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35377 Commits

Author SHA1 Message Date
Ricardo Wurmus 1189c7f1b0
gnu: Add python-hicexplorer. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 5bb9e0af8d
gnu: Add python-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 80f4db91b1
gnu: Add python-pyfaidx. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 1f41f01c14
gnu: Add python-pypairix. 
* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a9d496b353
gnu: Add python-intervaltree. 
* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus a6a7156aa9
gnu: Add python-dask. 
* gnu/packages/python.scm (python-dask): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 035989c403
gnu: Add python-partd. 
* gnu/packages/python.scm (python-partd): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus c27a9d8a88
gnu: Add python-blosc. 
* gnu/packages/python.scm (python-blosc): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus b2b8226244
gnu: Add python-locket. 
* gnu/packages/python.scm (python-locket): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 930ba31d20
gnu: Add python-cloudpickle. 
* gnu/packages/python.scm (python-cloudpickle): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 3d352cb9cf
gnu: Add python-sortedcontainers. 
* gnu/packages/python.scm (python-sortedcontainers): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 098cb1e9c4
gnu: Add python-cytoolz. 
* gnu/packages/python.scm (python-cytoolz): New variable.
 2018-09-10 16:50:26 +02:00
Ricardo Wurmus 7cd51cd28e
gnu: Add python-toolz. 
* gnu/packages/python.scm (python-toolz): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus 943a4cb601
gnu: Add python-multiprocess. 
* gnu/packages/python.scm (python-multiprocess): New variable.
 2018-09-10 16:50:25 +02:00
Ricardo Wurmus fc62567251
gnu: Add python-dill. 
* gnu/packages/python.scm (python-dill): New variable.
 2018-09-10 16:50:25 +02:00
Tobias Geerinckx-Rice 82d5c7c6de
gnu: python-typing: Update to 3.6.6. 
* gnu/packages/python.scm (python-typing): Update to 3.6.6.
 2018-09-10 15:29:13 +02:00
Tobias Geerinckx-Rice 419aa05e1b
gnu: tinyproxy: Update to 1.10.0. 
* gnu/packages/web.scm (tinyproxy): Update to 1.10.0.
[native-inputs]: Remove asciidoc.
 2018-09-10 15:29:12 +02:00
Tobias Geerinckx-Rice f6c8a97a04
gnu: spectrwm: Update to 3.2.0. 
* gnu/packages/wm.scm (spectrwm): Update to 3.2.0.
[arguments]: Remove 'fix-freetype-include' phase.
 2018-09-10 15:29:12 +02:00
Marius Bakke f2d4944086
gnu: guile-xcb: Install compiled files to "lib" instead of "share". 
This follows up commit b03f270e3d which removes
the previous install location from Guiles search path.

* gnu/packages/guile-wm.scm (guile-xcb)[arguments]: Amend #:configure-flags.
 2018-09-10 14:49:46 +02:00
Mădălin Ionel Patrașcu 57d70dbabc
gnu: Add yad. 
* gnu/packages/gtk.scm (yad): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-10 14:45:15 +02:00
Marius Bakke 4d19a14e77
gnu: python-llfuse: Update to 1.3.5. 
* gnu/packages/python.scm (python-llfuse): Update to 1.3.5.
 2018-09-10 14:29:40 +02:00
Marius Bakke 073705e725
gnu: python2-contextlib2: Use 'invoke' instead of 'system*'. 
* gnu/packages/python.scm (python2-contextlib2)[arguments]: Use INVOKE.
 2018-09-10 14:28:42 +02:00
Marius Bakke d06940882d
gnu: python2-contextlib2: Update to 0.5.5. 
* gnu/packages/python.scm (python2-contextlib2): Update to 0.5.5.
[native-inputs]: Add PYTHON2-UNITTEST2.
 2018-09-10 14:25:25 +02:00
Marius Bakke d4c04e509b
gnu: Remove python-contextlib2. 
This package is part of the Python standard library since version 3.2.

* gnu/packages/python.scm (python-contextlib2): Rename to ...
(python2-contextlib2): ... this.  Remove previous incarnation.
[arguments]: Set #:python.
 2018-09-10 14:24:34 +02:00
Marius Bakke e5eef32445
gnu: perl-module-runtime: Update to 0.016. 
* gnu/packages/perl.scm (perl-module-runtime): Update to 0.016.
 2018-09-10 14:13:36 +02:00
Ludovic Courtès 94b3b6041d
gnu: hpcguix-web: Update to 53e09ea. 
* gnu/packages/web.scm (hpcguix-web): Update to 53e09ea.
 2018-09-10 12:18:14 +02:00
Ludovic Courtès 81317071fb
services: hpcguix-web: Produce a log file and rotate it. 
* gnu/services/web.scm (%hpcguix-web-log-file)
(%hpcguix-web-log-rotations): New variables.
(hpcguix-web-shepherd-service): Pass #:log-file.
(hpcguix-web-service-type): Extend ROTTLOG-SERVICE-TYPE.
 2018-09-10 12:12:52 +02:00
Ludovic Courtès 19de8273ee
services: tailon: Move to (gnu services web). 
This allows (gnu services admin) to remain deeper in the module graph
and to be used by (gnu services web).

* gnu/services/admin.scm (<tailon-configuration-file>)
(tailon-configuration-files-string)
(tailon-configuration-file-compiler, <tailon-configuration>)
(tailon-shepherd-service, %tailon-accounts)
(tailon-service-type): Move to...
* gnu/services/web.scm: ... here.
* gnu/tests/admin.scm: Remove.  Move test to...
* gnu/tests/web.scm (%tailon-os)
(run-tailon-test, %test-tailon): ... here.
 2018-09-10 12:12:50 +02:00
Alex Vong d930374014
gnu: youtube-dl: Update to 2018.08.04. 
* gnu/packages/video.scm (youtube-dl): Update to 2018.08.04.
 2018-09-10 11:31:34 +02:00
Leo Famulari de15ff1a6c
gnu: Add asignify. 
* gnu/packages/crypto.scm (asignify): New variable.
 2018-09-09 20:05:47 -04:00
Marius Bakke 02107081da
gnu: double-conversion: Update to 3.1.0. 
* gnu/packages/maths.scm (double-conversion): Update to 3.1.0.
 2018-09-10 01:41:29 +02:00
Marius Bakke 2bdc73fb26
gnu: double-conversion: Don't use unstable tarball. 
* gnu/packages/maths.scm (double-conversion)[source]: Use GIT-FETCH.
 2018-09-10 01:41:29 +02:00
Marius Bakke 68a08dfbe5
gnu: libgd: Incorporate grafted changes. 
* gnu/packages/gd.scm (gd)[replacement]: Remove field.
[source](patches): Add "gd-CVE-2018-5711.patch" and
"gd-CVE-2018-1000222.patch".
(gd/fixed): Remove variable.
* gnu/packages/php.scm (gd-for-php): Remove variable.
(php)[inputs]: Change GD-FOR-PHP to GD.
 2018-09-10 01:39:01 +02:00
Marius Bakke fe79ce3b1f
Merge branch 'master' into core-updates 2018-09-10 01:37:32 +02:00
Marius Bakke fb94354a69
gnu: jbig2dec: Remove graft for 0.15. 
* gnu/packages/image.scm (jbig2dec): Update to 0.15.
[source]: Reindent.
(jbig2dec-0.15): Remove variable.
 2018-09-10 01:00:26 +02:00
Marius Bakke 18784d8f11
gnu: OpenSSL: Remove obsolete workaround. 
* gnu/packages/tls.scm (openssl)[arguments]: Remove workaround that is not
needed for GCC version 5.3 and later.
 2018-09-10 00:54:03 +02:00
Leo Famulari d4bd2453ec
gnu: certbot: Update to 0.27.1. 
* gnu/packages/tls.scm (python-acme): Update to 0.27.1.
[arguments]: Use invoke.
(certbot): Update to 0.27.1.
[native-inputs]: Use python-sphinx-1.6.
 2018-09-09 18:52:04 -04:00
Leo Famulari ced98c7e89
gnu: libgd: Fix CVE-2018-{5711,1000222}. 
* gnu/packages/patches/gd-CVE-2018-1000222.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd/fixed): New variable.
* gnu/packages/php.scm (gd-for-php)[source]: Use 'gd-CVE-2018-1000222.patch'.
 2018-09-09 18:13:19 -04:00
Ricardo Wurmus 15cc7e6adf
ui: Add soft port for styling and filtering build output. 
* guix/ui.scm (build-output-port): New procedure.
* guix/scripts/package.scm (%default-options): Print build trace.
(guix-package): Use build-output-port.
* guix/scripts/build.scm (guix-build): Use build-output-port.

Co-authored-by: Sahithi Yarlagadda <sahi@swecha.net>
 2018-09-09 23:18:21 +02:00
Sahithi Yarlagadda 80ec1b73d2
ui: Add support for colorization. 
* guix/ui.scm (ansi-color-tables): New variable.
(color, colorize-string): New procedures.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2018-09-09 22:26:54 +02:00
Ricardo Wurmus 45350539aa
gnu: r-chron: Update to 2.3-53. 
* gnu/packages/statistics.scm (r-chron): Update to 2.3-53.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus ab50580a9d
gnu: r-annotationhub: Update to 2.12.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
 2018-09-09 22:26:02 +02:00
Ricardo Wurmus 35c076e619
gnu: r-chippeakanno: Update to 3.14.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2.
 2018-09-09 22:26:02 +02:00
Roel Janssen c36d972531
gnu: Update texmaker to 5.0.2. 
* gnu/packages/tex.scm (texmaker): Update to 5.0.2.
 2018-09-09 21:59:08 +02:00
Marius Bakke 4333d48a82
gnu: mariadb: Move unbundle substitutions to source snippet. 
* gnu/packages/databases.scm (mariadb)[source](snippet): Add two substitutions
from ...
[arguments]: The 'unbundle' phase here.  Rename to 'fix-pcre-detection.
 2018-09-09 17:59:37 +02:00
Marius Bakke 1d957c79b6
gnu: mariadb: Update to 10.1.36. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.36.
[arguments]: Disable one new test.
 2018-09-09 17:59:36 +02:00
Marius Bakke 5e53722249
gnu: jbig2dec: Don't build libjbig2dec.a. 
* gnu/packages/image.scm (jbig2dec)[arguments]: New field.
 2018-09-09 17:59:36 +02:00
Marius Bakke de781c05e7
gnu: util-linux: Remove static library reference from '.la' files. 
* gnu/packages/linux.scm (util-linux)[arguments]: Substitute all '.la' files.
 2018-09-09 17:59:36 +02:00
Marius Bakke 334bd08c42
gnu: cmake: Update to 3.12.2. 
* gnu/packages/cmake.scm (cmake): Update to 3.12.2.
 2018-09-09 17:59:36 +02:00
Marius Bakke a34ce3308e
gnu: gdk-pixbuf: Update to 2.38.0. 
* gnu/packages/gtk.scm (gdk-pixbuf): Update to 2.38.0.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[arguments]: Don't explicitly enable x11 in #:configure-flags.  Prevent tests
from getting installed.  Adjust test substitutions.  Add phase to fix install.
[native-inputs]: Add GETTEXT-MINIMAL.
(gdk-pixbuf+svg)[arguments]: Adjust accordingly.
 2018-09-09 17:59:36 +02:00