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Author SHA1 Message Date
Timo Kaufmann f0ea741a9a
Merge pull request #51786 from symphorien/giac-1.5 
giac: 1.4.9 -> 1.5.0
 2018-12-10 13:40:03 +01:00
Maximilian Bosch de02111a51
Merge pull request #51534 from jbedo/bowtie2 
bowtie2: fix missing dependencies
 2018-12-10 00:58:51 +01:00
Symphorien Gibol 29242e472e giac: build with nauty support 2018-12-09 23:18:58 +01:00
Symphorien Gibol 2253b3e760 nauty: also install libs 2018-12-09 23:18:53 +01:00
Symphorien Gibol 8b4f885264 giac: add missing optional dependencies 2018-12-09 23:18:53 +01:00
Symphorien Gibol e7801461e0 giac: don't split in multiple outputs for when gui enabled 
This breaks the Phys and Turtle menu, among other things.
 2018-12-09 23:18:53 +01:00
Symphorien Gibol b5435d0551 giac: 1.4.9 -> 1.5.0 2018-12-09 23:18:46 +01:00
Frederik Rietdijk e0950ae9ad Merge master into staging-next 2018-12-08 12:40:13 +01:00
Sebastien Maret da314a44ea gildas: 20181101_a -> 20181201_a 2018-12-06 12:02:05 +01:00
Justin Bedo 8c5251e3c0
bowtie2: fix missing dependencies 2018-12-05 10:51:30 +11:00
Frederik Rietdijk a510aa2672 Merge master into staging-next 2018-12-03 12:18:43 +01:00
Timo Kaufmann 5f2b8de75c
Revert "pythonPackages.cypari2: 1.3.1 -> 2.0.1 (#49446)" (#51414) 
This reverts commit d9b650f4cc.

The update is causing segfaults. See
https://trac.sagemath.org/ticket/26442.
 2018-12-03 00:44:33 +01:00
markuskowa 506d4c7e44
Merge pull request #51329 from c0bw3b/cleanup/gnu-https 
Favor HTTPS URLs - the GNU edition
 2018-12-02 16:52:33 +01:00
c0bw3b 0498ccd076 Treewide: use HTTPS on GNU domains 
HTTP -> HTTPS for :
- http://gnu.org/
- http://www.gnu.org/
- http://elpa.gnu.org/
- http://lists.gnu.org/
- http://gcc.gnu.org/
- http://ftp.gnu.org/ (except in fetchurl mirrors)
- http://bugs.gnu.org/
 2018-12-02 15:51:59 +01:00
c0bw3b 0f868d8116 Treewide: use HTTPS on SourceForge 2018-12-02 15:33:08 +01:00
Jan Tojnar a51a99c690
gobject-introspection: rename package 
camelCase package name was a huge inconsistency in GNOME package set.
 2018-12-02 12:42:29 +01:00
Brenton Horne 10f40f3ac6 scilab-bin: adding application launchers 
Moving the desktop configuration files from
opt/scilab-$ver/share/applications to share/applications, making the
required changes, and moving the icons in opt/scilab-$ver/share/icons to
share/icons. Moving locales, appdata and mime out of there
opt/scilab-${ver} too. Also removing unneeded scilab-${ver} and
scilab-${majorVer} symlinks from bin/.
 2018-12-02 17:53:40 +10:00
Brenton Horne 7041972128 scilab-bin: adding bin/scilab symlink (#51346) 
Should fix #51343, merely adding a scilab symlink within the bin/ directory, so that it can be detected by SageMath.
 2018-12-01 23:25:40 +01:00
Timo Kaufmann 88b69a0d40
Merge pull request #51337 from timokau/sagenb-matplotlib-fix 
sage: misc fixes
 2018-12-01 22:04:48 +01:00
Timo Kaufmann 0e570199de sage: fix jmol integration 2018-12-01 21:31:29 +01:00
Timo Kaufmann cb73495f02 sagenb: fix matplotlib path 2018-12-01 20:41:40 +01:00
Timo Kaufmann d9b650f4cc
pythonPackages.cypari2: 1.3.1 -> 2.0.1 (#49446) 2018-12-01 12:57:55 +01:00
Jan Tojnar c5881ec2c9
Merge remote-tracking branch 'upstream/master' into staging 2018-11-30 20:09:45 +01:00
Frederik Rietdijk 1828a5c5ba Merge master into staging-next 2018-11-30 17:46:21 +01:00
Matthew Bauer 76c7a8bac0
Merge pull request #51205 from matthewbauer/more-setup-hooks 
Add premake & imake setup hook
 2018-11-29 19:36:25 -06:00
Frederik Rietdijk 9b81c7e455 Merge staging-next into staging 2018-11-29 09:18:35 +01:00
Frederik Rietdijk 9db2421d1f Merge master into staging-next 2018-11-29 08:12:56 +01:00
Matthew Bauer c0a804c747 treewide: add dontUseImakeConfigure where needed 
We need to set dontUseImakeConfigure in a few places to prevent imake
from overriding the default configure phase. This packages all have a
configure script that needs to get run:

- Xaw3d
- R
- tkgate
- ssvnc
 2018-11-28 20:14:45 -06:00
Matthew Bauer 8a4da41849 xearth: use imake setup hook 2018-11-28 20:14:36 -06:00
Will Dietz d7a0e03cfa
Merge pull request #51162 from dtzWill/update/z3-4.8.3 
z3: 4.8.1 -> 4.8.3
 2018-11-28 18:15:31 -06:00
Timo Kaufmann aa053197de
Merge pull request #51191 from timokau/sage-fixes 
sage: fix test timeout and downgraded R tests
 2018-11-28 23:10:32 +01:00
Timo Kaufmann d6376bca6d sage: don't test the downgraded R 
Fails transiently. See https://github.com/NixOS/nixpkgs/pull/49249. The
failures look harmless and are fixed with R 3.5 which will be used in
sage 8.5.
 2018-11-28 22:52:15 +01:00
Timo Kaufmann 359bf7f1e3 sage: disable test timeout 
Hydra build failed due to timeout:
https://hydra.nixos.org/build/84870983
 2018-11-28 22:37:24 +01:00
Renaud d209180c78
Merge pull request #51087 from Luz/librepcb 
librepcb: 20181031 -> 0.1.0
 2018-11-28 08:19:13 +01:00
Will Dietz a034d90e3b z3: 4.8.1 -> 4.8.3 
https://github.com/Z3Prover/z3/releases/tag/z3-4.8.3
 2018-11-27 22:00:19 -06:00
R. RyanTM 36a0335d02 picard-tools: 2.18.14 -> 2.18.17 (#50647) 
* picard-tools: 2.18.14 -> 2.18.16

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.16
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions

* picard-tools: 2.18.16 -> 2.18.17

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.17
 2018-11-27 14:31:09 +01:00
Nick Hu 583911a0b2 quantomatic: init at 0.7 2018-11-26 21:51:58 +00:00
Luz 021b6e86fa librepcb: 20181031 -> 0.1.0 2018-11-26 22:33:39 +01:00
Vladimír Čunát a5de78b7d7
Merge branch 'master' into staging-next 2018-11-26 10:28:00 +01:00
Timo Kaufmann 2fbde72556
sage: add tkinter as matplotlib backend (#51032) 
Fixes #50959.
 2018-11-25 17:38:45 +01:00
Timo Kaufmann 98c94d3d7d sage: add jupyter notebook support 
Fixes #48544.
 2018-11-25 15:54:31 +01:00
Timo Kaufmann 0c23fa9aaf
Merge pull request #50998 from timokau/sage-refactor 
Sage refactor
 2018-11-24 23:59:28 +01:00
Timo Kaufmann a0723f1285 sage: don't fix node version 2018-11-24 23:14:38 +01:00
Timo Kaufmann e28a8ed287 sage: add some flexibility to the test runner 
Make it possible to run individual tests. This is very useful while
git-bisecting.
 2018-11-24 23:14:38 +01:00
Timo Kaufmann 21f9123ea6 sage: remove openblas hack 
The pc files have since been included into the openblas package.
 2018-11-24 23:14:38 +01:00
Timo Kaufmann 3832ddedb9 sage: refactor 2018-11-24 23:14:33 +01:00
c0bw3b 0ea604ac1d Treewide: use https for SourceForge 2018-11-24 19:58:03 +01:00
Timo Kaufmann 9b4a518465 sage: drop known-padics-failure patch 
The failure was not observed for a while and is probably fixed now.
 2018-11-24 19:01:57 +01:00
Timo Kaufmann ca6475b5e8 sage: drop unused patches 2018-11-24 19:01:57 +01:00
Frederik Rietdijk c1792242ef Merge staging-next into staging 2018-11-24 10:44:50 +01:00