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188 Commits

Author SHA1 Message Date
Timo Kaufmann
9f434d7080 sage: 8.8.beta5 -> 8.8.beta6 2019-06-27 22:01:40 +02:00
Timo Kaufmann
325a5037bf sage: 8.8.beta4 -> 8.8.beta5 2019-06-27 22:01:37 +02:00
Timo Kaufmann
240d4c31d2 sage: 8.8.beta3 -> 8.8.beta4 2019-06-27 21:57:33 +02:00
Timo Kaufmann
608948e3e9 sage: 8.8.beta2 -> 8.8.beta3 2019-06-27 21:57:33 +02:00
Timo Kaufmann
21c1ab6776 sage: 8.7 -> 8.8.beta2 2019-06-27 21:57:27 +02:00
Timo Kaufmann
9955657209 sage: fix online threejs 2019-06-20 12:50:00 +02:00
Timo Kaufmann
2d78d928cd sage: backport threejs r100 compatibility 
https://github.com/NixOS/nixpkgs/issues/62736#issuecomment-503757429
 2019-06-20 12:50:00 +02:00
Timo Kaufmann
6e74109b13
sage: fix threejs integration (#63375) 
Before this it didn't find the correct files. Unfortunately, the
interactive parts of sage are hard to test automatically.
 2019-06-18 11:50:41 +02:00
volth
f3282c8d1e treewide: remove unused variables (#63177) 
* treewide: remove unused variables

* making ofborg happy
 2019-06-16 19:59:05 +00:00
Robin Gloster
6cf583cf2f
Merge pull request #60406 from JohnAZoidberg/remove-isnull 
treewide: Remove usage of isNull
 2019-05-18 09:36:24 +00:00
Timo Kaufmann
3814d7b14a
givaro: 4.0.4 -> 4.1.0, fflas-ffpack: 2.3.2 -> 2.4.0, linbox: 1.5.2 -> 1.6.0 (#61285) 
The three packages are interdependent and need to be updated together,
like the main contributor did for sage:

https://trac.sagemath.org/ticket/24214
 2019-05-11 16:09:07 +02:00
Daniel Schaefer
786f02f7a4 treewide: Remove usage of isNull 
isNull "is deprecated; just write e == null instead" says the Nix manual
 2019-04-29 14:05:50 +02:00
Timo Kaufmann
6dabc28cd0 sage: add compatibility for R 3.6.0 
The random number generator seems to have changed. Because of this, a
trivial test adjustment is needed.
 2019-04-29 13:37:07 +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
Timo Kaufmann
62c288ec20
python.pkgs.sympy: 1.3 -> 1.4 (#59482) 2019-04-14 17:52:03 +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
69555825f8
eclib: 20180815 -> 20190226 (#58801) 
Needs a sage patch, see
https://trac.sagemath.org/ticket/27360.
 2019-04-02 15:39:20 +00:00
Timo Kaufmann
5fc5881221
sage: backport bugfix (#57794) 2019-03-17 14:36:01 +00:00
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
23908a0ee3 sage: downgrade maxima to 5.41 
See discussion at
82254747af.
 2019-03-09 17:23:57 +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
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
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
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
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
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
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
Timo Kaufmann
e379ee67c3 sage: 8.5 -> 8.6 2019-01-17 20:39:02 +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
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
Timo Kaufmann
b09967d812 sage: 8.5.rc0 -> 8.5.rc1 2018-12-16 21:33:28 +01:00
Timo Kaufmann
90bc5ce04d sage: 8.5.beta5 -> 8.5.beta6 2018-12-10 19:36:24 +01:00
Symphorien Gibol
b5435d0551 giac: 1.4.9 -> 1.5.0 2018-12-09 23:18:46 +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
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
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
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
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
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
Frederik Rietdijk
53d00c3351 Merge master into staging-next 2018-11-10 11:08:54 +01:00
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
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
7ca1c31dfa sage: 8.4.rc1 -> 8.4 2018-10-18 09:58:36 +02:00
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
Timo Kaufmann
a13eb29485 sage: 8.4.beta6 -> 8.4.beta7 2018-10-01 17:38:20 +02:00
Timo Kaufmann
0be6ca9e71 sage: 8.4.beta5 -> 8.4.beta6 2018-09-27 12:08:15 +02:00
Timo Kaufmann
1217882907 sage: 8.4.beta4 -> 8.4.beta5 2018-09-15 17:23:14 +02:00
Timo Kaufmann
c3f652d5a8 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-15 17:22:11 +02:00
Timo Kaufmann
db784d883c sage: re-add pkg-config aliases 
Those were removed because they were added to openblas itself. There was
an error with that however and it will take some time until the fix
makes its way through staging. For the time being, reverting this part
of 26d5d030fe will fix the sage build.
This commit should be reverted once
408eacbc89 is in master.
 2018-09-07 21:55:41 +02:00
Timo Kaufmann
770c5b8a69 sage: 8.4.beta3 -> 8.4.beta4 2018-09-07 20:56:37 +02:00
Timo Kaufmann
4ab832d6e7 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-07 20:54:09 +02:00
Timo Kaufmann
7521f2863d sage: fix numpy and scipy integration 2018-09-07 18:36:52 +02:00
Timo Kaufmann
46e653673e sage: 8.4.beta2 -> 8.4.beta3 2018-09-02 12:42:44 +02:00
Frederik Rietdijk
7945295410 Merge master into staging 2018-08-27 08:21:50 +02:00
Timo Kaufmann
0e4160a3a1 pythonPackages.sympy: 1.1.1 -> 1.2 2018-08-26 19:56:44 +02:00
Timo Kaufmann
1b42a1ba1e sage: 8.4.beta1 -> 8.4.beta2 2018-08-26 13:09:22 +02:00
Timo Kaufmann
26d5d030fe openblas: add pkg-config aliases 2018-08-21 16:39:57 +02:00
Timo Kaufmann
52b9217b50 sage: 8.4.beta0 -> 8.4.beta1 2018-08-16 00:17:14 +02:00
Timo Kaufmann
df97127114 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-08-15 13:51:07 +02:00
Timo Kaufmann
291018b34e arb: 2.13.0 -> 2.14.0 (#44600) 2018-08-07 16:38:34 +02:00
Timo Kaufmann
a8b048c686 sage: 8.3 -> 8.4.beta0 2018-08-05 21:09:56 +02:00
Michael Raskin
75cb04672f
Merge pull request #44508 from timokau/cddlib-0.94j 
cddlib: 0.94i -> 0.94j
 2018-08-05 19:03:47 +00:00
Timo Kaufmann
0a44ff7676 cddlib: 0.94i -> 0.94j 
cddlib was autotoolized, incorporated equivalents to the sage patches
and moved to GitHub.
 2018-08-05 19:02:45 +02:00
Timo Kaufmann
30c822189d sage: don't override pari 
Sage assumes that pari does not use threads. However instead of
disabling them at compile time, we can diable them at runtime instead.
As a result, sage doesn't need its own version of pari anymore. That
means less rebuilds, less complexity and easier debugging.
 2018-08-05 13:48:14 +02:00
Timo Kaufmann
834a24e0ff sage: don't pin ntl 
Now possible because of the lcalc c++11 patch.
 2018-08-04 14:22:58 +02:00