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843 Commits

Author SHA1 Message Date
Timo Kaufmann
31709b611f R: add timokau as a maintainer 
I'm interested in R as a dependency for sage. R changes are likely to
impact sage, so I'd like to get notified on those changes.
 2019-04-28 13:20:47 +02:00
Renaud
9f26d537e8
Merge pull request #59516 from r-ryantm/auto-update/gmsh 
gmsh: 4.2.2 -> 4.2.3
 2019-04-24 20:40:56 +02:00
Timo Kaufmann
9c7f774a39 gap: mark as broken on darwin 
Has been failing to build for a while.
 2019-04-20 12:36:11 +02:00
Timo Kaufmann
af6739fdd7 gap: 4.10.0 -> 4.10.1 2019-04-20 09:54:27 +02:00
Timo Kaufmann
49b8efcb84 sage: 8.6 -> 8.7 
https://groups.google.com/forum/#!topic/sage-release/3m8PV9JkFro
 2019-04-17 22:44:32 +02:00
Timo Kaufmann
e0e5445667 sage: fix another transient sig_on bug 
Caused a test failure on hydra, backporting upstream fix.
 2019-04-17 19:58:07 +02:00
R. RyanTM
00d17e36ea gmsh: 4.2.2 -> 4.2.3 
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
 2019-04-14 13:15:32 -07:00
Timo Kaufmann
62c288ec20
python.pkgs.sympy: 1.3 -> 1.4 (#59482) 2019-04-14 17:52:03 +02:00
markuskowa
87f595a1f0
Merge pull request #56615 from r-ryantm/auto-update/clp 
clp: 1.16.11 -> 1.17.0
 2019-04-14 12:05:32 +02:00
Markus Kowalewski
19dfffff3c
clp: restrict to x86_64-linux + darwin 2019-04-14 00:17:25 +02:00
Markus Kowalewski
e879991e1b
clp: 1.17.0 -> 1.17.11 2019-04-14 00:04:06 +02:00
Julien Dehos
a13f5d0da1 mxnet: fix cuda support enabled build (#48781) 2019-04-12 10:31:22 +00:00
Vladimír Čunát
f7ddff5c6d
R: fix regression from commit cbade453 #58989 
Normally the directory is created in fixup phase.
 2019-04-07 17:38:45 +02:00
rhokue
cbade453ac R: explicitly declare which as a run-time dependency 
Fixes https://github.com/NixOS/nixpkgs/issues/58963.
Closes https://github.com/NixOS/nixpkgs/pull/58989.
 2019-04-07 11:12:43 +02:00
Timo Kaufmann
ceede33ddf
python.pkgs.cypari2: 2.0.3 -> 2.1.0 (#59085) 2019-04-06 21:46:13 +00:00
Timo Kaufmann
7f22a42976 nauty: disable cpu feature detection 2019-04-04 14:54:55 +02:00
Timo Kaufmann
15045e6233 nauty: add timokau as a maintainer 
I'm interested in this package as a sage dependency.
 2019-04-04 14:54:31 +02:00
Timo Kaufmann
5880c449dd nauty: small refactoring 2019-04-04 14:54:05 +02:00
Timo Kaufmann
69555825f8
eclib: 20180815 -> 20190226 (#58801) 
Needs a sage patch, see
https://trac.sagemath.org/ticket/27360.
 2019-04-02 15:39:20 +00:00
markuskowa
7701fd7603
Merge pull request #58097 from r-ryantm/auto-update/ginac 
ginac: 1.7.4 -> 1.7.5
 2019-03-29 20:27:39 +01:00
markuskowa
403aa2dfed
Merge pull request #58180 from luzpaz/gmsh4.2.2 
gmsh 4.2.1->4.2.2
 2019-03-28 18:11:58 +01:00
luz.paz
13158c692c gmsh 4.2.1->4.2.2 2019-03-23 12:51:12 -04:00
Will Dietz
24484b216a qalculate-gtk: 2.9.0 -> 3.0.0 
http://qalculate.github.io/news.html
 2019-03-23 01:09:17 -05:00
R. RyanTM
34cba0b001 ginac: 1.7.4 -> 1.7.5 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
 2019-03-21 17:54:31 -07:00
worldofpeace
0353967957 nasc: 0.5.1 -> 0.5.2 
Main improvment is that libqalculatenasc.so is now properly linked

Changelog: https://github.com/parnold-x/nasc/compare/0.5.1...0.5.2
 2019-03-20 23:10:33 -04:00
Timo Kaufmann
5fc5881221
sage: backport bugfix (#57794) 2019-03-17 14:36:01 +00:00
Timo Kaufmann
8fc3c033cb
pynac: 0.7.23 -> 0.7.24 (#57791) 
Apparently some python3 related fixes: https://trac.sagemath.org/ticket/27241

Also switch to using pname.
 2019-03-17 14:35:28 +00:00
Alex Branham
1e354a7e40 R: 3.5.2 -> 3.5.3 
Closes https://github.com/NixOS/nixpkgs/pull/57400.
 2019-03-14 19:50:37 +01:00
Timo Kaufmann
ce96994032
sage: fix docbuild (#57294) 
The docbuild (or rather its tests) failed because sphinx built some
English parts of the documentation in Russian. The added debian patch
fixes that by isolating docbuilding threads in sphinx using
proper subprocesses.
 2019-03-10 21:42:54 +00:00
Timo Kaufmann
3b7fb15182
Merge pull request #57126 from timokau/sage-maxima-downgrade 
sage: downgrade maxima to 5.41
 2019-03-09 20:05:01 +00:00
Timo Kaufmann
23908a0ee3 sage: downgrade maxima to 5.41 
See discussion at
82254747af.
 2019-03-09 17:23:57 +01:00
luz.paz
77cb537712 gmsh: 4.1.5 -> 4.2.1 2019-03-08 05:24:15 -05:00
Timo Kaufmann
e2b287b32a maxima: remove ecl known-failures patch 
It doesn't apply anymore since the recent update. Since the testsuite is
completely disabled now, there is little point in rebasing it.
 2019-03-07 16:08:10 +01:00
Jörg Thalheim
9b57d852af
Merge pull request #56905 from timokau/pari-fix 
pari: fix off-by-one error
 2019-03-06 11:00:07 +00:00
Timo Kaufmann
a648b8c714 pari: fix off-by-one error 
Done by applying upstream patch. Will be included in the next release.

Upstream: https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2117
 2019-03-05 21:50:44 +01:00
Timo Kaufmann
00fa98f012 pari: add timokau as maintainer 
I'm mostly interested in this package because it is a dependency of
sage. I'd like to be notified on changes (which ofBorg will do when I'm
listed as a maintainer).
 2019-03-05 20:23:04 +01:00
Timo Kaufmann
5a23cb575e pari: slight refactoring 
Use pname, one line per argument.
 2019-03-05 20:21:26 +01:00
Peter Simons
1c6a193b3e wxmaxima: update to version 19.03.0 2019-03-05 12:53:05 +01:00
Peter Simons
82254747af maxima: update to version 5.42.2 2019-03-05 12:53:04 +01:00
R. RyanTM
6a987f5730 form: 4.2.0 -> 4.2.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/form/versions
 2019-03-03 20:49:36 +01:00
Timo Kaufmann
9e3754786b sage: fix strictDeps fallout 
See https://github.com/NixOS/nixpkgs/pull/54182 and
https://github.com/NixOS/nixpkgs/pull/55757.
 2019-03-03 13:25:40 +01:00
Timo Kaufmann
2de81ee78f sage: patch for pip 19 
pip 19 introduced a deprecation warning for python 2.7. Since sage
internally uses pip to query for installed packages, this deprecation
warning will show up at unexpected times. That is ugly and messes with
the testsuite.

Upstream: https://trac.sagemath.org/ticket/27405
 2019-03-03 13:21:22 +01:00
R. RyanTM
e869b87dbb clp: 1.16.11 -> 1.17.0 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/clp/versions
 2019-03-01 16:08:32 -08:00
Frederik Rietdijk
2fcb11a244 Merge staging-next into master 2019-03-01 09:06:20 +01:00
Jörg Thalheim
dadc7eb329
treewide: use runtimeShell instead of stdenv.shell whenever possible 
Whenever we create scripts that are installed to $out, we must use runtimeShell
in order to get the shell that can be executed on the machine we create the
package for. This is relevant for cross-compiling. The only use case for
stdenv.shell are scripts that are executed as part of the build system.
Usages in checkPhase are borderline however to decrease the likelyhood
of people copying the wrong examples, I decided to use runtimeShell as well.
 2019-02-26 14:10:49 +00:00
Vladimír Čunát
71f4ba29a3
Merge branch 'master' into staging-next 
Hydra nixpkgs: ?compare=1506218
 2019-02-22 17:51:01 +01:00
luz.paz
add7b20858 gmsh: 4.1.3 -> 4.1.5 2019-02-21 22:55:48 -05:00
Frederik Rietdijk
e2cd07b997 Merge staging-next into staging 2019-02-21 07:54:33 +01:00
Vladimír Čunát
32767d139f
Merge branch 'staging-next' 
This round is without the systemd CVE,
as we don't have binaries for that yet.
BTW, I just ignore darwin binaries these days,
as I'd have to wait for weeks for them.
 2019-02-20 09:38:45 +01:00
Michael Raskin
446520bb9b
Merge pull request #56026 from oxij/tree/move-defaults-to-package-files-half-cuda 
all-packages.nix: move defaults to package files continues^2
 2019-02-19 21:54:02 +00:00
Matthew Bauer
b1bbd94bb6 Merge remote-tracking branch 'NixOS/master' into staging 2019-02-18 20:36:48 -05:00
Frederik Rietdijk
815b77cbe6 Merge master into staging-next 2019-02-18 14:18:04 +01:00
Frederik Rietdijk
4b2336ea28 python.pkgs.caffe: fix build, closes #8749 2019-02-17 10:13:22 +01:00
Vladimír Čunát
f7f1a2f54e
Merge branch 'master' into staging-next 
A mass darwin rebuild from master (#55784).
 2019-02-17 08:05:24 +01:00
Gabriel Ebner
7cbc76a3e6 Merge branch 'auto-update/qalculate-gtk' 2019-02-16 17:25:47 +01:00
Frederik Rietdijk
fd48a94b62 Merge staging-next into staging 2019-02-16 09:30:46 +01:00
Frederik Rietdijk
6fe10d2779 Merge master into staging-next 2019-02-16 09:29:54 +01:00
R. RyanTM
ef405c5b67 qalculate-gtk: 2.8.2 -> 2.9.0 
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
 2019-02-15 11:39:04 -08:00
Timo Kaufmann
9243e85fbc
sage: fix fetchSageDiff (#55783) 
For some reason I changed it to use `cgit`s `rawdiff` instead of `patch`
in the update to sage 8.6. Probably commited that by accident, at least
I can't remember the reason. Also changed the excludes filter, the
leading slash prevented it from working.

As a result, the cypari2 patch changed. Only didn't notice because it
was cached.

Fixes #55780
 2019-02-14 21:48:03 +01:00
Frederik Rietdijk
a25d48cd4f Merge master into staging 2019-02-14 11:35:50 +01:00
Jan Tojnar
606ceda352
gnome3: stop using aliases 2019-02-14 02:31:15 +01:00
Michael Raskin
8384cfe455
Merge pull request #55129 from oxij/tree/move-defaults-to-package-files 
all-packages.nix: move defaults to package files
 2019-02-13 20:04:08 +00:00
Frederik Rietdijk
7257dedd7c Merge master into staging-next 2019-02-13 12:33:29 +01:00
Timo Kaufmann
5728028916 sage: add numpy 1.16 compatibility patch 
https://trac.sagemath.org/ticket/27000
 2019-02-11 21:43:56 +01:00
Timo Kaufmann
342333c0ab
sage: add compatibility for sphinx 1.8.3 (#55078) (#55560) 
Since https://github.com/NixOS/nixpkgs/pull/48841 was replaced by
https://github.com/NixOS/nixpkgs/pull/54186, this needs to be done
separately.

(cherry picked from commit 33db01e6d9)
 2019-02-11 13:18:16 +01:00
Florian Franzen
f470720aa8 Merge branch 'staging-next' into staging 2019-02-10 14:37:31 +01:00
Vladimír Čunát
d2c4b5777b
sagelib: fix missing pkgs.pkgconfig 
Again: eb3f0aef43 #54306
Apparently the derivation needs both pkgconfigs
(it fails when missing either).
 2019-02-09 10:36:47 +01:00
Jan Malakhovski
4bc66b1994 cntk: move defaults to package file 2019-02-03 15:32:16 +00:00
Jan Malakhovski
31aa884b7f caffe: move defaults to package file 2019-02-03 15:32:15 +00:00
Jan Malakhovski
49148a3ea2 mxnet: move defaults to package file 2019-02-03 15:32:14 +00:00
Jan Malakhovski
88ca6dd78a cplex: move defaults to package file 2019-02-03 15:30:47 +00:00
Jan Malakhovski
ec2452dac1 scilab: move defaults to package file 2019-02-03 15:30:45 +00:00
Timo Kaufmann
33db01e6d9
sage: add compatibility for sphinx 1.8.3 (#55078) 
Since https://github.com/NixOS/nixpkgs/pull/48841 was replaced by
https://github.com/NixOS/nixpkgs/pull/54186, this needs to be done
separately.
 2019-02-02 13:02:07 +01:00
Vladimír Čunát
8ba516664b
Merge branch 'staging-next' into staging 2019-02-01 09:42:53 +01:00
Robert Schütz
052acfe930 sage: python-openid: move django and twill to checkInputs (#54949) 
A search through the source code
(https://github.com/openid/python-openid/search?q=django and
https://github.com/openid/python-openid/search?q=twill) reveals
that they are only used in examples and tests.
 2019-01-31 10:14:36 +01:00
markuskowa
ca13dc163b
Merge pull request #49871 from wucke13/getdp 
getdp: init at 3.0.4
 2019-01-31 00:43:08 +01:00
R. RyanTM
2b03ef0521 gmsh: 4.1.0 -> 4.1.3 
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
 2019-01-28 10:33:36 -08:00
wucke13
4f40b5e00e getdp: init at 3.0.4 2019-01-28 16:45:13 +01:00
Matthew Bauer
92f0f8dd68 Merge remote-tracking branch 'NixOS/master' into staging 2019-01-27 00:01:13 -05:00
Artemis Tosini
51a2a08d6e
mathematica: 11.2.0 -> 11.3.0 
Note that this only affects the English version, as I do not have access
to the hash for the Japanese version.
 2019-01-25 15:29:02 +00:00
worldofpeace
78da8d668b pantheon: init a 5.0 2019-01-24 20:54:14 +00:00
Timo Kaufmann
d34f44db45
sage: fix transient ecl error (#54285) 
Sometimes the doctests fail because ecl races to create a directory.
This should fix that by making sure each process has its own directory.
 2019-01-18 23:02:03 +01:00
markuskowa
4545aaa671
Merge pull request #54209 from r-ryantm/auto-update/gmsh 
gmsh: 4.0.7 -> 4.1.0
 2019-01-18 11:40:48 +01:00
R. RyanTM
55ea7b1bbe gmsh: 4.0.7 -> 4.1.0 
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
 2019-01-17 12:55:54 -08:00
Timo Kaufmann
e379ee67c3 sage: 8.5 -> 8.6 2019-01-17 20:39:02 +01:00
Timo Kaufmann
29e150d85f
Merge pull request #54127 from timokau/gap-improvements 
gap: install libgap, add packageSet option
 2019-01-17 20:38:38 +01:00
Timo Kaufmann
cf63a8c94c gap: add packageSet option 
Two reasons for this:

- more fine-grained space/functionality tradeoff

- preparation for the sage 8.6 update, which finally doesn't need a
  downgraded gap anymore but does break when unexpected (non-standard)
  packages are installed. Details: https://trac.sagemath.org/ticket/26983

The proper way to deal with gap packages would be to create a package
set, package each one individually and have something like gap
equivalent of `python.withPackages`. I am not willing to do that
however.
 2019-01-17 10:10:24 +01:00
Timo Kaufmann
bb173ec8e3 gap: install libgap 
There are some starts of a `make install`, but nothing complete yet.
Upstream now ships a `libgap` as a replacement of the custom one used by
sagemath.
 2019-01-17 10:10:21 +01:00
Timo Kaufmann
6bbd0596dd gap: add timokau as maintainer 
So that I'll be notified on changes which likely impact sage.
 2019-01-16 23:41:31 +01:00
Timo Kaufmann
a8dbc5e313
python.pkgs.cypari2: 1.3.1 -> 2.0.3 (#54093) 
Upstream issues should be fixed now, see https://trac.sagemath.org/ticket/26442.
Sage needs a patch to adapt.
 2019-01-16 22:15:40 +01:00
Johannes Frankenau
bebf305c1b gurobi: 8.0.1 -> 8.1 (#53884) 2019-01-13 23:22:55 +01:00
R. RyanTM
bd7eec5d9c pynac: 0.7.22 -> 0.7.23 (#53559) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/pynac/versions
 2019-01-07 14:52:18 +01:00
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