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2022-01-31gnu: ruby-mustache: Fix race condition.Danny Milosavljevic
* gnu/packages/patches/ruby-mustache-1.1.1-fix-race-condition-tests.patch: New file. * gnu/packages/ruby.scm (ruby-mustache)[source]<#:origin>: Add it. * gnu/local.mk (dist_patch_DATA): Add it.
2022-01-31gnu: Add scvelo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31gnu: python-seaborn: Fix build.Ricardo Wurmus
* 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.
2022-01-31gnu: python-anndata: Update to 0.7.8.Ricardo Wurmus
* 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.
2022-01-31gnu: Add python-xlrd-1.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-xlrd-1): New variable.
2022-01-31gnu: python-louvain-0.6: Update to 0.7.1.Ricardo Wurmus
* 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.
2022-01-31gnu: python-louvain: Update to 0.16.Ricardo Wurmus
* gnu/packages/graph.scm (python-louvain): Update to 0.16.
2022-01-31gnu: bwa-meth: Remove trailing #T from build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase.
2022-01-31gnu: bwa-meth: Update to 0.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-31gnu: fontmanager: Add missing input.Julien Lepiller
* gnu/packages/fontutils.scm (fontmanager)[native-inputs]: Add python-wrapper.
2022-01-31gnu: java-log4j-api: Update to 2.17.1.Julien Lepiller
* gnu/packages/java.scm (java-log4j-api): Update to 2.17.1.
2022-01-31gnu: pre-commit: Update to 2.17.0.Vinicius Monego
* gnu/packages/version-control.scm (pre-commit): Update to 2.17.0.
2022-01-31gnu: shotcut: Update to 22.01.30.Vinicius Monego
* gnu/packages/video.scm (shotcut): Update to 22.01.30.
2022-01-31gnu: texlive-bin: Fix building on riscv64-linux.Efraim Flashner
* gnu/packages/tex.scm (texlive-bin)[arguments]: Adjust configure-flags for riscv64-linux to skip luajit based binaries. Add phase to skip some tests.
2022-01-30gnu: Remove OpenSSL 1.0.Marius Bakke
This package no longer has any users in Guix. * gnu/packages/tls.scm (openssl-1.0): Remove variable.
2022-01-30gnu: Remove unused patch.Marius Bakke
* gnu/packages/patches/openssl-CVE-2019-1559.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly.
2022-01-30gnu: OpenSSL: Add 3.0.Marius Bakke
* 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.
2022-01-30gnu: util-linux-with-udev: Remove input labels.Marius Bakke
* gnu/packages/linux.scm (util-linux+udev)[inputs]: Use MODIFY-INPUTS.
2022-01-30gnu: expat: Update replacement to 2.4.4 [fixes CVE-2022-23852, CVE-2022-23990].Marius Bakke
* gnu/packages/xml.scm (expat/fixed): Update to 2.4.4.
2022-01-30gnu: waylandpp: Update to 0.2.9.Marius Bakke
* gnu/packages/freedesktop.scm (waylandpp): Update to 0.2.9.
2022-01-30gnu: Add python-gwcs.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-gwcs): New variable. Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30gnu: Add python-asdf-wcs-schemas.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-asdf-wcs-schemas): New variable. Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30gnu: Add python-asdf-astropy.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-asdf-astropy): New variable. Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30gnu: Add python-asdf-coordinates-schemas.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-asdf-coordinates-schemas): New variable. Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30gnu: Add python-asdf-transform-schemas.Sharlatan Hellseher
* gnu/packages/astronomy.scm (python-asdf-transform-schemas): New variable. Signed-off-by: Vinicius Monego <monego@posteo.net>
2022-01-30gnu: python-asdf: Update to 2.8.3.Sharlatan Hellseher
* 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>
2022-01-30services: zabbix: Support gexps in configuration serializer.Marius Bakke
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.
2022-01-30gnu: patchelf: Add release-monitoring-url.Efraim Flashner
* gnu/packages/elf.scm (patchelf)[properties]: New field.
2022-01-30gnu: mesa: Add support for riscv64-linux.Efraim Flashner
* 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.
2022-01-30gnu: audacity: Add fallback to locate ffmpeg via pkg-config.Liliana Marie Prikler
* 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.
2022-01-29gnu: k3b: Do not depend on QtWebKit.Leo Famulari
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.
2022-01-29gnu: luminance-hdr: Replace dependency on QtWebKit with QtWebEngine.Leo Famulari
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.
2022-01-29gnu: python-black: Document the tomli version requirements.Leo Famulari
* gnu/packages/python-xyz.scm (python-black): Add comment.
2022-01-29gnu: choqok: Don't depend on QtWebKit.Leo Famulari
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.
2022-01-29gnu: fcitx5-chinese-addons: Replace the dependency on QtWebKit with QtWebEngine.Leo Famulari
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.
2022-01-29gnu: texmaker: Don't depend on QtWebKit.Leo Famulari
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.
2022-01-29gnu: wpewebkit: Update to 2.34.3 [security fixes].Liliana Marie Prikler
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.
2022-01-29gnu: wpebackend-fdo: Update to 1.12.0.Liliana Marie Prikler
* gnu/packages/webkit.scm (wpebackend-fdo): Update to 1.12.0. [build-system]: Use meson-build-system. [inputs]: Add libepoxy.
2022-01-29gnu: libwpe: Update to 1.12.0.Liliana Marie Prikler
* gnu/packages/webkit.scm (libwpe): Update to 1.12.0. [build-system]: Use meson-build-system.
2022-01-29gnu: WPE WebKit: Set the Common Platform Enumeration (CPE) name.Leo Famulari
* gnu/packages/webkit.scm (wpewebkit)[properties]: New field.
2022-01-29gnu: kdenlive: Don't depend on QtWebKit.Leo Famulari
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.
2022-01-29gnu: nextcloud-client: Don't depend on QtWebKit.Leo Famulari
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.
2022-01-29tests: Add system test for TimescaleDB.Marius Bakke
* gnu/tests/databases.scm (%timescaledb-os, run-timescaledb-test, %test-timescaledb): New variables.
2022-01-29services: postgresql: Export missing <postgresql-configuration> accessor.Marius Bakke
* gnu/services/databases.scm: Export POSTGRESQL-CONFIGURATION-EXTENSION-PACKAGES.
2022-01-29tests: postgresql: Test the default PostgreSQL.Marius Bakke
* gnu/tests/databases.scm (%postgresql-os): Change from POSTGRESQL-10 to POSTGRESQL.
2022-01-29gnu: zabbix: Update to 5.4.9.Marius Bakke
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 5.4.9.
2022-01-29services: zabbix-agent: Set the PATH variable.Marius Bakke
* gnu/services/monitoring.scm (zabbix-agent-shepherd-service)[start]: Set the PATH variable to the common values.
2022-01-29gnu: Add TimescaleDB.Marius Bakke
* gnu/packages/databases.scm (timescaledb): New variable.
2022-01-29services: zabbix-frontend: Adjust indentation.Marius Bakke
* gnu/services/monitoring.scm (zabbix-front-end-activation): Reindent.
2022-01-29services: zabbix-frontend: Enable IEEE754-compatible history values.Marius Bakke
* gnu/services/monitoring.scm (zabbix-front-end-config): Specify $DB['DOUBLE_IEEE754'] in the configuration file, as per current example.
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