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Author SHA1 Message Date
Ricardo Wurmus be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus bb38287570
gnu: salmon: Update to 1.4.0. 
* 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.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 483cdf36a5
gnu: cereal: Update to 1.3.0. 
* gnu/packages/serialization.scm (cereal): Update to 1.3.0.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 9875dae429
gnu: macs: Update to 2.2.7.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 1ace395f9c
gnu: libgff: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
 2021-06-07 16:50:33 +02:00
Ricardo Wurmus 176513f5f3
gnu: jellyfish: Update to 2.3.0. 
* 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.
 2021-06-07 16:50:33 +02:00
Pierre Neidhardt e3611cc412
gnu: sbcl-fof: Update to 0.2.0. 
* gnu/packages/lisp-xyz.scm (sbcl-fof): Update to 0.2.0.
 2021-06-07 14:00:18 +02:00
Christopher Baines 26499816a9
etc: Add "bordeaux.guix.gnu.org.pub" public key file. 
* 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".
 2021-06-07 11:31:17 +01:00
Christopher Baines e536fc1786
gnu: guix-build-coordinator: Update to 0-31.4a47417. 
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-31.4a47417.
 2021-06-07 10:35:42 +01:00
Ricardo Wurmus 1ac8f05103
gnu: multiqc: Update to 1.10.1. 
* 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.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 856de4f61c
gnu: Add python-rich. 
* gnu/packages/python-xyz.scm (python-rich): New variable.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 17f3194150
gnu: python-dataclasses: Update to 0.8. 
* gnu/packages/python-xyz.scm (python-dataclasses): Update to 0.8.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus f41e56dcf1
gnu: python-attrs: Update to 21.2.0. 
* 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.
 2021-06-07 10:53:16 +02:00
Ricardo Wurmus 12964df69a
gnu: python-attrs: Conditionally execute tests. 
* gnu/packages/python-xyz.scm (python-attrs)[arguments]: Wrap "check" phase in
conditional expression.
 2021-06-07 10:53:16 +02:00
Mădălin Ionel Patrașcu a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3. 
* 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>
 2021-06-07 10:38:54 +03:00
Vinicius Monego e05100aafd
gnu: gtg: Update to 0.5. 
* 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>
 2021-06-07 10:38:54 +03:00
Vinicius Monego 1acc0cfbb9
gnu: srain: Update to 1.2.2. 
* 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>
 2021-06-07 10:38:54 +03:00
Matthew James Kraai d0b3af53e0
gnu: xf86-video-vesa: Update to 2.5.0. 
* gnu/packages/xorg.scm (xf86-video-vesa): Update to 2.5.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-06-07 10:38:54 +03:00
Lars-Dominik Braun dbe607925a
gnu: xpra: Update to 4.2. 
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>
 2021-06-07 09:33:57 +02:00
Ludovic Courtès 4604d43c0e
gnu: gnutls@3.6.16: Fix cross-compilation. 
Fixes <https://bugs.gnu.org/48771>.
Reported by Eric Brown <ecbrown@ericcbrown.com>.

* gnu/packages/tls.scm (gnutls-3.6.16)[arguments]: New field.
 2021-06-06 23:12:18 +02:00
Vinicius Monego c335fbf3cb
gnu: libheif: Update to 1.12.0. 
* gnu/packages/image.scm (libheif): Update to 1.12.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:18 +02:00
Vinicius Monego 13d8443acf
gnu: homebank: Update to 5.5.2. 
* gnu/packages/finance.scm (homebank): Update to 5.5.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:18 +02:00
Vinicius Monego 436dcb4ffa
gnu: cozy: Update to 1.0.3. 
* gnu/packages/ebook.scm (cozy): Update to 1.0.3.
[inputs]: Add granite, libgee.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:18 +02:00
Vinicius Monego a3082797b3
gnu: drawing: Update to 0.8.0. 
* gnu/packages/gnome.scm (drawing): Update to 0.8.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:18 +02:00
c4droid 018e09d4c8
gnu: Add pwntools. 
* gnu/packages/cybersecurity.scm (pwntools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-06-06 23:12:17 +02:00
Xinglu Chen b8baebae6a
doc: Add reference for ‘git-version’ and ‘hg-version’. 
* 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>
 2021-06-06 23:12:17 +02:00
Leo Prikler bde4fc00c0
gnu: komikku: Update to 0.29.1. 
* gnu/packages/gnome.scm (komikku): Update to 0.29.1.
 2021-06-06 21:56:35 +02:00
Tobias Geerinckx-Rice d102e9a139
gnu: dash: Update to 0.5.11.4. 
* gnu/packages/shells.scm (dash): Update to 0.5.11.4.
 2021-06-06 20:51:21 +02:00
Tobias Geerinckx-Rice 5c38e5e24e
gnu: pidgin: Update to 2.14.5. 
* gnu/packages/messaging.scm (pidgin): Update to 2.14.5.
 2021-06-06 20:51:20 +02:00
Mathieu Othacehe a068ed6a5f
scripts: substitute: Cache connection when looking for narinfos. 
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.
 2021-06-06 18:54:29 +02:00
Maxime Devos 82b0e27de1
lint: tests-true: Check if tests are enabled when cross-compiling. 
* 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>
 2021-06-06 18:49:12 +02:00
Solene Rapenne via Guix-patches via e2ad110f4c
gnu: vlc: Update to 3.0.14. 
* gnu/packages/video.scm (vlc): Update to 3.0.14.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2021-06-06 18:34:12 +02:00
Tobias Geerinckx-Rice d00713d49e
gnu: git: Update to 2.32.0. 
* gnu/packages/version-control.scm (git): Update to 2.32.0.
 2021-06-06 18:34:12 +02:00
Denis 'GNUtoo' Carikli 3c401ca6df
gnu: Add matterbridge. 
* gnu/packages/messaging.scm (matterbridge): New variable.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2021-06-06 18:29:36 +02:00
Hartmut Goebel 5d4bd2ee94
gnu: Add python-pytest-mp. 
* gnu/packages/python-check.scm (python-pytest-mp): New variable.
 2021-06-06 17:50:33 +02:00
Hartmut Goebel d8fed768a8
gnu: Add python-asn1tools. 
* gnu/packages/python-xyz.scm (python-asn1tools): New variable.
 2021-06-06 17:50:33 +02:00
pukkamustard 52dc188e12
gnu: Add ocaml-ppx-cold. 
* gnu/packages/ocaml.scm (ocaml-ppx-cold): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:17:22 +02:00
pukkamustard 7cf518ee85
gnu: Add ocaml-ppx-here. 
* gnu/packages/ocaml.scm (ocaml-ppx-here): New variable.
  (ocaml4.07-ppx-here): Inherit from ocaml-ppx-here.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:58 +02:00
pukkamustard c35fd0374d
gnu: Add ocaml-ppx-compare. 
* gnu/packages/ocaml.scm (ocaml-ppx-compare): New variable.
  (ocaml4.07-ppx-compare): Inherit from ocaml-ppx-compare.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:56 +02:00
pukkamustard 5b61a1472b
gnu: Add ocaml-syntax-shims. 
* gnu/packages/ocaml.scm (ocaml-syntax-shims): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:52 +02:00
pukkamustard 3649c56a5f
gnu: Add ocaml-ppx-let. 
* gnu/packages/ocaml.scm (ocaml-ppx-let): New variable.
  (ocaml4.07-ppx-let): Inherit from ocaml-ppx-let.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:50 +02:00
pukkamustard 6f4f9c4d55
gnu: Add ocaml-bigstringaf. 
* gnu/ocaml/packages.scm (ocaml-bigstringaf): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:48 +02:00
pukkamustard c729d98610
gnu: Add ocaml-ppx-sexp-conv. 
* gnu/packages/ocaml.scm (ocaml-ppx-sexp-conv): New variable.
  (ocaml4.07-ppx-sexp-conv): Inherit from ocaml-ppx-sexp-conv.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:45 +02:00
pukkamustard ec31363e22
gnu: Add ocaml-uunf. 
* gnu/packages/ocaml.scm (ocaml-uunf): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:43 +02:00
pukkamustard 59a39ec61b
gnu: Add ocaml-sedlex. 
* gnu/packages/ocaml.scm (ocaml-sedlex): New variable.
  (ocaml4.07-sedlex): Inherit from ocaml-sedlex.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:41 +02:00
pukkamustard 262683250c
gnu: Add ocaml-ppxlib. 
* gnu/packages/ocaml.scm (ocaml-ppxlib): New variable.
  (ocaml4.07-ppxlib): Inherit from ocaml-ppxlib.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:39 +02:00
pukkamustard 3c8899160b
gnu: ocaml-migrate-parsetree: Update to 2.1.0. 
* gnu/packages/ocaml.scm (ocaml-migrate-parsetree): Update to 2.1.0.
  (ocaml-migrate-parsetree-1): New variable.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:37 +02:00
pukkamustard cfa65d7770
gnu: Add ocaml-compiler-libs. 
* gnu/packages/ocaml.scm (ocaml-compiler-libs): New variable.
  (ocaml4.07-compiler-libs): Inherit from ocaml-compiler-libs.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:35 +02:00
pukkamustard 8f5aa879de
gnu: Add ocaml-stdio. 
* gnu/packages/ocaml.scm (ocaml-stdio): New variable.
  (ocaml4.07-stdio): Inherit from ocaml-stdio.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:33 +02:00
pukkamustard 4b6e1fba5a
gnu: Add ocaml-gen. 
* gnu/packages/ocaml.scm (ocaml-gen): New variable.
  (ocaml4.07-gen): Remove variable.
  (ocaml4.07-sedlex): Replace ocaml4.07-gen with ocaml-gen.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
 2021-06-06 17:16:31 +02:00