Commit graph

92975 commits

Author SHA1 Message Date
Ricardo Wurmus
7fc8a6faf6
gnu: Add scvelo.
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31 16:07:40 +01:00
Ricardo Wurmus
9686c828ed
gnu: python-seaborn: Fix build.
* gnu/packages/python-xyz.scm (python-seaborn)[source]: Add patch.
[arguments]: Add build phase 'patch-more-tests.
* gnu/packages/patches/python-seaborn-2690.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2022-01-31 16:07:40 +01:00
Ricardo Wurmus
f383aca408
gnu: python-anndata: Update to 0.7.8.
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.8.
[arguments]: Embed the appropriate version string instead of letting it
try (and fail) to discover the correct string at load time.
[propagated-inputs]: Add python-xlrd-1.
2022-01-31 16:07:40 +01:00
Ricardo Wurmus
ad516f4009
gnu: Add python-xlrd-1.
* gnu/packages/python-xyz.scm (python-xlrd-1): New variable.
2022-01-31 16:07:39 +01:00
Ricardo Wurmus
cd4bf5ecb4
gnu: python-louvain-0.6: Update to 0.7.1.
* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1.
[arguments]: Add build phases 'find-igraph and 'pretend-version.
[native-inputs]: Add python-setuptools-scm and python-wheel.
Rename this variable...
(python-louvain-0.7): ...to this, naturally.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update
reference to python-louvain-0.6.
2022-01-31 16:07:39 +01:00
Ricardo Wurmus
90b6b857fd
gnu: python-louvain: Update to 0.16.
* gnu/packages/graph.scm (python-louvain): Update to 0.16.
2022-01-31 16:07:39 +01:00
Ricardo Wurmus
9ce1fd24e3
gnu: bwa-meth: Remove trailing #T from build phase.
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
2022-01-31 16:07:39 +01:00
Ricardo Wurmus
f32a49fceb
gnu: bwa-meth: Update to 0.2.3.
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-31 16:07:39 +01:00
Julien Lepiller
9295b91116
gnu: fontmanager: Add missing input.
* gnu/packages/fontutils.scm (fontmanager)[native-inputs]: Add
python-wrapper.
2022-01-31 15:53:48 +01:00
Julien Lepiller
c636a8786e
gnu: java-log4j-api: Update to 2.17.1.
* gnu/packages/java.scm (java-log4j-api): Update to 2.17.1.
2022-01-31 15:29:14 +01:00
Vinicius Monego
1b778f03e0
gnu: pre-commit: Update to 2.17.0.
* gnu/packages/version-control.scm (pre-commit): Update to 2.17.0.
2022-01-31 10:56:33 -03:00
Vinicius Monego
4014672172
gnu: shotcut: Update to 22.01.30.
* gnu/packages/video.scm (shotcut): Update to 22.01.30.
2022-01-31 10:55:48 -03:00
Efraim Flashner
e217174b7b
gnu: texlive-bin: Fix building on riscv64-linux.
* gnu/packages/tex.scm (texlive-bin)[arguments]: Adjust configure-flags
for riscv64-linux to skip luajit based binaries. Add phase to skip some
tests.
2022-01-31 09:22:49 +02:00
Marius Bakke
43dd34c777
gnu: Remove OpenSSL 1.0.
This package no longer has any users in Guix.

* gnu/packages/tls.scm (openssl-1.0): Remove variable.
2022-01-30 17:04:34 +01:00
Marius Bakke
9b8839099e
gnu: Remove unused patch.
* gnu/packages/patches/openssl-CVE-2019-1559.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2022-01-30 17:04:34 +01:00
Marius Bakke
2932c421a3
gnu: OpenSSL: Add 3.0.
* gnu/packages/tls.scm (openssl-3.0): New variable.
* gnu/packages/patches/openssl-3.0-c-rehash-in.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2022-01-30 17:04:34 +01:00
Marius Bakke
753cacb1ad
gnu: util-linux-with-udev: Remove input labels.
* gnu/packages/linux.scm (util-linux+udev)[inputs]: Use MODIFY-INPUTS.
2022-01-30 17:04:34 +01:00
Marius Bakke
5c9c7856a6
gnu: expat: Update replacement to 2.4.4 [fixes CVE-2022-23852, CVE-2022-23990].
* gnu/packages/xml.scm (expat/fixed): Update to 2.4.4.
2022-01-30 17:04:34 +01:00
Marius Bakke
bb5f6d8cef
gnu: waylandpp: Update to 0.2.9.
* gnu/packages/freedesktop.scm (waylandpp): Update to 0.2.9.
2022-01-30 17:04:34 +01:00
Sharlatan Hellseher
3e497b3a4c
gnu: Add python-gwcs.
* gnu/packages/astronomy.scm (python-gwcs): New variable.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:19 -03:00
Sharlatan Hellseher
007495210d
gnu: Add python-asdf-wcs-schemas.
* gnu/packages/astronomy.scm (python-asdf-wcs-schemas): New variable.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:19 -03:00
Sharlatan Hellseher
7b2747c81d
gnu: Add python-asdf-astropy.
* gnu/packages/astronomy.scm (python-asdf-astropy): New variable.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:18 -03:00
Sharlatan Hellseher
527ee1bdc8
gnu: Add python-asdf-coordinates-schemas.
* gnu/packages/astronomy.scm (python-asdf-coordinates-schemas): New variable.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:18 -03:00
Sharlatan Hellseher
89a5c53f38
gnu: Add python-asdf-transform-schemas.
* gnu/packages/astronomy.scm (python-asdf-transform-schemas): New variable.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:17 -03:00
Sharlatan Hellseher
e1437e7ec1
gnu: python-asdf: Update to 2.8.3.
* gnu/packages/astronomy.scm: (python-asdf): Update to 2.8.3.
[inputs]: Use the new style. Move python-importlib-resources,
python-jsonschema, python-numpy, python-pyyaml to ...
[propagated-inputs]: ... here. Use the new style. Add python-jmespath.

Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30 11:46:17 -03:00
Marius Bakke
ab8b76b735
services: zabbix: Support gexps in configuration serializer.
This makes it possible to do e.g. (include-files (list (local-file "foo.conf"))).

* gnu/services/monitoring.scm (serialize-field, serialize-list,
serialize-include-files, serialize-extra-options): Rewrite as gexps.
(zabbix-server-config-file, zabbix-agent-config-file): Simplify builders by
using FORMAT.
2022-01-30 14:47:43 +01:00
Efraim Flashner
dea8810036
gnu: patchelf: Add release-monitoring-url.
* gnu/packages/elf.scm (patchelf)[properties]: New field.
2022-01-30 14:58:28 +02:00
Efraim Flashner
0b1be21d1f
gnu: mesa: Add support for riscv64-linux.
* gnu/packages/gl.scm (mesa)[inputs]: Add llvm-11 on riscv64-linux.
[native-inputs]: Add glslang on riscv64-linux.
[arguments]: In configure-flags adjust gallium-drivers to swap the
power* and intel drivers for the fallback option. Specify riscv64-linux
configure options for vulkan-drivers. Enable the vulkan-overlay-layer
and llvm support. Adjust the custom 'disable-failing-test phase to have
a riscv64-linux section.
2022-01-30 12:28:08 +02:00
Liliana Marie Prikler
6589966b97
gnu: audacity: Add fallback to locate ffmpeg via pkg-config.
* gnu/packages/patches/audacity-ffmpeg-fallback.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it here.
* gnu/packages/audio.scm (audacity)[patches]: Use it here.
[inputs]: Add back ffmpeg.
2022-01-30 08:11:00 +01:00
Leo Famulari
090e925816
gnu: k3b: Do not depend on QtWebKit.
According to CMakelists.txt, "Qt5WebKitWidgets is used for prettier
k3bdiskinfoview."

See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/kde-multimedia.scm (k3b)[inputs]: Remove qtwebkit.
2022-01-29 19:18:46 -05:00
Leo Famulari
4bd060909d
gnu: luminance-hdr: Replace dependency on QtWebKit with QtWebEngine.
See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/image-viewers.scm (luminance-hdr)[inputs]: Remove qtwebkit. Add
qtwebengine, qtdeclarative, and qtwebchannel.
2022-01-29 18:43:13 -05:00
Leo Famulari
f3d0ed37ea
gnu: python-black: Document the tomli version requirements.
* gnu/packages/python-xyz.scm (python-black): Add comment.
2022-01-29 18:29:32 -05:00
Leo Famulari
f928b56d13
gnu: choqok: Don't depend on QtWebKit.
These dependencies were only used to create a plugin for Konqueror, which Guix
does not include.

See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/kde-internet.scm (choqok)[inputs]: Remove kdewebkit and qtwebkit.
2022-01-29 18:16:48 -05:00
Leo Famulari
db17f8b502
gnu: fcitx5-chinese-addons: Replace the dependency on QtWebKit with QtWebEngine.
See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/fcitx5.scm (fcitx5-chinese-addons)[inputs]: Remove qtwebkit. Add
qtdeclarative, qtwebchannel, and qtwebengine.
[arguments]: Pass "-DUSE_WEBKIT=off" to #:configure-flags.
2022-01-29 17:59:30 -05:00
Leo Famulari
f8bfb2d856
gnu: texmaker: Don't depend on QtWebKit.
The program stopped using QtWebKit in version 5.0.

See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/tex.scm (texmaker)[inputs]: Remove qtwebkit.
2022-01-29 17:31:17 -05:00
Liliana Marie Prikler
07f45615c3
gnu: wpewebkit: Update to 2.34.3 [security fixes].
This update fixes all the security issues fixed upstream between
versions 2.30.5 and 2.34.3:

https://webkitgtk.org/news.html

* gnu/packages/webkit.scm (wpewebkit): Update to 2.34.3.
[#:phases]: Add ‘patch-cmake’ phase to fix an error in the install directories
of the documentation.
[inputs]: Add lcms.
2022-01-29 16:39:56 -05:00
Liliana Marie Prikler
f0bc429a52
gnu: wpebackend-fdo: Update to 1.12.0.
* gnu/packages/webkit.scm (wpebackend-fdo): Update to 1.12.0.
[build-system]: Use meson-build-system.
[inputs]: Add libepoxy.
2022-01-29 16:39:55 -05:00
Liliana Marie Prikler
c97e07be56
gnu: libwpe: Update to 1.12.0.
* gnu/packages/webkit.scm (libwpe): Update to 1.12.0.
[build-system]: Use meson-build-system.
2022-01-29 16:39:51 -05:00
Leo Famulari
08875dd556
gnu: WPE WebKit: Set the Common Platform Enumeration (CPE) name.
* gnu/packages/webkit.scm (wpewebkit)[properties]: New field.
2022-01-29 15:37:17 -05:00
Leo Famulari
0442d683c3
gnu: kdenlive: Don't depend on QtWebKit.
Kdenlive no longer uses QtWebKit.

See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/kde.scm (kdenlive)[inputs]: Remove qtwebkit.
2022-01-29 15:29:12 -05:00
Leo Famulari
9d13747fc2
gnu: nextcloud-client: Don't depend on QtWebKit.
This package propagates QtWebEngine and doesn't keep a reference to QtWebKit.

See <https://issues.guix.gnu.org/53289> for more information about this change.

* gnu/packages/sync.scm (qtwebkit)[inputs]: Remove qtwebkit.
[arguments]: Remove related #:configure-flag that is not recognized by
our version of nextcloud-client.
2022-01-29 13:38:56 -05:00
Marius Bakke
b6b0cfa2f8
tests: Add system test for TimescaleDB.
* gnu/tests/databases.scm (%timescaledb-os, run-timescaledb-test,
%test-timescaledb): New variables.
2022-01-29 16:09:03 +01:00
Marius Bakke
59847afda7
services: postgresql: Export missing <postgresql-configuration> accessor.
* gnu/services/databases.scm: Export POSTGRESQL-CONFIGURATION-EXTENSION-PACKAGES.
2022-01-29 16:09:03 +01:00
Marius Bakke
765be3dcef
tests: postgresql: Test the default PostgreSQL.
* gnu/tests/databases.scm (%postgresql-os): Change from POSTGRESQL-10 to
POSTGRESQL.
2022-01-29 16:09:03 +01:00
Marius Bakke
45681b89a8
gnu: zabbix: Update to 5.4.9.
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 5.4.9.
2022-01-29 12:52:38 +01:00
Marius Bakke
756f16aa01
services: zabbix-agent: Set the PATH variable.
* gnu/services/monitoring.scm (zabbix-agent-shepherd-service)[start]: Set the
PATH variable to the common values.
2022-01-29 12:52:38 +01:00
Marius Bakke
81873cbc5d
gnu: Add TimescaleDB.
* gnu/packages/databases.scm (timescaledb): New variable.
2022-01-29 12:52:38 +01:00
Marius Bakke
8fa6f975d4
services: zabbix-frontend: Adjust indentation.
* gnu/services/monitoring.scm (zabbix-front-end-activation): Reindent.
2022-01-29 12:52:37 +01:00
Marius Bakke
7f12a40e9a
services: zabbix-frontend: Enable IEEE754-compatible history values.
* gnu/services/monitoring.scm (zabbix-front-end-config): Specify
$DB['DOUBLE_IEEE754'] in the configuration file, as per current example.
2022-01-29 12:52:37 +01:00
Marius Bakke
5122805c48
services: zabbix-server: Add shepherd actions for runtime control commands.
* gnu/services/monitoring.scm (zabbix-server-runtime-control-procedure,
zabbix-server-actions): New variables.
(zabbix-server-shepherd-service)[actions]: New field.  Let-bind variables
common between actions and the start procedure.
2022-01-29 12:52:37 +01:00