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Author SHA1 Message Date
Ricardo Wurmus 35aa90a1fd
gnu: Add Infernal. 
* gnu/packages/bioinformatics.scm (infernal): New variable.
 2016-09-02 16:46:37 +02:00
Leo Famulari d058708e86
gnu: libidn: Replace with 1.33 [fixes CVE-2015-8948 and CVE-2016-{6261,6263}]. 
* gnu/packages/libidn.scm (libidn)[replacement]: New field.
(libidn-1.33): New variable.
 2016-09-02 09:52:56 -04:00
Efraim Flashner 135ba811c6
gnu: python2-ipython: Use strip-python2-variant. 
* gnu/packages/python.scm (python2-ipython): Inherit using
strip-python2-variant.
[propagated-inputs]: Remove work-around for python2-terminado.
[inputs]: Remove work-around for python2-jsonschema, python2-matplotlib,
python2-numpy, python2-requests.
(python-inputs)[properties]: New field.
 2016-09-02 06:44:37 +03:00
Efraim Flashner fc1a170e65
gnu: python2-numexpr: Use strip-python2-variant. 
* gnu/packages/python.scm (python2-numexpr): Replace package definition
with 'package-with-python2', using 'strip-python2-variant'.
 2016-09-02 06:44:36 +03:00
Efraim Flashner 2b031d3fc1
gnu: python2-scikit-image: Use strip-python2-variant. 
* gnu/packages/python.scm (python2-scikit-image): Inherit using
strip-python2-variant.
[propagated-inputs]: Remove work-around for python2-matplotlib,
python2-numpy, python2-scipy.
 2016-09-02 06:44:36 +03:00
Efraim Flashner 7e21b9fb26
gnu: python-scikit-learn: Set source file name. 
* gnu/packages/python.scm (python-scikit-learn)[source]: Add 'file-name'
field.
 2016-09-02 06:44:36 +03:00
Efraim Flashner 25a2f81f9b
gnu: python2-scikit-learn: Use strip-python2-variant. 
* gnu/packages/python.scm (python2-scikit-learn): Replace package
definition with 'package-with-python2', using 'strip-python2-variant'
to simplify the package definition.
 2016-09-02 06:44:35 +03:00
Efraim Flashner d44a618384
gnu: python-requests-mock: Update to 1.0.0. 
* gnu/packages/openstack.scm (python-requests-mock): Update to 1.0.0.
[inputs]: Remove python-setuptools. Move python-mock ...
[native-inputs]: ... to here.  Add python-discover, python-fixtures,
python-sphinx, python-testrepostory, python-testtools.
[properties]: Add python2-variant.
(python2-requests-mock): inherit stripped variant.
[native-inputs]: Use python2-setuptools.
 2016-09-02 06:44:25 +03:00
Mark H Weaver bb76ef9d8b
Revert "gnu: gsl: Update to 2.2." 
This reverts commit b16b16e6c2.

Rationale: gsl-2.2 consistently fails its test suite on i686.  Inkscape
depends on gsl, and the grub background image is converted using
inkscape, so i686 systems can no longer be built.
 2016-09-01 20:17:01 -04:00
Danny Milosavljevic f63e5eaaeb
gnu: dtc: Add missing symbols patch from debian. 
* gnu/packages/u-boot.scm (dtc)[source]: Add patch.
* gnu/packages/patches/dtc-add-missing-symbols-to-lds.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: David Craven <david@craven.ch>
 2016-09-02 00:16:34 +02:00
Ludovic Courtès 4e49163f76
guix build: Rewrite '--with-input' in terms of 'package-input-rewriting'. 
* guix/scripts/build.scm (transform-package-inputs): Rewrite in terms of
'package-input-rewriting'.
 2016-09-01 23:07:54 +02:00
Ludovic Courtès 2a75b0b63d
packages: Add 'package-input-rewriting'. 
* guix/packages.scm (package-input-rewriting): New procedure.
* tests/packages.scm ("package-input-rewriting"): New test.
* doc/guix.texi (Defining Packages): Document it.
(Package Transformation Options): Add cross-reference.
 2016-09-01 23:07:54 +02:00
John Darrington 705b971477
gnu: Fix typo in description of xfce-desktop-service. 
* gnu/services/desktop.scm (xfce-desktop-service) abilit --> ability.
 2016-09-01 17:55:49 +02:00
John Darrington 7e348e6c0d
gnu: Add rpcbind 
* gnu/packages/onc-rpc.scm (rpcbind): New variable.
 2016-09-01 17:55:39 +02:00
Kei Kebreau 261b3da532
gnu: Add telepathy-mission-control. 
* gnu/packages/freedesktop.scm (telepathy-mission-control): New variable.
 2016-09-01 11:24:51 -04:00
Danny Milosavljevic 71d4676069
gnu: Add u-boot. 
* gnu/packages/u-boot.scm (u-boot, make-u-boot-package,
  u-boot-vexpress_ca9x4, u-boot-malta): New variables.

Co-authored-by: David Craven <david@craven.ch>
 2016-09-01 17:17:42 +02:00
Danny Milosavljevic d62ed73239
gnu: Add dtc. 
* gnu/packages/u-boot.scm (dtc): New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add file.

Co-authored-by: David Craven <david@craven.ch>
 2016-09-01 17:17:42 +02:00
Vincent Legoll e5cd149f68
Update 'TODO'. 
* TODO: Remove items about guix challenge & guix publish.

Signed-off-by: Vincent Legoll <vincent.legoll@gmail.com>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-09-01 14:57:03 +02:00
Ludovic Courtès 38c2b50354
Reinstate "services: elogind: Provide '%elogind-file-systems' by extension." 
This reverts commit 17073dafc5.
 2016-09-01 14:57:03 +02:00
Marius Bakke 5fd66a37d5
gnu: slim: Move to display-managers.scm. 
* gnu/packages/display-managers.scm: New file.
* gnu/packages/slim.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
* gnu/services/xorg.scm: Likewise.
 2016-09-01 14:36:49 +02:00
Efraim Flashner 7060b28171
tests: hackage: Fix mock urls. 
Followup to 18f7473504.

* tests/hackage.scm (hackage->guix-package): Use 'https' in mock urls.
 2016-09-01 13:40:49 +03:00
Mark H Weaver 307347fe1b
gnu: Fix typo in copyright notice in (gnu packages networking). 
* gnu/packages/networking.scm: "Coypright" --> "Copyright".
 2016-09-01 04:27:08 -04:00
Leo Famulari 7335ca1d71
gnu: icedtea-6: Update to 1.13.12 [security fixes]. 
Fixes CVE-2016-{3458,3485,3500,3508,3550,3606}.

* gnu/packages/java.scm (icedtea-6): Update to 1.13.12.
[source]: Remove 'icedtea-remove-overrides' patch.
[arguments]: Move ALSA header substitution to 'patch-paths' phase.
* gnu/packages/patches/icedtea-remove-overrides.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-08-31 19:04:46 -04:00
Marius Bakke 68c35ba96e
gnu: rofi: Update to 1.2.0. 
* gnu/packages/xdisorg.scm (rofi): Update to 1.2.0.
  [inputs]: Drop libx11 and add xcb-util-xrm.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-08-31 15:12:29 -04:00
Marius Bakke 4493a3c2ef
gnu: Add xcb-util-xrm. 
* gnu/packages/xdisorg.scm (xcb-util-xrm): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-08-31 15:12:25 -04:00
John Darrington a7074f47ad
gnu: wcslib: Correct formatting and grammar. 
* gnu/packages/astronomy.scm (wcslib): Minor whitespace and grammatical
changes.
 2016-08-31 20:57:23 +02:00
Eric Bavier 46a0622481
gnu: bambam: Remove wrap-binary phase. 
Functionality provided already by python-build-system.

* gnu/packages/games.scm (bambam)[arguments]: Remove 'wrap-binary phase.
[synopsis]: Capitalize first word.
 2016-08-31 12:16:19 -05:00
Eric Bavier 83ab1a812f
tests: cpan: Fix mock urls. 
Followup to 7a62263ee5.

* tests/cpan.scm (cpan->guix-package): Use "https" in mock urls.
 2016-08-31 09:58:39 -05:00
Ludovic Courtès 7b44cae50a
services: shepherd: Add 'shepherd-service-upgrade', from 'guix system'. 
* guix/scripts/system.scm (service-upgrade): Move to...
* gnu/services/shepherd.scm (shepherd-service-upgrade): ... here.
* tests/system.scm ("service-upgrade: nothing to do", "service-upgrade:
one unchanged, one upgraded, one new", "service-upgrade: service
depended on is not unloaded", "service-upgrade: obsolete services that
depend on each other"): Move to...
* tests/services.scm: ... here.  Adjust to 'service-upgrade' rename.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès d4f8884fdb
guix system: Do not unload services depended on. 
Reported by Mark H Weaver <mhw@netris.org>
at <https://lists.gnu.org/archive/html/guix-devel/2016-08/msg01470.html>.

* guix/scripts/system.scm (service-upgrade)[live-service-required?]: New
procedure.
[obsolete?]: Use it.
* tests/system.scm ("service-upgrade: service depended on is not
unloaded", "service-upgrade: obsolete services that depend on each
other"): New tests.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès 6673bddc9a
services: shepherd: Parameterize 'shepherd-service-back-edges'. 
* gnu/services/shepherd.scm (shepherd-service-back-edges): Add
  #:provision and #:requirement parameter.  Honor them.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès f20a7b8696
guix system: Use 'shepherd-service-lookup-procedure' in 'service-upgrade'. 
* guix/scripts/system.scm (service-upgrade)[essential?]: SERVICE is now
a <live-service>.
[lookup-target, lookup-live, running?, stopped, obsolete?]: New
procedures.
[to-load, to-unload]: Use them.  TO-UNLOAD is now a list of
<live-service>.
(call-with-service-upgrade-info): Extract symbols from TO-UNLOAD.
* tests/system.scm ("service-upgrade: one unchanged, one upgraded, one
new"): Adjust accordingly.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès a5d78eb64b
services: shepherd: Add 'shepherd-service-lookup-procedure'. 
* gnu/services/shepherd.scm (shepherd-service-lookup-procedure): New
procedure.
(shepherd-service-back-edges)[provision->service]: Use it.
* tests/services.scm ("shepherd-service-lookup-procedure"): New test.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès b8692e4696
guix system: Extract and test the service upgrade procedure. 
* guix/scripts/system.scm (service-upgrade): New procedure, with code
from...
(call-with-service-upgrade-info): ... here.  Use it.
* tests/system.scm (live-service, service-upgrade): New variables.
("service-upgrade: nothing to do", "service-upgrade: one unchanged, one
upgraded, one new"): New tests.
 2016-08-31 15:44:20 +02:00
Ludovic Courtès 183605c853
services: herd: Provide <live-service> objects. 
* gnu/services/herd.scm (<live-service>): New record type.
(current-services): Change to return a single value: #f or a list of
<live-service>.
* guix/scripts/system.scm (call-with-service-upgrade-info): Adjust
accordingly.
* gnu/tests/base.scm (run-basic-test)["shepherd services"]: Adjust
accordingly.
 2016-08-31 15:44:19 +02:00
Ludovic Courtès 1bc4d0c266
doc: Fix 'ntp-service' typo. 
Reported by Vincent Legoll <vincent.legoll@gmail.com>.

* doc/guix.texi (Networking Services): Change #:name-service to
  #:servers in 'ntp-service' documentation.
 2016-08-31 15:44:19 +02:00
Ricardo Wurmus c180533bb5
gnu: subread: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (subread): Update to 1.5.1.
 2016-08-31 15:23:03 +02:00
ng0 840224aadc
gnu: Add emacs-auto-complete. 
* gnu/packages/emacs.scm (emacs-auto-complete): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-08-31 10:10:30 +03:00
ng0 9657aba4ed
gnu: Add emacs-cyberpunk-theme. 
* gnu/packages/emacs.scm (emacs-cyberpunk-theme): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-08-31 10:10:30 +03:00
ng0 41392b9a3d
gnu: Add emacs-flx. 
* gnu/packages/emacs.scm (emacs-flx): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-08-31 10:10:30 +03:00
Ben Woodcroft 7d57ebaa7c
gnu: aragorn: Update to 1.2.37. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.37.
 2016-08-31 15:52:49 +10:00
Eric Bavier 0c4520d686
gnu: autojump: Fix failing tests. 
This is a followup to 1d33b9e; test script was moved in upgrade to
version 22.3.4.

* gnu/packages/admin.scm (autojump)[arguments]: Adjust unit test script
file name.
 2016-08-31 00:46:59 -05:00
Efraim Flashner b0488fe549
gnu: Add bambam. 
* gnu/packages/games.scm (bambam): New variable.
 2016-08-31 00:46:59 -05:00
Efraim Flashner 4916514503
gnu: alsa-utils: Use 'modify-phases'. 
* gnu/packages/linux.scm (alsa-utils)[arguments]: Use 'modify-phases'
syntax.
 2016-08-31 08:38:18 +03:00
Efraim Flashner 43043f23f5
gnu: alsa-utils: Update to 1.1.2. 
* gnu/packages/linux.scm (alsa-utils): Update to 1.1.2.
 2016-08-31 08:38:17 +03:00
John Darrington c9bd15c1d8
gnu: Add gnuastro 
* gnu/packages/astronomy.scm (gnuastro): New variable.
 2016-08-31 06:17:13 +02:00
John Darrington 2be83f6e8d
gnu: Add wcslib 
* gnu/packages/astronomy.scm (wcslib): New variable.
 2016-08-31 06:17:07 +02:00
John Darrington 82e4557d56
gnu: Add cfitsio 
* gnu/packages/astronomy.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2016-08-31 06:16:54 +02:00
Efraim Flashner 7a3f940541
gnu: fossil: Update to 1.35. 
* gnu/packages/version-control.scm (fossil): Update to 1.35.
[source]: Download from fossil-scm.org, remove patch, remove snippet.
* gnu/packages/patches/fossil-test-fixes.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-08-31 00:57:05 +03:00
Kei Kebreau bb8b543a48
gnu: Add telepathy-idle. 
* gnu/packages/freedesktop.scm (telepathy-idle): New variable.
 2016-08-30 17:35:53 -04:00