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Author SHA1 Message Date
Timo Kaufmann e371a02b6c sage: disable test timeout
I already did that once in 359bf7f1e3.
That change mysteriously got lost somehow (presumably in some merge
commit).

Nix has its own timeout settings, so there is no risk in running
forever. At the same time, some tests can exceed the default timeout
(30minutes per file for --long tests) when run on many weak cores (like
the aarch64 community builder or some hydra builders).
2019-12-01 13:23:54 +01:00
Timo Kaufmann afb9887dbd sage: backport fix for threejs r109 2019-11-06 14:40:16 +01:00
Timo Kaufmann f64885b9ca sage: fix pkgconfig errors in tests
python.pkgs.pkgconfig raises an exception on missing packages since
version 1.5.0. Previously those errors were just silently ignored. That
worked fine, since the packages are only missing at runtime (when they
are not really needed) but present at buildtime.

Since this fails the tests now, we just add the packages to
PKG_CONFIG_PATH at runtime. This does not add additional runtime
dependencies. Still, it would be nicer if the sage testssuite would not
test the buildsystem at runtime in the first place.

The breakage was originally caused by the pkgconfig update in
1efa71616f.
2019-11-06 14:40:13 +01:00
Timo Kaufmann da7ec1c139 sage: ignore werkzeug immutable dict deprecation 2019-11-06 14:40:13 +01:00
Timo Kaufmann f85ce834ce sage: ignore deprecation warnings in rst2sws
Needs to be fixed upstream (by werkzeug, twisted). Doesn't impact the
functionality and the tests are soon to be removed with the py3 update
anyway.
2019-11-06 14:40:13 +01:00
Timo Kaufmann af480796c9 sage: ignore cmp deprecation in sagenb 2019-11-06 14:40:13 +01:00
Timo Kaufmann 32827e35d8 sage: ignore attrs deprecation warning
cmp is deprecated since attrs 19.2.0:
http://www.attrs.org/en/19.2.0/changelog.html

The deprecation warning breaks the doctests.  Fortunately they have a
rather long deprecation window, so we can just wait until upstream(s)
fix this.
2019-10-30 22:27:00 +01:00
Timo Kaufmann 7a7e9c1b27
Merge pull request from timokau/sage-8.9
sage: 8.8 -> 8.9
2019-09-30 11:13:46 +00:00
Timo Kaufmann d9176bee70 sage: 8.9.rc1 -> 8.9 2019-09-30 11:10:10 +02:00
R. RyanTM faf9a73e2f eclib: 20190226 -> 20190909
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eclib/versions

Relevant sage upstream ticket: https://trac.sagemath.org/ticket/28472
2019-09-26 16:41:50 +02:00
Timo Kaufmann 78741fc409 sage: 8.9.rc0 -> 8.9.rc1 2019-09-25 10:19:04 +02:00
Timo Kaufmann 1797c9c295 sage: 8.9.beta9 -> 8.9.rc0
Sage now by default expects the lcalc library to be named Lfunction
(instead of libLfunction). This could be changed by an environment
variable (https://trac.sagemath.org/ticket/28224), but various distros
seem to agree on this standard
(https://groups.google.com/forum/#!topic/sage-packaging/xvh55IxHTZg) so
it's best just to follow it. The old standard was set by sage anyway and
sage is the only consumer of lcalc in nixpkgs.
2019-09-24 17:51:09 +02:00
Timo Kaufmann 5aba3be6f9 sage: 8.9.beta8 -> 8.9.beta9 2019-09-23 18:50:59 +02:00
Timo Kaufmann 8593d468ae Merge remote-tracking branch 'upstream/master' into sage-8.9 2019-09-23 17:11:15 +02:00
Timo Kaufmann cbe12344ca sage: add pager to environment
Temporary fixup while waiting for an upstream fix.
2019-09-23 15:14:43 +02:00
volth 7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Timo Kaufmann 84578046aa sage: 8.9.beta7 -> 8.9.beta8 2019-09-03 15:34:28 +02:00
volth 08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Timo Kaufmann 071a4db33e sage: 8.9.beta6 -> 8.9.beta7 2019-08-19 00:16:06 +02:00
Timo Kaufmann e8436f5e23 sage: 8.9.beta5 -> 8.9.beta6 2019-08-18 21:52:27 +02:00
Frederik Rietdijk fe9a3e3e63 Merge staging-next into staging 2019-08-17 09:39:23 +02:00
Timo Kaufmann 192197dc6c
Merge pull request from timokau/sage-transient-debug
sage: add patch to debug transient issue
2019-08-17 00:33:05 +02:00
Timo Kaufmann 41bb319462 sage: avoid running out of memory during tests 2019-08-16 23:50:55 +02:00
volth 46420bbaa3 treewide: name -> pname (easy cases) ()
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
2019-08-15 13:41:18 +01:00
Timo Kaufmann f6265b0da5 sage: default to long tests again
Changed by accident in 5e58c5f900.
2019-08-09 18:42:14 +02:00
Timo Kaufmann 9ef44b3431 sage: move sympow cache to .sage 2019-08-09 17:45:14 +02:00
Timo Kaufmann 5e58c5f900 sympow: 1.018.1 -> 2.023.4
Maintenance taken over by debian package maintainer jgmbenoit:
https://trac.sagemath.org/ticket/3360#comment:17

This moves sympow to his fork, since there is no offical
version-controlled source repository from the original author and they
do not seem to maintain sympow anymore. We had already accumulated quite
some patches from debian, who have effectively maintained sympow for a
while now.
2019-08-09 17:45:08 +02:00
Timo Kaufmann ddd3faf08e sage: 8.9.beta4 -> 8.9.beta5 2019-08-07 15:33:15 +02:00
Timo Kaufmann f6a1fe64eb sage: 8.9.beta3 -> 8.9.beta4 2019-08-02 23:50:45 +02:00
Timo Kaufmann 69d9700c61 sage: add list of past test failures 2019-08-02 18:09:18 +02:00
Timo Kaufmann dac4719e0b sage: add patch to debug transient issue 2019-08-02 18:09:15 +02:00
Timo Kaufmann b884552c35 sage: 8.9.beta2 -> 8.9.beta3 2019-08-02 01:03:33 +02:00
Timo Kaufmann 56bd506e42 sage: 8.9.beta0 -> 8.9.beta2 2019-07-11 19:42:01 +02:00
Frederik Rietdijk 25a77b7210 Merge staging-next into staging 2019-07-03 08:59:42 +02:00
Timo Kaufmann 924c321e8a sage: 8.8 -> 8.9.beta0 2019-07-02 23:02:36 +02:00
worldofpeace 3f4a353737 treewide: use dontUnpack 2019-07-01 04:23:51 -04:00
Timo Kaufmann 5b2db39c49 sage: 8.8.rc2 -> 8.8 2019-06-27 22:05:30 +02:00
Timo Kaufmann e7d4386e0e sage: 8.8.rc1 -> 8.8.rc2 2019-06-27 22:03:00 +02:00
Timo Kaufmann 218fd843a3 sage: 8.8.rc0 -> 8.8.rc1 2019-06-27 22:03:00 +02:00
Timo Kaufmann 409bee28b6 sage: 8.8.beta7 -> 8.8.rc0 2019-06-27 22:03:00 +02:00
Timo Kaufmann c76e8fa86e sage: 8.8.beta6 -> 8.8.beta7 2019-06-27 22:02:57 +02:00
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 ()
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 ()
* treewide: remove unused variables

* making ofborg happy
2019-06-16 19:59:05 +00:00
Robin Gloster 6cf583cf2f
Merge pull request 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 ()
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 () 2019-04-14 17:52:03 +02:00
Timo Kaufmann ceede33ddf
python.pkgs.cypari2: 2.0.3 -> 2.1.0 () 2019-04-06 21:46:13 +00:00
Timo Kaufmann 69555825f8
eclib: 20180815 -> 20190226 ()
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 () 2019-03-17 14:36:01 +00:00
Timo Kaufmann ce96994032
sage: fix docbuild ()
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 ()
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 
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 () ()
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 
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 ()
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 ()
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 ()
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 ()" ()
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 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 () 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 ()
Fixes .
2018-11-25 17:38:45 +01:00
Timo Kaufmann 98c94d3d7d sage: add jupyter notebook support
Fixes .
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