alioth/nixpkgs
3
0
Fork 0
forked from mirrors/nixpkgs
Code Releases Activity
323289 commits 217 branches 121 tags 4.5 GiB
Commit graph

229 commits

Author SHA1 Message Date
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
Timo Kaufmann e550e5d0c7 lcalc: apply c++11 patch 2018-08-04 14:22:29 +02:00
Timo Kaufmann fa34f6d41c sage: don't pin pari 2018-08-04 14:22:28 +02:00
Timo Kaufmann e82c26af9b sage: don't pin singular 2018-08-04 14:22:28 +02:00
Timo Kaufmann 840b64fdb8 sage: 8.2 -> 8.3 2018-08-04 14:22:21 +02:00
Timo Kaufmann ae821e09e7 glpk: adopt error recovery patch (#44201) 
This makes it possible to use "vanilla" glpk for sage and shouldn't
affect anything else.
 2018-07-29 20:53:56 +02:00
Jörg Thalheim 218298b30f
Merge branch 'master' into unused5 2018-07-21 15:41:22 +01:00
volth 52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
volth 6d2857a311 [bot] treewide: remove unused 'inherit' in let blocks 2018-07-20 19:38:19 +00:00
Matthew Bauer fddd90e9ea
Merge pull request #43538 from timokau/fetchpatch-fix 
fetchpatch: quote excludes
 2018-07-19 00:35:09 -04:00
Timo Kaufmann cad446513e ntl: 9.11.0 -> 11.2.1 
ntl hasn't been updated in a while. So I'm doing that and adding myself
as the maintainer. I'm also adding some options and pinning the sage
dependency, since it is unfortunately not compatible with the latest ntl
yet.

I've also enabled the tests, since they don't take terribly long and are
worth the time in my opinion.
 2018-07-18 14:58:38 +02:00
Timo Kaufmann 3058513941 fetchpatch: add option to revert a patch 2018-07-16 22:46:54 +02:00
Timo Kaufmann c77d1e5b31 eclib: 20171219 -> 20180710 
Also includes the necessary sage compatibility patch, borrowed from
ArchLinux.
 2018-07-15 14:59:28 +02:00
Timo Kaufmann 85f7fa93bc pythonPackages.cypari2: 1.1.4 -> 1.2.1 (#43496) 2018-07-14 00:17:55 +02:00
Timo Kaufmann 35896e3506 sage: replace flask-babel version pin by patch 2018-07-12 22:55:16 +02:00
Timo Kaufmann dcc1013f6b pythonPackages.backports_shutil_get_terminal_size: 1.0 -> 2016-02-21 (#42840) 2018-07-02 18:03:05 +02:00
Timo Kaufmann 70ba695777 sage: replace JUPYTER_PATH patch by upstream patch 
The patch was replaced by a better upstream patch that doesn't mvoe the
jupyter dir to the user's home.
 2018-06-30 22:30:30 +02:00
Timo Kaufmann 398dad270a sage, arb: update sage dependencies arb and pynac 
Removes the version pinning for arb and pynac by backporting the
upstream (sage) package upgrades. This necessitates a new patch for arb,
which was however already proposed and accepted upstream.
 2018-06-30 17:05:56 +02:00
Timo Kaufmann 17e6b391eb sage: 8.1 -> 8.2, use system packages 2018-06-30 01:21:31 +02:00
Silvan Mosberger 57bccb3cb8 treewide: http -> https sources (#42676) 
* treewide: http -> https sources

This updates the source urls of all top-level packages from http to
https where possible.

* buildtorrent: fix url and tab -> spaces
 2018-06-28 20:43:35 +02:00
Michael Raskin 2093d4781d sage: set platforms to the set where I can build it; Hydra ARM builds seem to fail 2018-03-10 13:50:11 +01:00
Timo Kaufmann 4f239f9d49 sage: Make build more platform independant 2018-03-04 01:36:31 +01:00
Timo Kaufmann 89162cdd29 sage: explicitly use gfortran6 
The recent change from gfortran=gfortran6 to gfortran=gfortran7 broke
the build.
 2018-02-23 17:00:21 +01:00
Timo Kaufmann 0713bde50f sage: Don't build docs by default 
This makes the HTML-docs an default-off option. Inline documentation
(`matrix-plot??`) is still available and HTML docs are available online.

Motivation: Get below the Hydra output size limit.
 2018-02-13 17:52:41 +01:00
Timo Kaufmann 272e930827 sage: fix non-deterministic build failures 
The build was failing on some machines because of a `find` command that
touched files in different orders on different machines.

That confused `make`s timestamp mechanism.
 2018-02-05 15:03:24 +01:00
Timo Kaufmann b223662ad1 sage: 8.0 -> 8.1, fix sandbox build 
The sandboxed build was failing, because it relied heavily on
/usr/bin/env. This is fixed with a lot of shebang patching (both
to system packages and to sage-internal packages).
 2018-01-26 14:42:24 +01:00
Michael Raskin 85eac6ff73
Restrict platforms to what is known to work. 2017-11-06 01:25:04 +00:00
Timo Kaufmann fe68ba81d2 sage: 6.8 -> 8.0 
This "un-breaks" sage while also updating it to 8.0.

It compiles sage with its dependencies as one big pile, which is not
the best approach but definately better than nothing for now.

To be able to shrink the huge output pile a little, it also splits
docs from the rest of the output.
 2017-11-05 17:37:40 -06:00
Silvan Mosberger f5fa5fa4d6 pkgs: refactor needless quoting of homepage meta attribute (#27809) 
* pkgs: refactor needless quoting of homepage meta attribute

A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.

* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit

* Fixed some instances
 2017-08-01 22:03:30 +02:00
Robin Gloster f87de53883
sage: mark as broken 2017-03-30 12:06:08 +02:00
Mikhail Volkhov 78c0cecc5f
sage: fix build at 6.8 2017-03-13 10:34:55 +03:00
Robin Gloster 005a147f92
sage: fix build 
closes #17842
 2016-08-29 12:46:51 +00:00
cmfwyp 179d992427
sage: fix TeX Live input 
The Sage derivation had texLive, the old TeX Live packaging which
is now marked as broken, as a build input. This replaces it by the
current TeX Live packaging.

However, the build remains broken. One of the problems can be
solved by patching the hashbangs at the beginning of build scripts,
but the build still gets stuck while building ncurses.
 2016-08-07 23:18:47 -04:00
Florent Becker b860b106c5 sage: 6.1.1 -> 6.8 2015-09-22 09:01:33 +00:00
Joachim Fasting 71a443c1b2 Add mirrors for sage 2014-11-03 23:04:44 +01:00
Joachim Fasting 6f7822ddda sage: fix download url for version 6.1.1 2014-11-02 20:55:08 +01:00
Joachim Fasting 82ec13eaa3 sage: fix meta information 
Correct homagepage, description, and license.
 2014-11-02 20:55:02 +01:00
Eelco Dolstra fe4bc3cc80 Fix evaluation error 
http://hydra.nixos.org/build/10697257
 2014-04-29 20:40:28 +02:00
John Wiegley 7ce39b067a Add expression for sage 2014-04-22 14:10:36 -05:00