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* grafts: Record cache lookups for profiling.Ludovic Courtès2021-06-08
| | | | | * guix/grafts.scm (record-cache-lookup!): New procedure. (with-cache): Use it.
* store: Generalize cache lookup recording.Ludovic Courtès2021-06-08
| | | | | * guix/store.scm (cache-lookup-recorder): New procedure. (record-cache-lookup!): Define in terms of it.
* store: Support dynamic allocation of per-connection caches.Ludovic Courtès2021-06-08
| | | | | | | | | | | | | | | | | * guix/store.scm (<store-connection>)[object-cache]: Remove. [caches]: New field. (open-connection, port->connection): Adjust '%make-store-connection' calls accordingly. (%store-connection-caches, %object-cache-id): New variables. (allocate-store-connection-cache, vector-set) (store-connection-cache, set-store-connection-cache) (set-store-connection-caches!, set-store-connection-cache!): New procedures. (cache-object-mapping): Add #:cache parameter. (set-store-connection-object-cache!): Remove. (lookup-cached-object): Use 'store-connection-cache'. (run-with-store): Use 'store-connection-caches' and 'set-store-connection-caches!'.
* gnu: pantheon: Use modern 'define-module' syntax.Ludovic Courtès2021-06-08
| | | | | | | The :prefix bit introduced in 9f59a9b4bc93b3ef6cd3bd1c9eed04c30ba2d2d4 led to a test failure in 'tests/graph.scm'. * gnu/packages/pantheon.scm: Write #:prefix, not :prefix.
* doc: Update minimum Guile-Git version.Ludovic Courtès2021-06-08
| | | | * doc/guix.texi (Requirements): Update Guile-Git version.
* news: Fix typo.Ludovic Courtès2021-06-08
| | | | | * etc/news.scm: Remove 'x' introduced by mistake in dfdcd9d812d20a86babc4da8a01bc17e44900c3c.
* gnu: python-mappy: Move to (gnu packages bioinformatics).Efraim Flashner2021-06-08
| | | | | * gnu/packages/python-xyz.scm (python-mappy): Move to ... * gnu/packages/bioinformatics.scm: ... here.
* gnu: jami: Update to 20210606.1.e2f9490.Maxim Cournoyer2021-06-08
| | | | | | | * gnu/packages/jami.scm (jami): Update to 20210606.1.e2f9490. (pjproject-jami)[0019-ignore-down-interfaces]: Apply new custom patch. (jami-qt)[source]: Use %jami-sources, which now includes the Qt client. [phases]{change-directory}: New phase.
* gnu: jami: Always include the custom Jami patches with the sources.Maxim Cournoyer2021-06-08
| | | | | | | | | | | | | | | | | | | Before this change, there was a Jami origin containing the sources with the patches, and another one containing the sources but with the patches removed. Unify the source to always contain the patches, which adds just 1 MiB to the corresponding tarball and simplifies things. * gnu/packages/jami.scm (%jami-sources): Make it a simple variable. Move the docstring to a comment. Only remove the tarballs, always keeping the patches with the sources. Adjust the comments. (%sfl-patches): Remove variable. (jami-apply-dependency-patches): Rename to... (jami-apply-custom-patches): ... this. Adjust the input label used to 'jami-sources'. (pjproject-jami): Replace %sfl-patches by %jami-sources. Adjust following the renaming of the jami-apply-custom-patches procedure. (ffmpeg-jami): Likewise. Do not make a temporary binding, simply call the unquoted jami-apply-custom-patches procedure.
* gnu: opendht: Update to 2.2.0rc7-1.c8a0b44.Maxim Cournoyer2021-06-08
| | | | * gnu/packages/networking.scm (opendht): Update to 2.2.0rc7-1.c8a0b44.
* gnu: Add l3afpad.Leo Famulari2021-06-07
| | | | * gnu/packages/text-editors.scm (l3afpad): New variable.
* gnu: pigx-rnaseq: Update to 0.0.17.Ricardo Wurmus2021-06-08
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17. [arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase. [inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and python-deeptools. [native-inputs]: Add tzdata.
* gnu: ghostwriter: Update to 2.0.1.Leo Famulari2021-06-07
| | | | * gnu/packages/text-editors.scm (ghostwriter): Update to 2.0.1.
* gnu: python-pikepdf: Update to 2.12.2.Nicolas Goaziou2021-06-07
| | | | * gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.12.2.
* gnu: dino: Update to 0.2.1 [fixes CVE-2021-33896].Jack Hill2021-06-07
| | | | | | * gnu/packages/messaging.scm (dino): Update to 0.2.1. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: qtwebengine: Enable H.264 WebRTC encoding.Sergey Trofimov2021-06-07
| | | | | | | | | * gnu/packages/qt.scm (qtwebengine)[inputs]: Add openh264. [source]: Remove bundled openh264. [arguments]: Adjust build scripts accordingly in the 'substitute-source' phase. Pass '-webengine-proprietary-codecs' in the custom 'configure' phase. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: youtube-dl: Update to 2021.06.06.Xinglu Chen2021-06-07
| | | | | | * gnu/packages/video.scm (youtube-dl): Update to 2021.06.06. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
* gnu: isync: Update to 1.4.2.Xinglu Chen2021-06-07
| | | | | | * gnu/packages/mail.scm (isync): Update to 1.4.2. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
* gnu: pigx-rnaseq: Adjust to upgrade of salmon.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase "use-latest-salmon".
* gnu: salmon: Update to 1.4.0.Ricardo Wurmus2021-06-07
| | | | | | | | | * gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0. [arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags; remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add "fix-error-message-in-tests" phase, simplify "use-system-libraries" phase. [inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap sources.
* gnu: cereal: Update to 1.3.0.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/serialization.scm (cereal): Update to 1.3.0.
* gnu: macs: Update to 2.2.7.1.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
* gnu: libgff: Update to 2.0.0.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0. [home-page]: Update to new home.
* gnu: jellyfish: Update to 2.3.0.Ricardo Wurmus2021-06-07
| | | | | | | * gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0. [arguments]: Disable SSE to avoid tuning to the build node's CPU. [native-inputs]: Replace python-2 with python-wrapper. [license]: Update.
* gnu: sbcl-fof: Update to 0.2.0.Pierre Neidhardt2021-06-07
| | | | * gnu/packages/lisp-xyz.scm (sbcl-fof): Update to 0.2.0.
* etc: Add "bordeaux.guix.gnu.org.pub" public key file.Christopher Baines2021-06-07
| | | | | | | * etc/substitutes/bordeaux.guix.gnu.org.pub: New file. * Makefile.am (dist_pkgdata_DATA): Add it. * guix/self.scm (miscellaneous-files): Add "share/guix/bordeaux.guix.gnu.org.pub".
* gnu: guix-build-coordinator: Update to 0-31.4a47417.Christopher Baines2021-06-07
| | | | | * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-31.4a47417.
* gnu: multiqc: Update to 1.10.1.Ricardo Wurmus2021-06-07
| | | | | | | | * gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1. [arguments]: Remove build phase "relax-requirements"; replace "check" phase. [propagated-inputs]: Add python-coloredlogs, python-future, python-networkx, and python-rich; remove python-nose. [native-inputs]: Add python-pytest and the test suite.
* gnu: Add python-rich.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/python-xyz.scm (python-rich): New variable.
* gnu: python-dataclasses: Update to 0.8.Ricardo Wurmus2021-06-07
| | | | * gnu/packages/python-xyz.scm (python-dataclasses): Update to 0.8.
* gnu: python-attrs: Update to 21.2.0.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/python-xyz.scm (python-attrs): Update to 21.2.0. (python-attrs-bootstrap): Keep this at 19.3.0 to avoid mass rebuilds.
* gnu: python-attrs: Conditionally execute tests.Ricardo Wurmus2021-06-07
| | | | | * gnu/packages/python-xyz.scm (python-attrs)[arguments]: Wrap "check" phase in conditional expression.
* gnu: python-hic2cool: Update to 0.8.3.Mădălin Ionel Patrașcu2021-06-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. [source]: Download using git-fetch. [arguments]: Enable tests. Add phase to make test data writable. [propagated-inputs]: Add python-h5py, python-numpy, python-pandas, python-scipy. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: gtg: Update to 0.5.Vinicius Monego2021-06-07
| | | | | | | * gnu/packages/gnome.scm (gtg): Update to 0.5. [inputs]: Add gdk-pixbuf+svg, pango, python-lxml. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: srain: Update to 1.2.2.Vinicius Monego2021-06-07
| | | | | | | | | * gnu/packages/irc.scm (srain): Update to 1.2.2. [build-system]: Switch to meson-build-system. [arguments]: Add #:glib-or-gtk?. Remove 'fix-permissions phase. [native-inputs]: Add python-sphinx. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: xf86-video-vesa: Update to 2.5.0.Matthew James Kraai2021-06-07
| | | | | | * gnu/packages/xorg.scm (xf86-video-vesa): Update to 2.5.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: xpra: Update to 4.2.Lars-Dominik Braun2021-06-07
| | | | | | | | | | | | | | Fixes <https://issues.guix.gnu.org/issue/48890>. * gnu/packages/xorg.scm (xpra): Update to 4.2. [source]: Switch to ".tar.gz" archive and update patch file. [native-inputs]: Add pandoc. [arguments]: Adjust custom 'fix-paths phase for changes in source. * gnu/packages/patches/xpra-4.2-systemd-run.patch: Adapt to new version and rename file. * gnu/local.mk (dist_patch_DATA): Rename file. Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
* gnu: gnutls@3.6.16: Fix cross-compilation.Ludovic Courtès2021-06-06
| | | | | | | Fixes <https://bugs.gnu.org/48771>. Reported by Eric Brown <ecbrown@ericcbrown.com>. * gnu/packages/tls.scm (gnutls-3.6.16)[arguments]: New field.
* gnu: libheif: Update to 1.12.0.Vinicius Monego2021-06-06
| | | | | | * gnu/packages/image.scm (libheif): Update to 1.12.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: homebank: Update to 5.5.2.Vinicius Monego2021-06-06
| | | | | | * gnu/packages/finance.scm (homebank): Update to 5.5.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: cozy: Update to 1.0.3.Vinicius Monego2021-06-06
| | | | | | | * gnu/packages/ebook.scm (cozy): Update to 1.0.3. [inputs]: Add granite, libgee. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: drawing: Update to 0.8.0.Vinicius Monego2021-06-06
| | | | | | * gnu/packages/gnome.scm (drawing): Update to 0.8.0. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add pwntools.c4droid2021-06-06
| | | | | | * gnu/packages/cybersecurity.scm (pwntools): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* doc: Add reference for ‘git-version’ and ‘hg-version’.Xinglu Chen2021-06-06
| | | | | | | | | * doc/contributing.texi (Version Numbers): Document ‘git-version’ and ‘hg-version’. * doc/guix.texi (package Reference): Reference ‘Version Numbers’ section for version naming guidelines. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: komikku: Update to 0.29.1.Leo Prikler2021-06-06
| | | | * gnu/packages/gnome.scm (komikku): Update to 0.29.1.
* gnu: dash: Update to 0.5.11.4.Tobias Geerinckx-Rice2021-06-06
| | | | * gnu/packages/shells.scm (dash): Update to 0.5.11.4.
* gnu: pidgin: Update to 2.14.5.Tobias Geerinckx-Rice2021-06-06
| | | | * gnu/packages/messaging.scm (pidgin): Update to 2.14.5.
* scripts: substitute: Cache connection when looking for narinfos.Mathieu Othacehe2021-06-06
| | | | | | | | | | | | The process-substitution procedure is opening two distinct connections. The first one when looking for narinfo by calling lookup-narinfo and the other one when fetching nar files. Cache the connection when looking for narinfos so that process-substitution only opens one connection. * guix/scripts/substitute.scm (lookup-narinfo): Cache connection by using open-connection-for-uri/cached.
* lint: tests-true: Check if tests are enabled when cross-compiling.Maxime Devos2021-06-06
| | | | | | | | | | | * guix/lint.scm (check-tests-true): New linter. (%local-checkers)[tests-true]: Add it. * tests/lint.scm ("tests-true: #:tests? must not be set to #t") ("tests-true: absent #:tests? is acceptable") ("tests-true: #:tests? #f is acceptable") ("tests-true: #:tests? #t acceptable when compiling natively"): Test it. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
* gnu: vlc: Update to 3.0.14.Solene Rapenne via Guix-patches via2021-06-06
| | | | | | * gnu/packages/video.scm (vlc): Update to 3.0.14. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
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