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Author SHA1 Message Date
Tobias Geerinckx-Rice 7214dc8449
gnu: python-duniterpy: Update to 0.60.1. 
* gnu/packages/finance.scm (python-duniterpy): Update to 0.60.1.
 2020-11-14 01:50:28 +01:00
Tobias Geerinckx-Rice 647d1ece49
gnu: inxi-minimal: Update to 3.1.09-1. 
* gnu/packages/admin.scm (inxi-minimal): Update to 3.1.09-1.
 2020-11-14 01:50:27 +01:00
Ludovic Courtès c6e8f40f2c
maint: Rebuild '.version' when 'config.status' changes. 
* Makefile.am ($(top_srcdir)/.version): Depend on 'config.status'.  Use
$(AM_V_GEN).
 2020-11-13 22:48:34 +01:00
Ricardo Wurmus 4e9b2e8ba2
gnu: inspekt3d: Build with Guile 3. 
* gnu/packages/engineering.scm (inspekt3d)
[source]: Add snippet to allow building with Guile 3.0.
[inputs]: Replace guile-2.2 with guile-3.0.
[propagated-inputs]: Replace guile-opengl with guile3.0-opengl.
 2020-11-13 21:42:45 +01:00
Ricardo Wurmus dd012afde4
gnu: libfive: Update to 0-4.8ca1b86. 
* gnu/packages/engineering.scm (libfive): Update to 0-4.8ca1b86.
[inputs]: Replace guile-2.2 with guile-3.0.
 2020-11-13 21:42:45 +01:00
Ludovic Courtès 627e61f1a8
maint: Add '.guix-authorizations' to the distribution. 
Reported by Vagrant Cascadian.

* Makefile.am (EXTRA_DIST): Add .guix-authorizations.
 2020-11-13 21:31:22 +01:00
Tobias Geerinckx-Rice f6e031ab36
gnu: julia: Update to 1.5.3. 
* gnu/packages/julia.scm (julia): Update to 1.5.3.
(libuv-julia): Update to 1fcc6d66f9df74189c74d3d390f02202bb7db953.
(julia-patch): Update version.  No change to patches.
 2020-11-13 19:43:25 +01:00
Tobias Geerinckx-Rice db2f95f1c2
gnu: libwhich: Compile natively, too. 
This follows up on commit 12424b3ecf.

* gnu/packages/julia.scm (libwhich)[arguments]: Fix non-cross
compilation.
 2020-11-13 19:43:25 +01:00
John Soo 0cdc13ce43
guix build: Expose log-url for third parties. 
* guix/scripts/build.scm (log-url): Expose it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-11-13 18:11:30 +01:00
John Soo e783cd51ba
pack: Expose some bindings for third-party use. 
* guix/scripts/pack.scm (compressor-name, compressor-extension,
compressor-command, %compressors, %formats): Export.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-11-13 18:10:11 +01:00
Ludovic Courtès 0b146ceaab
Merge branch 'version-1.2.0' of ssh://git.sv.gnu.org/srv/git/guix into version-1.2.0 2020-11-13 17:02:49 +01:00
Maxim Cournoyer 4e01bc440a
gnu: python-pysam: Update to version 0.16.0.1. 
The check phase was failing with:

starting phase `check'
make: Entering directory '...drv-0/python-pysam-0.15.1-checkout/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[main] "samtools import" has been removed. Please use "samtools view" instead.
make: *** [Makefile:56: ex1.bam] Error 1

* gnu/packages/bioinformatics.scm (python-pysam): Update to version 0.16.0.1.
[phases]{check}: Delete a couple more failing test files.
[native-inputs]: Add python-pytest.
 2020-11-13 10:17:00 -05:00
Roel Janssen 37ba374a53
gnu: Fix build for python-pysam. 
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
  samtools-1.9, and bcftools-1.9.
 2020-11-13 16:16:43 +01:00
Roel Janssen ecc309c142
gnu: Add bcftools-1.9. 
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
 2020-11-13 16:14:01 +01:00
Ekaitz Zarraga 3a15847685
gnu: dino: Update to 0.2.0 
Update of the recently released Dino 0.2.0 version.

Thanks!

From 0b764d48996f3851ee2596a25f1fd42a8d3f4063 Mon Sep 17 00:00:00 2001
From: Ekaitz Zarraga <ekaitz@elenq.tech>
Date: Fri, 13 Nov 2020 12:18:11 +0100
Subject: [PATCH] gnu: dino: Update to 0.2.0

    * gnu/packages/messaging.scm (dino): Update to 0.2.0

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2020-11-13 15:02:33 +01:00
Tobias Geerinckx-Rice 12424b3ecf
gnu: libwhich: Cross-compile. 
* gnu/packages/julia.scm (libwhich)[arguments]: Use CC-FOR-TARGET.
Look for zlib in NATIVE-INPUTS.
 2020-11-13 15:02:32 +01:00
Ludovic Courtès 4b2ce77ca0
gnu: guix: Update to 3ba6ffd. 2020-11-13 15:01:25 +01:00
Roel Janssen c3232fcc77
gnu: bedtools: Use samtools-1.9. 
The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814

* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
 2020-11-13 14:49:31 +01:00
Roel Janssen da4a38edad
gnu: Add samtools-1.9. 
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
 2020-11-13 14:49:27 +01:00
Roel Janssen 3ede804f6d
gnu: Add htslib-1.9. 
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
 2020-11-13 14:49:20 +01:00
Ludovic Courtès 3ba6ffd0dd
gnu: guix: Update to 1.2.0rc1. 2020-11-13 14:40:28 +01:00
Ludovic Courtès 1e272d42f6
Update NEWS. 2020-11-13 09:13:56 +01:00
Ludovic Courtès ae10ec441a
gnu: glib: Graft patch to detect changes to the installed applications. 
Fixes <https://bugs.gnu.org/35594>.
Reported by sirgazil <sirgazil@zoho.com> and others.

* gnu/packages/patches/glib-appinfo-watch.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/glib.scm (glib)[replacement]: New field.
(glib-with-gio-patch): New variable.
(glib-with-documentation): Use 'package/inherit'.
 2020-11-13 09:13:56 +01:00
Ludovic Courtès a30e7a72fc
maint: Use 'guix' instead of 'guile3.0-guix' for the binary tarball. 
* Makefile.am (GUIX_FOR_BINARY_TARBALL): Change to 'guix'.
 2020-11-13 09:13:56 +01:00
Tobias Geerinckx-Rice 2646b9d6d3
gnu: vim: Update to 8.2.1980. 
* gnu/packages/vim.scm (vim): Update to 8.2.1980.
 2020-11-13 01:52:16 +01:00
Tobias Geerinckx-Rice bb2232206c
gnu: criu: Support nftables. 
* gnu/packages/virtualization.scm (criu)[inputs]: Add nftables.
 2020-11-13 01:43:57 +01:00
Tobias Geerinckx-Rice 0a46a1e918
gnu: criu: Update to 3.15. 
* gnu/packages/virtualization.scm (criu): Update to 3.15.
 2020-11-13 01:43:56 +01:00
Tobias Geerinckx-Rice c645d44f01
gnu: youtube-dl: Update to 2020.11.12. 
* gnu/packages/video.scm (youtube-dl): Update to 2020.11.12.
 2020-11-13 01:43:56 +01:00
Tobias Geerinckx-Rice a400ab4f14
gnu: knot: Update to 3.0.2. 
* gnu/packages/dns.scm (knot): Update to 3.0.2.
 2020-11-13 01:27:24 +01:00
Tobias Geerinckx-Rice 72ee78a6bf
gnu: muchsync: Update to 6. 
* gnu/packages/mail.scm (muchsync): Update to 6.
 2020-11-13 01:27:23 +01:00
Tobias Geerinckx-Rice f41c9ab4c3
gnu: gpxsee: Update to 7.36. 
* gnu/packages/gps.scm (gpxsee): Update to 7.36.
 2020-11-13 01:27:23 +01:00
Tanguy Le Carrour 5f72da5f8a
gnu: alot: Update to 0.9.1. 
* gnu/packages/mail.scm (alot): Update to 0.9.1.
[arguments]: Fix some tests and disable some others.
[native-inputs]: Add procps.
[inputs]: Remove python2-magic, python2-configobj, python2-twisted,
python2-urwid, python2-urwidtrees, python2-pygpgme and python2-notmuch.
Add gnupg, python-magic, python-configobj, python-twisted,
python-service-identity, python-urwid, python-urwidtrees,
python-gpg and python-notmuch.
[synopsis]: Update synopsis.
[description]: Update description.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-11-12 23:31:26 +01:00
Tanguy Le Carrour 30a1476bbc
gnu: afew: Update to 3.0.1. 
* gnu/packages/mail.scm (afew): Update to 3.0.1.
[inputs]: Add notmuch and python-dkimpy.
[native-inputs]: Add python-freezegun.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2020-11-12 23:24:16 +01:00
Marius Bakke 1ed9a078e1
gnu: ungoogled-chromium: Update to 86.0.4240.198-0.b68e17f [security fixes]. 
This fixes CVE-2020-16013 and CVE-2020-16017.

* gnu/packages/chromium.scm (%chromium-version): Set to 86.0.4240.198.
(ungoogled-chromium): Update hash.
 2020-11-12 21:54:17 +01:00
Maxim Cournoyer c410e9e531
gnu: python-flask-basicauth: Fix indentation. 
* gnu/packages/python-web.scm (python-flask-basicauth): Fix indentation.
 2020-11-12 15:17:57 -05:00
Maxim Cournoyer a4cfdab56a
gnu: python-flask-basicauth: Fix build. 
* gnu/packages/python-web.scm (python-flask-basicauth)[phases]: Add a
'fix-imports phase.
 2020-11-12 15:17:29 -05:00
Tobias Geerinckx-Rice 66479da5e2
gnu: tor: Update to 0.4.4.6 [fixes TROVE-2020-005]. 
* gnu/packages/tor.scm (tor): Update to 0.4.4.6.
 2020-11-12 19:01:13 +01:00
Maxim Cournoyer 3de898b43c
maint: update-guix-package: Optionally add sources to store. 
Following discussions in <https://issues.guix.gnu.org/43893>, keeping a copy
of the updated package source is desirable when generating a release.

* build-aux/update-guix-package.scm (version-controlled?): Remove variable.
(call-with-temporary-git-worktree): Renamed from
'with-temporary-git-worktree'.  Update doc.  Do not change directory
implicitly.  Define as a procedure, not a syntax.
(keep-source-in-store): New procedure.
(main): Adjust to use with call-with-temporary-git-worktree.  Add the sources
to the store when GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT is set.  Exit gracefully
when FIND-ORIGIN-REMOTE returns #f.
(%savannah-guix-git-repo-push-url-regexp): Adjust match for a potential colon
separator.
* Makefile.am (GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT): Adjust.
* .dir-locals.el (scheme-mode): Remove entry for with-temporary-git-worktree.
* doc/contributing.texi (Updating the Guix Package): Update doc.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2020-11-12 09:23:27 -05:00
Pierre Neidhardt a002e8a4f5
gnu: emacs-lispy: Update to 20201109. 
* gnu/packages/emacs-xyz.scm (emacs-lispy): Update to 20201109.
[native-inputs]: Add which.
[arguments]: Fix test command to not use straight.el and disable
failing test related to Clojure.
 2020-11-12 15:21:57 +01:00
Ludovic Courtès 07914def98
Merge branch 'version-1.2.0' 2020-11-12 10:47:25 +01:00
Ludovic Courtès ef1107e2cc
nls: Update string translations. 2020-11-12 10:13:45 +01:00
Ludovic Courtès 7547be7d99
nls: Update translations of the manual. 2020-11-12 10:12:45 +01:00
Julien Lepiller 74fdbbfaad
nls: Update translations of the manual. 2020-11-12 09:39:17 +01:00
Julien Lepiller e55f6418cd
nls: Update 'ta' translation. 2020-11-12 09:39:10 +01:00
Ludovic Courtès b73981369e
lint: patch-file-names: Simplify 'search-patch' error handling. 
* guix/lint.scm (check-patch-file-names): Remove 'message-condition?'
guard, which is useless since d51bfe242f.
Remove call to 'format' in the 'formatted-message?' case.
 2020-11-12 09:29:05 +01:00
Efraim Flashner a13063d6ac
gnu: sbcl-cffi-libffi: Fix building on ARM hardware. 
* gnu/packages/lisp-xyz.scm (sbcl-cffi-libffi-bootstrap)[arguments]: Add
phase to adapt code to changes in libffi.
 2020-11-11 22:49:22 +02:00
Efraim Flashner 4ce58ac0ed
gnu: sbcl-cffi-grovel: End all phases with #t. 
* gnu/packages/lisp-xyz.scm (sbcl-cffi-grovel)[arguments]: End custom
'install-headers phase with #t.
 2020-11-11 22:49:19 +02:00
Marius Bakke 5f799dd119
gnu: python-matplotlib: Remove unused input. 
* gnu/packages/python-xyz.scm (python-matplotlib)[inputs]: Remove IMAGEMAGICK.
 2020-11-11 21:37:12 +01:00
Marius Bakke 184598a43c
gnu: i3lock-fancy: Fix defunct substitution. 
* gnu/packages/wm.scm (i3lock-fancy)[arguments]: Fix faulty regular expression.
 2020-11-11 21:37:12 +01:00
Marius Bakke 1aa765fd52
gnu: i3lock-fancy: Inputs are not native. 
* gnu/packages/wm.scm (i3lock-fancy)[native-inputs]: Move everything ...
[inputs]: ... here.
 2020-11-11 21:37:12 +01:00