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Timo Kaufmann b8a299c910 python.pkgs.entrypoints: simplify tests 
The upstream issue requiring one test to be disabled was fixed:
https://github.com/takluyver/entrypoints/issues/23
 2019-02-17 14:40:49 +01:00
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 a27de564b9 python.pkgs.matplotlib: add numpy 1.6 compat patch (#55577) 
* python.pkgs.matplotlib: add numpy 1.6 compat patch

Numpy deprecated asscalar in 1.16. This will be fixed in the next
matplotlib version, but to avoid deprecation warnings (and because they
are breaking the sage testsuite), it can't hurt to backport the fix
already.

Upstream: https://github.com/matplotlib/matplotlib/pull/12478

* sage: add numpy 1.16 compatibility patch

https://trac.sagemath.org/ticket/27000
 2019-02-11 23:43:46 +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 56d92ba70c python.pkgs.matplotlib: add numpy 1.6 compat patch 
Numpy deprecated asscalar in 1.16. This will be fixed in the next
matplotlib version, but to avoid deprecation warnings (and because they
are breaking the sage testsuite), it can't hurt to backport the fix
already.

Upstream: https://github.com/matplotlib/matplotlib/pull/12478
 2019-02-11 21:39:21 +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
Timo Kaufmann 295acfcb33 Revert "rustfmt: 1.0.0 -> 1.0.1" (#55437) 
This reverts commit 7fff567ee9. It depends
on the rustc update I reverted in #55379. It should be re-introduced
after that rustc update has gone through staging.
 2019-02-08 12:24:15 +01:00
Timo Kaufmann 882131e7db Revert "rustc: 1.31.0 -> 1.32.0" (#55379) 
This reverts commit 56dba36eb5.
 2019-02-07 12:49:37 +01:00
Timo Kaufmann dbc771f2e1 Merge pull request #55299 from r-ryantm/auto-update/jmol 
jmol: 14.29.29 -> 14.29.31
 2019-02-06 13:15:46 +01:00
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
Timo Kaufmann 2564e780b5 vimPlugins: update (#54889) 
Auto-generated update.
 2019-01-29 20:55:52 +01:00
Timo Kaufmann ed1a8277ce vimPlugins: add pname to remaining plugins (#54311) 
This makes it possible to access plugin name and version seperately (and
reliably), e.g. for accessing the plugin directory using pname.
 2019-01-19 13:18:27 +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 2bc0e00372 vimUtils.buildVimPlugin: write vim errors to stderr 
Previously vim would silently fail when help tags couldn't be generated.
We need to pass the "verbose" flag (with verbose level 1) to convince
vim to print errors to standard error.
 2019-01-18 21:18:35 +01:00
Timo Kaufmann ab22e8cc9c neovim: generate remote plugin manifest 
This makes sure the user doesn't have to call `UpdateRemotePlugins`
manually for plugins installed through nix. A minor patch to neovim is
necessary, but it should be harmless. See
https://github.com/neovim/neovim/issues/9413 for a discussion about
the patch.
 2019-01-18 21:18:32 +01:00
Timo Kaufmann 51c4768f67 neovim: fix indentation 2019-01-18 21:15:17 +01:00
Timo Kaufmann a1169afded youtube-dl: 2019.01.16 -> 2019.01.17 
Fixes an issue with youtube, see
https://github.com/rg3/youtube-dl/issues/18891
 2019-01-18 16:05:39 +01:00
Timo Kaufmann 73368f468a Merge pull request #54202 from timokau/sage-8.6 
sage: 8.5 -> 8.6
 2019-01-17 21:12:17 +01:00
Timo Kaufmann 471ba67013 libgap, gap-libgap-compatible: remove 
They were only used by sage, which now (since version 8.6) uses gaps own
(new) libgap.
 2019-01-17 20:39:02 +01:00
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
Timo Kaufmann c74b019ab2 python.pkgs.cypari2: fix build (#53966) 
Broken by a typo in f665828fa3 causing the
sitePackages path to be wrong.
 2019-01-14 22:50:27 +01:00
Timo Kaufmann 3dc0a1b7a7 spotify: 1.0.94.262.g3d5c231c-9 -> 1.0.96.181.gf6bc1b6b-12 (#53930) 
spotify now requires "libatk-bridge-2.0.so", which is provided by
at-spi2-atk.
 2019-01-14 11:05:13 +01:00
Timo Kaufmann b54d9e27cb python.pkgs.pygal: fix build (#53833) 
`pytestrunner` is a required build input.

Also we need to explicitly set the locale to pass the tests on darwin.
 2019-01-12 15:08:21 +01:00
Timo Kaufmann 6359e9baf0 python3.pkgs.tinycss: fix build (#53831) 
The build was broken by the python 3.7 switch, which caused an
incompatible change in the way cython generates files:

https://github.com/Kozea/tinycss/issues/17

This is solved by removing the pre-generated file and re-generating it
at build time.
 2019-01-12 11:24:31 +01:00
Timo Kaufmann 0d028c3bee neovim-qt: add desktop file to wrapper (#53777) 
My recent change in #53447 caused neovim-qt to no longer be recognized
as a desktop application.
 2019-01-10 22:18:04 +01:00
Timo Kaufmann 8dd63a67e9 python3.pkgs.graph-tool: fix with python3.7 (#53719) 
"async" is now reserved, there is an upstream fix but no release yet.
 2019-01-10 00:10:34 +01:00
Timo Kaufmann e012ec5b14 Merge pull request #53670 from timokau/vim-plugins-update 
vimPlugins: update, init neoterm and vim-slime
 2019-01-08 22:27:42 +01:00
Timo Kaufmann 67cf32751c vimPlugins.vim-slime: init at 2019-01-03 2019-01-08 22:04:27 +01:00
Timo Kaufmann f7113786af vimPlugins.neoterm: init at 2018-12-21 2019-01-08 21:59:31 +01:00
Timo Kaufmann 8c81099cda radare2: add propagated build inputs (#53667) 
Fixes the cutter build which was broken when radare2 was moved away from
vendored dependencies in #51837.
 2019-01-08 21:55:44 +01:00
Timo Kaufmann 114a9e6bd4 vimPlugins: update 2019-01-08 17:55:56 +01:00
Timo Kaufmann a2ffb3fcd8 python.pkgs.r2pipe: init at 1.2.0 (#53504) 2019-01-06 19:10:47 +01:00
Timo Kaufmann c52c4a00a2 doc: add neovim-qt configuration 2019-01-06 10:56:28 +01:00
Timo Kaufmann ee9bc405b9 neovim-qt: wrap in separate derivation 
This makes it possible to swap out the (wrapped) neovim without
recompiling neovim-qt. In particular, the user can use `neovim.override`
to configure their neovim and then use that same configuration for
neovim-qt, without having to give up binary caching.
 2019-01-06 10:56:27 +01:00
Timo Kaufmann e33d6364f6 Merge pull request #53240 from timokau/vim-drv-recursively 
vimUtils: apply pluginToDrv recursively
 2019-01-03 11:56:44 +01:00
Timo Kaufmann 801a548183 vimUtils: fix map parentheses 2019-01-02 22:59:19 +01:00
Timo Kaufmann f38363387e vimUtils: apply pluginToDrv recursively 
This is necessary to handle plugin dependencies which also may be
strings.
 2019-01-02 22:12:27 +01:00
Timo Kaufmann 04ba895ecd suitesparse: 5.3.0 -> 5.4.0 (#53128) 2019-01-01 15:47:55 +01:00
Timo Kaufmann a0dc57e27b vimUtils: derive pname from the plugin string (#53121) 
For backwards compatibility. The user may specify their own plugins
without the pname attribute. In that case the attrname of the plugin
(given as a string) is the pname.

Fixes #53112
 2018-12-31 16:26:06 +01:00
Timo Kaufmann 42575040fc Merge pull request #53113 from timokau/neovim-requiredPlugins-fix 
vimUtils: fix requiredPlugins
 2018-12-31 11:45:41 +01:00
Timo Kaufmann d9d9ac989a neovim: mark as broken for aarch64 
Has always been broken.
 2018-12-31 11:12:51 +01:00
Timo Kaufmann 093cfde1e0 vimUtils: fix requiredPlugins 
I broke this in #52767 and didn't notice because I only tested with vim
and `requiredPlugins` is only used by neovim. This would break setups
that use string-plugins (like pathogen) with neovim.
 2018-12-31 10:31:14 +01:00
Timo Kaufmann 30ff3e0f39 vimUtils.buildVimPlugin: fix helptag generation (#53071) 
I messed that up in my refactoring in #52767, since I moved the relevant
bash code out of a function and failed to adjust the shell variable
name. Now the plugin build will fail loudly when help tag generation
fails to make sure this doesn't happen again.
 2018-12-30 12:22:17 +01:00
Timo Kaufmann 92bd86383f python.pkgs.cysignals: 1.8.0 -> 1.8.1 (#53039) 2018-12-29 16:16:23 +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
Timo Kaufmann d84ac4f43f fflas-ffpack: add patch to fix flaky test (#53005) 2018-12-28 14:02:43 +01:00
Timo Kaufmann 22d0f320e8 Merge pull request #52767 from timokau/vim-plugin-updates 
Fix vim-plugin dependencies
 2018-12-28 13:48:21 +01:00
Timo Kaufmann 58b4351b38 vimPlugins.taglist-vim: fix build 
The override actually broke the build, no idea why it was added
originally. The build works fine without it.
 2018-12-28 13:31:58 +01:00
Timo Kaufmann af465293f1 vimPlugins: use fixed point 2018-12-27 11:55:53 +01:00
Timo Kaufmann 96b6396101 vimUtils.buildVimPlugin: derive name from pname and version 2018-12-27 10:34:14 +01:00
Timo Kaufmann edf8b984fa vimPlugins: Update 2018-12-27 10:32:27 +01:00
Timo Kaufmann 8e8a09bfc9 vimUtils: add dependency logic to nativeImpl 
nativeImpl previously simply ignored dependency information.
 2018-12-24 23:41:44 +01:00
Timo Kaufmann b352318cd1 vimUtils: represent vim plugins as derivations 
Vim plugins were previously represented as strings by default,
necessitating a `knownPlugins` set. Backwards compatibility is kept
(strings are still accepted), so vam plugins should continue to work.
 2018-12-24 23:41:41 +01:00
Timo Kaufmann ce7899bea5 vimPlugins.ncm2-jedi: init at 2018-07-18 2018-12-24 23:40:44 +01:00
Timo Kaufmann 1e25b748fa vimPlugins: Update 2018-12-23 23:30:11 +01:00
Timo Kaufmann c7de873f94 Merge pull request #52658 from r-ryantm/auto-update/zim 
zim: 0.68 -> 0.69
 2018-12-22 14:37:30 +01:00
Timo Kaufmann 1d04be420c zim: mark as broken for darwin 
Has been broken for about a year already.
 2018-12-22 14:10:09 +01:00
Timo Kaufmann bfca7082d4 Merge pull request #52613 from nyanloutre/pyqt5-fix 
pythonPackages.pyqt5: fix sip dependency
 2018-12-21 15:28:50 +01:00
Timo Kaufmann c5398741e0 Revert "collectd: fix build with lm_sensors" (#52619) 2018-12-21 13:11:22 +01:00
Timo Kaufmann 64b9df085d Revert "python: cypari2: 1.3.1 -> 2.0.0" (#52596) 
This reverts commit 7c9ca65480. The
cypari2 update is not ready. The package is pretty much only used for
sage and the update causes problems:
https://trac.sagemath.org/ticket/26442#comment:33
I've already reverted this once before.
 2018-12-20 23:51:48 +01:00
Timo Kaufmann 51fdee8b92 pythonPackages.jupytext: init at 0.8.4 (#52545) 2018-12-20 12:18:30 +01:00
Timo Kaufmann 4040b43a25 Merge pull request #52557 from etu/php-codesniffer-updates 
Php codesniffer updates
 2018-12-20 12:06:11 +01:00
Timo Kaufmann 979b88b2bc pythonPackages.pathpy: skip performance test (#52548) 
The test may fail non-deterministically, as it does right now on hydra.
 2018-12-19 23:53:17 +01:00
Timo Kaufmann af83f8b398 pythonPackages.absl-py: fix python2 build (#52544) 2018-12-19 23:19:16 +01:00
Timo Kaufmann b09967d812 sage: 8.5.rc0 -> 8.5.rc1 2018-12-16 21:33:28 +01:00
Timo Kaufmann 314fc8390b arb: 2.15.1 -> 2.16.0 (#52394) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/arb/versions
 2018-12-16 20:01:10 +01:00
Timo Kaufmann 066614a526 pythonPackages.graph-tool: fix build (#52261) 
The new version of cgal introduced in #47826 requires a patch (that will
be included in the next graph-tool version).

Fixes #50446
 2018-12-16 00:10:33 +01:00
Timo Kaufmann 79642ebd77 Merge pull request #52202 from timokau/cysignals-1.8.0 
pythonPackages.cysignals: 1.7.2 -> 1.8.0
 2018-12-15 12:57:41 +01:00
Timo Kaufmann 0cca124b04 pythonPackages.cysignals: 1.7.2 -> 1.8.0 2018-12-15 10:42:40 +01:00
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
Timo Kaufmann 2f98b1c112 spotify: 1.0.93.242.gc2341a27-15 -> 1.0.94.262.g3d5c231c-9 2018-12-04 13:33:34 +01:00
Timo Kaufmann 21de751e74 python.pkgs.pygraphviz: add graphviz path 2018-12-04 11:44:40 +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 aa053197de Merge pull request #51191 from timokau/sage-fixes 
sage: fix test timeout and downgraded R tests
 2018-11-28 23:10:32 +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 63b39af496 pythonPackages.rpy2: various fixes (#51084) 
- make sure libreadline is found at runtime
- make sure python libraries are found at runtime
- add libraries necessary to pass the testsuite and standard libraries
 2018-11-27 18:24:37 +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