Commit graph

751 commits

Author SHA1 Message Date
Timo Kaufmann 7abdacc4f2
Merge pull request #51039 from timokau/sage-8.5
sage: 8.4 -> 8.5
2018-12-29 16:15:38 +01:00
Timo Kaufmann 8cd7b5aab3
gap: 4r8p10 -> 4.10.0 (#53037)
This new version also has a libgap replacement, so after the next sage
update gap-libgap-compatible and libgap won't be necessary anymore.
2018-12-29 16:05:56 +01:00
Timo Kaufmann 22c16ed300 Merge remote-tracking branch 'upstream/master' into sage-8.5 2018-12-29 12:16:02 +01:00
Timo Kaufmann 95909d4fb6 Revert "sage: preload openblasCompat"
This reverts commit 4900bbee17.

The issue that was supposed to fix is now fixed by lazy-loading rpy2 and
makign sure scipy is loaded before that.
That is not quite as nice, but preloading is now causing its own issues
with openblas 0.3.4:
https://github.com/xianyi/OpenBLAS/issues/1936
2018-12-28 23:06:05 +01:00
Timo Kaufmann 360eddd3a3 sage: remove outdated patch files 2018-12-28 23:06:05 +01:00
Timo Kaufmann 6f0f06ec89 sage: 8.5.rc1 -> 8.5 2018-12-28 23:06:05 +01:00
Alex Branham a5fc513079 R: 3.5.1 -> 3.5.2
Closes https://github.com/NixOS/nixpkgs/pull/52571.
2018-12-21 13:59:36 +01:00
Gabriel Ebner 21597583f9
Merge pull request #52067 from r-ryantm/auto-update/qalculate-gtk
qalculate-gtk: 2.8.1 -> 2.8.2
2018-12-17 09:46:32 +01:00
Timo Kaufmann b09967d812 sage: 8.5.rc0 -> 8.5.rc1 2018-12-16 21:33:28 +01:00
Jörg Thalheim 33c227c23b
Merge pull request #52392 from r-ryantm/auto-update/calc
calc: 2.12.7.1 -> 2.12.7.2
2018-12-16 17:33:43 +00:00
R. RyanTM 67536060ac calc: 2.12.7.1 -> 2.12.7.2
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/calc/versions
2018-12-16 07:44:09 -08:00
Michael Raskin 2f0cbb34cf
Merge pull request #52171 from r-ryantm/auto-update/pari
pari: 2.11.0 -> 2.11.1
2018-12-15 12:08:50 +00:00
R. RyanTM 943e6fa283 pari: 2.11.0 -> 2.11.1
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/pari/versions
2018-12-14 22:17:15 -08:00
R. RyanTM a7e1717d4b qalculate-gtk: 2.8.1 -> 2.8.2
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/qalculate-gtk/versions
2018-12-14 07:37:22 -08:00
luz.paz ab9532b1fe gmsh: 4.0.5 -> 4.0.7 2018-12-14 08:01:20 -05:00
Timo Kaufmann 90bc5ce04d sage: 8.5.beta5 -> 8.5.beta6 2018-12-10 19:36:24 +01:00
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
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 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
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
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
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
Timo Kaufmann 4900bbee17 sage: preload openblasCompat 2018-11-28 20:44:09 +01:00
Timo Kaufmann 7ca2915a50 sage: 8.5.beta4 -> 8.5.beta5 2018-11-27 18:26:16 +01:00
Timo Kaufmann 2dd9a0ed72 Merge remote-tracking branch 'upstream/master' into sage-8.5 2018-11-27 18:25:39 +01:00
Timo Kaufmann 90cebaf828 sage: 8.5.beta3 -> 8.5.beta4 2018-11-25 19:39:18 +01:00
Timo Kaufmann 2a87caa892 sage: 8.5.beta2 -> 8.5.beta3 2018-11-25 19:39:17 +01:00
Timo Kaufmann 3370247f7f sage: 8.5.beta1 -> 8.5.beta2 2018-11-25 19:39:17 +01:00
Timo Kaufmann 883aa99226 sage: add short tests 2018-11-25 19:39:13 +01:00
Timo Kaufmann 8e7da1b8a4 sage: 8.5.beta0 -> 8.5.beta1 2018-11-25 19:36:21 +01:00
Timo Kaufmann 6138f5d5eb sage: 8.4 -> 8.5.beta0 2018-11-25 19:36:21 +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
Michael Raskin 6fe39605df polymake: init at 3.2r4 2018-11-22 12:29:14 +03:00
Frederik Rietdijk fd26e7be2a Merge master into staging-next 2018-11-20 11:47:26 +01:00
luzpaz 0ec2af3736
gmsh: 4.0.4 -> 4.0.5
Manually updated
2018-11-19 11:12:38 -05:00
Frederik Rietdijk 63c6875f26 Merge master into staging-next 2018-11-18 10:32:12 +01:00
Jörg Thalheim 131f2e93b6
sage: unpin nodePackage version 2018-11-16 21:24:25 +00:00
Renaud 650036f022
Merge pull request #50359 from jfrankenau/gurobi-java
gurobi: install Java library files
2018-11-15 14:13:47 +01:00
Johannes Frankenau b4e13e6257 gurobi: install Java library files 2018-11-14 19:38:18 +01:00
Renaud 7ca9d67948
Merge pull request #50102 from r-ryantm/auto-update/gp2c
gp2c: 0.0.11 -> 0.0.11pl1
2018-11-14 16:07:49 +01:00
markuskowa f597a88542
Merge pull request #50101 from r-ryantm/auto-update/gmsh
gmsh: 4.0.2 -> 4.0.4
2018-11-14 12:46:48 +01:00
Markus Kowalewski 644ab709e7
gmsh: restrict platform to x86_64-linux 2018-11-14 12:33:37 +01:00
Markus Kowalewski ced40eabfd
gmsh: use openblas instead of atlas/lapack
* openblas is properly recognized by cmake
* the cmake patch is no longer neccessary
2018-11-14 11:41:46 +01:00
Matthew Bauer 2e18ba6c5a
Merge pull request #49776 from matthewbauer/atlas-remove
atlas: remove
2018-11-13 19:18:35 -06:00
Frederik Rietdijk daf3297cb4 Merge master into staging-next 2018-11-12 18:59:08 +01:00
Peter Simons 22a802584f
Merge pull request #50179 from Thra11/r-without-jdk
R: Remove jdk dependency on aarch32/64
2018-11-12 12:42:39 +01:00
Frederik Rietdijk 7863aae5b2 Merge master into staging-next 2018-11-11 08:59:44 +01:00
markuskowa 45a4adb1b3
Merge branch 'master' into atlas-remove 2018-11-11 02:22:04 +01:00
Markus Kowalewski 6533d7588d
colpack: set platform to linux 2018-11-11 02:17:49 +01:00
Tom Hall b51018ed2e R: Remove jdk dependency on aarch32/64
Add javaSupport as an argument for R. Default to false on arm as there is no free jdk on arm.
2018-11-10 20:53:26 +00:00
R. RyanTM 2fd0c31673 calc: 2.12.6.8 -> 2.12.7.1 (#50173)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/calc/versions
2018-11-10 15:32:06 +01:00
Gabriel Ebner 698ad2dd4d nasc: 0.5.0 -> 0.5.1 2018-11-10 14:18:31 +01:00
Gabriel Ebner 5f2a7607fa qalculate-gtk: 2.6.2 -> 2.8.1 2018-11-10 13:17:17 +01:00
Frederik Rietdijk 53d00c3351 Merge master into staging-next 2018-11-10 11:08:54 +01:00
R. RyanTM f5b4eb63f3 gp2c: 0.0.11 -> 0.0.11pl1
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gp2c/versions
2018-11-09 17:56:17 -08:00
R. RyanTM 6f2bb3c275 gmsh: 4.0.2 -> 4.0.4
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions
2018-11-09 17:41:49 -08:00
Timo Kaufmann efe6322ce4 pythonPackages.networkx: 2.1 -> 2.2 2018-11-07 20:15:37 +01:00
Timo Kaufmann 72e6e792f6 sage: add fetchSageDiff utility function 2018-11-07 20:15:37 +01:00
Matthew Bauer 95373d3634 atlas: remove
atlas is broken and can apparently be removed.

Fixes #49594
2018-11-04 20:23:12 -06:00
Matthew Bauer 7f4b26681d
Merge pull request #49417 from matthewbauer/disallow-native-build-inputs
Disallow references to nativeBuildInputs
2018-11-02 20:26:48 -05:00
Jan Tojnar 3493f44727
Merge pull request #49560 from worldofpeace/eos-third-update
update some elementary thirdparty apps
2018-11-02 21:29:57 +01:00
worldofpeace 0a2420bccd nasc: 0.4.7 -> 0.5.0 2018-11-02 16:01:05 -04:00
Tuomas Tynkkynen 067d1cf330 Merge remote-tracking branch 'upstream/master' into staging
Conflicts:
	pkgs/applications/science/math/sage/sage-src.nix
2018-10-27 19:58:03 +03:00
Timo Kaufmann 2513747356 sage: fix attrname
This is a minimal change mainly to make sure repology recognizes this
package as sage. I plan a bit more refactoring later, but this is
intentionally kept minimally invasive so that it won't break anything
and can be backported to 18.09.
2018-10-27 14:18:08 +02:00
Timo Kaufmann fbea2cd77a arb: 2.14.0 -> 2.15.1 2018-10-27 11:27:03 +02:00
Timo Kaufmann 2ce2fcfc30 pythonPackages.cython: 0.28.5 -> 0.29
Needs a sage patch from
https://trac.sagemath.org/ticket/25292
2018-10-24 20:05:44 +02:00
Timo Kaufmann db75fe7313 sage: fix doctest
The test is depending on the "py2" tag always being added. I patched
that recently to make it possible to test sagedoc individually. Somehow
I missed this doctest.
2018-10-22 14:52:19 +02:00
Timo Kaufmann b39142cd1f sage: fix dochtml tests 2018-10-21 19:17:07 +02:00
Timo Kaufmann 38c2be5ffe sage: fix docbuild
This is only a hotfix without really knowing the issue. See
https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ
2018-10-21 14:16:06 +02:00
Timo Kaufmann a413dedde1
Merge pull request #44527 from timokau/sage-8.4
[WIP] sage: 8.3 -> 8.4
2018-10-20 01:34:34 +02:00
Timo Kaufmann 7ca1c31dfa sage: 8.4.rc1 -> 8.4 2018-10-18 09:58:36 +02:00
R. RyanTM eeb2ee296c gmsh: 4.0.1 -> 4.0.2
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions
2018-10-15 21:54:45 -07:00
Timo Kaufmann f89df0b556 sage: 8.4.rc0 -> 8.4.rc1 2018-10-13 13:27:10 +02:00
Timo Kaufmann 27919e06f1 sage: 8.4.beta7 -> 8.4.rc0 2018-10-07 12:23:10 +02:00
Jörg Thalheim 5200167f12
Merge pull request #47831 from r-ryantm/auto-update/calc
calc: 2.12.6.6 -> 2.12.6.8
2018-10-04 23:31:38 +01:00