-Id: I914071a90b4555d7d1218ce83337d49298effb01
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
e00314c406
gnu: Add python-hopcroftkarp. 
* gnu/packages/machine-learning.scm (python-hopcroftkarp): New variable.

Change-Id: I444f0371526d7a69d31363c228d5f7818bcf60dd
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
fe9a30f2f6
gnu: Add python-multimethod. 
* gnu/packages/python-xyz.scm (python-multimethod): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
185ebc01f6
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
 2024-01-09 10:19:43 +01:00
Troy Figiel
76470d47c5
gnu: python-h5py: Reformat with guix style. 
* gnu/packages/python-xyz.scm (python-h5py): Reformat with guix style.

Change-Id: I9c8fabcb8a438909ff70a2c98c9e01b3a82079f3
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
def734936f
gnu: python-h5py: Enable tests. 
* gnu/packages/python-xyz.scm (python-h5py)[native-inputs]: Add python-ipython and python-pytest.

Change-Id: Ia1cae8bce802805c9d9b38a3bf515423f9b719b4
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
67c3d230dc
gnu: Add python-portend. 
* gnu/packages/python-web.scm (python-portend): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
da2c300519
gnu: Add python-jaraco-collections. 
* gnu/packages/python-xyz.scm (python-jaraco-collections): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
5137af3e20
gnu: Add python-jaraco-text. 
* gnu/packages/python-xyz.scm (python-jaraco-text): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2024-01-09 10:19:43 +01:00
Troy Figiel
2de3f4d43c
gnu: Add python-zc-lockfile. 
* gnu/packages/python-web.scm (python-zc-lockfile): New variable.
 2024-01-09 10:19:43 +01:00