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Author SHA1 Message Date
Timo Kaufmann e39e304638 Merge pull request #78496 from r-ryantm/auto-update/brial 
brial: 1.2.6 -> 1.2.7
 2020-01-26 23:28:02 +01:00
Timo Kaufmann 7db53cc312 Merge pull request #78348 from timokau/pygments-lexer-fix 
python2.pkgs.ipython, python2.pkgs.sphinx: use proper python2 lexer
 2020-01-23 16:10:21 +01:00
Timo Kaufmann 0811a69fef python2.pkgs.sphinx: user proper python2 lexer 2020-01-23 09:40:26 +01:00
Timo Kaufmann 66675b5650 python2.pkgs.ipython: use the proper python2 lexer 
Since pygments 2.5 `PythonLexer` refers to python3 [1]. We have to be
explicit if we want to use python2.

[1] https://pygments.org/docs/changelog/
 2020-01-23 09:40:14 +01:00
Timo Kaufmann d62e410ccd Merge pull request #78222 from r-ryantm/auto-update/m4ri 
m4ri: 20140914 -> 20200115
 2020-01-22 17:43:44 +01:00
Timo Kaufmann d05843e841 Merge pull request #78302 from r-ryantm/auto-update/python2.7-jupytext 
python27Packages.jupytext: 1.3.1 -> 1.3.2
 2020-01-22 17:41:51 +01:00
Timo Kaufmann e8531b8ed4 Merge pull request #78220 from r-ryantm/auto-update/m4rie 
m4rie: 20150908 -> 20200115
 2020-01-22 09:57:07 +01:00
Timo Kaufmann 79f86d75d4 Merge pull request #78176 from r-ryantm/auto-update/fplll 
fplll: 5.3.1 -> 5.3.2
 2020-01-21 17:39:41 +01:00
Timo Kaufmann e8def5b1e0 Merge pull request #77130 from timokau/home-manager-2020-01-04 
home-manager: 2019-11-17 -> 2020-01-04
 2020-01-07 10:49:16 +01:00
Timo Kaufmann 5e9a3f4e4d home-manager: 2019-11-17 -> 2020-01-04 2020-01-06 21:24:32 +01:00
Timo Kaufmann bdbec90304 Merge pull request #76945 from prusnak/tensorflow-drop-bin2c-path 
python.pkgs.tensorflow: fix build with cudatoolkit 10.2
 2020-01-06 17:12:34 +01:00
Timo Kaufmann 2e216c3917 Merge pull request #76975 from timokau/ntl-11.4.3 
ntl: 11.4.2 -> 11.4.3
 2020-01-05 13:53:42 +01:00
Timo Kaufmann 58edcdc6ba ntl: 11.4.2 -> 11.4.3 
Upstream[1]:

> I uploaded NTL 11.4.3 to https://www.shoup.net/ntl/
> This fixes an embarrassing build problem in 11.4.2.

[1] https://groups.google.com/forum/#!topic/sage-devel/V5zHWIpRIJo
 2020-01-05 11:07:38 +01:00
Timo Kaufmann 552b38ed74 Merge pull request #76829 from timokau/gf2x-1.3.0 
ntl: 11.4.1 -> 11.4.2, gf2x: 1.2 -> 1.3.0
 2020-01-03 00:46:18 +01:00
Timo Kaufmann 45e3be9eca gf2x: 1.2 -> 1.3.0 
Switch source to fetchgit since it removes the requirements to manually
find the correct link for each version.

More information at
https://github.com/NixOS/nixpkgs/pull/45299
 2020-01-02 17:24:11 +01:00
Timo Kaufmann d41ff9b59f ntl: 11.4.1 -> 11.4.2 
Needed for gf2x 1.3.0 compatibility. Upstream says:

> I just uploaded NTL 11.4.2 to http://www.shoup.net/ntl

> This fixes a few small, obscure bugs, including one that  prevents using
> the gf2x-1.3 library.

At https://groups.google.com/d/msgid/sage-devel/992c77f6-ebf9-4049-8900-c45c6b89f4ed%40googlegroups.com
 2020-01-02 17:05:19 +01:00
Timo Kaufmann 98e6a8b579 Merge pull request #76531 from timokau/sympy-1.5 
python.pkgs.sympy: 1.4 -> 1.5
 2019-12-26 13:12:21 +01:00
Timo Kaufmann 8ac53ed0b1 python.pkgs.sympy: 1.4 -> 1.5 
Sage needs some doctest changes. The patch was included upstream.
Modelled after https://trac.sagemath.org/ticket/28911.
 2019-12-26 11:46:42 +01:00
Timo Kaufmann ef666d86fc Merge pull request #76187 from timokau/vimPlugins-2019-12-22 
vimPlugins: update
 2019-12-22 22:05:25 +01:00
Timo Kaufmann dfbe05d6c0 vimPlugins: update 2019-12-22 21:40:02 +01:00
Timo Kaufmann 53501c67c2 Merge pull request #76181 from timokau/fplll-5.3.1 
fplll: 5.3.0 -> 5.3.1
 2019-12-22 21:22:35 +01:00
Timo Kaufmann c8f49feafc Merge pull request #76176 from timokau/fpylll-aarch64-fix 
python.pkgs.fpylll: 0.5.0dev -> 0.5.1dev, fix tests on aarch64
 2019-12-22 19:46:29 +01:00
Timo Kaufmann 75fa016247 fplll: 5.3.0 -> 5.3.1 
Includes a patch we previously needed to apply.
 2019-12-22 18:20:36 +01:00
Timo Kaufmann 80b0639857 python.pkgs.fpylll: fix tests on aarch64 2019-12-22 17:05:21 +01:00
Timo Kaufmann c0871b5c48 python.pkgs.fpylll: 0.5.0dev -> 0.5.1dev 2019-12-22 16:46:14 +01:00
Timo Kaufmann b747a86f8f newsboat: fetch from vcs 
In hopes of working around
https://github.com/NixOS/nixpkgs/issues/60845. This fetches a gz archive
instead of xz and also fetches the archive from a different source,
hopefully avoiding the issue (whatever ist is caused by).

In addition to that, I think that building directly from VCS is
generally cleaner and more flexible for the following reasons:

- It cuts out and unnecessary middle step.

- It makes sure the version users install is equal to the version users
may have vetted.

- It makes it easy to develop patches or bisect changes by simply
checking out a different rev.

- It avoids using upstream-provided "binary" artifacts like those
generated by autotools.
 2019-12-22 16:31:10 +01:00
Timo Kaufmann db59e94059 Merge pull request #75801 from timokau/ecl-libffi-abi 
ecl: fix build with libffi 3.3
 2019-12-17 00:10:04 +01:00
Timo Kaufmann 00c3761322 ecl: fix build with libffi 3.3 
The build was broken by the recent libffi update
(53a04a2df0) because of this upstream
change:

https://github.com/libffi/libffi/commit/ef76205647bca77796882d31f6ab5e889f461f07

I have changed the usage of FFI_SYSV as gentoo suggests:

https://wiki.gentoo.org/wiki/Libffi_3.3_porting_notes/FFI_SYSV

I'm not entirely sure if that is the right call here, but I haven't
noticed any regressions in my testing and its definitely better than a
broken build.

Upstream: https://gitlab.com/embeddable-common-lisp/ecl/issues/302
 2019-12-16 23:02:26 +01:00
Timo Kaufmann ce013bb430 Merge pull request #75613 from timokau/brial-1.2.6 
brial: 1.2.5 -> 1.2.6, pybrial: use brial src
 2019-12-13 21:47:50 +01:00
Timo Kaufmann 135081a538 brial: 1.2.5 -> 1.2.6 
Motivation is mostly https://github.com/BRiAl/BRiAl/pull/37, which is a
pre-requiste for getting the sage tests to pass with python3.
 2019-12-13 20:31:31 +01:00
Timo Kaufmann 6a800927bb pybrial: 1.2.3 -> 1.2.5, directly use the brial src 
The pybrial package is a bit awkward. It doesn't have its own top-level
attribute, since it has a cyclic dependency with sage. That's one of the
reasons why it rarely gets updated. Its distributed along with brial, so
its best to keep the versions synchronized. The easiest way to do this
is to just re-use the source of brial.
 2019-12-13 20:29:16 +01:00
Timo Kaufmann 0dcd09b1b6 python.pkgs.fpylll: add changelog 2019-12-12 17:50:13 +01:00
Timo Kaufmann da7ca3fa87 fplll: 5.2.1 -> 5.3.0, python.pkgs.fpylll: 0.4.1dev -> 0.5.0dev 
The two packages need to be updated together, since fpylll 0.4.1
requires the old fplll version and fpylll 0.5.0 requires the new one.
 2019-12-12 17:50:13 +01:00
Timo Kaufmann d69b099f28 fplll: add timokau to the maintainers list 2019-12-12 17:50:13 +01:00
Timo Kaufmann cf0419e7d5 fplll: add changelog 2019-12-12 17:50:08 +01:00
Timo Kaufmann 0fa66219cc fplll: clean up dependencies 
autoreconfHook implies autotools.
 2019-12-11 10:32:46 +01:00
Timo Kaufmann ed8d53655f fplll: update formatting 
According to my perception of the current community standards.
 2019-12-11 10:32:32 +01:00
Timo Kaufmann 07266e20b5 Merge pull request #74767 from mkg20001/pkg/twinkle 
twinkle: init at 1.10.2
 2019-12-07 17:39:09 +01:00
Timo Kaufmann 3b16021adf Merge pull request #75148 from timokau/vimPlugins-2019-12-07 
vimPlugins: update
 2019-12-07 17:35:32 +01:00
Timo Kaufmann 85d10c9b48 vimPlugins: update 2019-12-07 12:03:16 +01:00
Timo Kaufmann cc6cf0a96a Merge pull request #74371 from bbigras/lego 
lego: 3.0.2 -> 3.2.0
 2019-12-05 09:39:52 +01:00
Timo Kaufmann 5c9000014e Merge pull request #74945 from timokau/sage-no-timeout 
sage: disable test timeout
 2019-12-04 09:55:34 +01:00
Timo Kaufmann f2393197d4 Merge pull request #74869 from timokau/cython-update-revert 
Revert "python.pkgs.Cython: 0.29.14 -> 0.29.15"
 2019-12-03 14:21:03 +01:00
Timo Kaufmann 12b167eeab Revert "python.pkgs.Cython: 0.29.14 -> 0.29.15" 
This reverts commit fa4bbefdfead8f76dbf2d1a890026fb15977c0bf.

The update seems to be no longer available. See
https://github.com/NixOS/nixpkgs/pull/74388#issuecomment-560490284.
 2019-12-03 00:37:13 +01:00
Timo Kaufmann 47f4ddf1ac python.pkgs.Cython: 0.29.14 -> 0.29.15 2019-12-01 18:54:38 +01:00
Timo Kaufmann a2407280d7 python.pkgs.Cython: backport fix for non-int hashes 
https://github.com/cython/cython/issues/2752 has already been accepted
upstream, is minimally invasive (only adds a feature, shouldn't break
any existing code) and is needed for the sage python3 update. Sage needs
this capability because it defines its own integer type.
 2019-12-01 18:54:38 +01:00
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 28cb34d538 Merge pull request #74537 from timokau/rpy2-3.2.2 
python3.pkgs.rpy2: 2.9.5 -> 3.2.2
 2019-12-01 00:38:43 +01:00
Timo Kaufmann ef43cd3d42 python3.pkgs.rpy2: 2.9.5 -> 3.2.2 
There have been significant changes, therefore it doesn't make sense
anymore to maintain the python2 and python3 version in the same file.
We'll be able to drop the python2 version soon, some time after we have
switched sage to python3.
 2019-12-01 00:07:12 +01:00
Timo Kaufmann 50b8b05368 Merge pull request #74185 from r-ryantm/auto-update/tridactyl-native 
tridactyl-native: 1.17.0 -> 1.17.1
 2019-11-26 00:24:00 +01:00
Timo Kaufmann 51751e1ac4 Merge pull request #73040 from marius851000/gnash 
gnash: fix compilation with libgif 5.2
 2019-11-21 22:37:12 +01:00
Timo Kaufmann 8c757f4dc9 vimPlugins: backoff on timeout in update.py 
Updating vim-plugins recently started timing out regularly for me. It
may have to do with an ISP switch on my side, but I don't think that
should cause timeouts. I guess I'm probably not the only one
experiencing this, so in this comment I introduce exponential backoff.
Every request will be retried up to 3 times (3 seconds, 6 seconds, 12
seconds delay).
 2019-11-19 21:10:32 +01:00
Timo Kaufmann 61c60bad22 vimPlugins: fix formatting and typing in update.py 2019-11-19 21:10:13 +01:00
Timo Kaufmann d17a25d190 Merge pull request #73448 from cw789/elixir_update 
elixir_1_9: 1.9.2 -> 1.9.4
 2019-11-18 21:30:10 +01:00
Timo Kaufmann c0a56ee711 Merge pull request #73611 from timokau/home-manager-2019-11-17 
home-manager: 2019-10-29 -> 2019-11-17
 2019-11-18 09:05:39 +01:00
Timo Kaufmann bee1fa9a20 home-manager: 2019-10-29 -> 2019-11-17 
The lorri module was recently added.
 2019-11-18 08:32:55 +01:00
Timo Kaufmann b41e2cf0c4 Merge pull request #73498 from timokau/vimPlugins-2019-11-16 
vimPlugins: update
 2019-11-16 15:23:56 +01:00
Timo Kaufmann 1defbf45cf vimPlugins: update 2019-11-16 14:17:52 +01:00
Timo Kaufmann 0ae46ca265 Merge pull request #71282 from timokau/tensorflow-1.15.0 
python.pkgs.tensorflow: 1.14.0 -> 1.15.0
 2019-11-13 17:11:31 +01:00
Timo Kaufmann 8e382a7ca7 python.pkgs.tensorflow: mark as broken for python2 2019-11-13 16:18:04 +01:00
Timo Kaufmann e4378d4641 python.pkgs.tensorflow: add more sanity checks 2019-11-13 16:18:01 +01:00
Timo Kaufmann 6832f1da6a python.pkgs.tensorflow: add functools32 dependency 
Now needed at runtime with the python2 build.
 2019-11-13 15:25:19 +01:00
Timo Kaufmann 4fb7831cb4 python.pkgs.tensorflow: fix build with newer gast 2019-11-12 23:43:10 +01:00
Timo Kaufmann 1fbd307880 python.pkgs.tensorflow: fix build with bazel 1.0 
The tensorflow build was broken by the bazel 1.0 update in
73eb01bde000c34b54764f6f2b9fd1d89a54ccfa.
 2019-11-12 23:43:07 +01:00
Timo Kaufmann 152d2fd22c python.pkgs.{tensorflow,tensorflow-estimator,tensorflow-tensorboard}: 1.14.0 -> 1.15.0 2019-11-12 23:42:47 +01:00
Timo Kaufmann c54848ee77 Merge pull request #72771 from timokau/sage-fixes 
sage: fix tests
 2019-11-06 16:21:51 +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 b5ac99fe00 Revert "python: notebook: 5.7.8 -> 6.0.1" 
This reverts commit ad53cf0a82.

I think this commit must have been by mistake. It updates the version of
notebook that was supposed to pin to an old, py2 compatible version.
 2019-11-02 12:11:12 +01:00
Timo Kaufmann bf946a808d Revert "pythonPackages.ipython: remove python2 frozen package" 
This reverts commit 0ccf10b955.

I think it was premature to drop the support a couple of weeks before
the official deadline. At least sage still depends on it.
 2019-11-02 12:11:12 +01:00
Timo Kaufmann f7c1e8f274 Merge pull request #72328 from timokau/sage-ignore-cmp-deprecation 
sage: ignore attrs deprecation warning
 2019-10-30 23:14:07 +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 fe625dcf76 Merge pull request #72031 from timokau/vimPlugins-2019-10-26 
vimPlugins: update
 2019-10-26 18:56:54 +02:00
Timo Kaufmann 162e1c5350 vimPlugins: update 2019-10-26 17:43:18 +02:00
Timo Kaufmann 43165b29e2 Merge pull request #71894 from timokau/home-manager-2019-10-23 
home-manager: 2019-09-20 -> 2019-10-23
 2019-10-26 12:05:58 +02:00
Timo Kaufmann 6fe7974a6c home-manager: 2019-09-20 -> 2019-10-23 2019-10-24 10:10:05 +02:00
Timo Kaufmann 1e00a97577 Merge pull request #71819 from timokau/vimPlugins-2019-10-23 
vimPlugins: update
 2019-10-23 17:36:13 +02:00
Timo Kaufmann 92e1b2142c vimPlugins: update 2019-10-23 16:28:31 +02:00
Timo Kaufmann a2aeec6c35 Merge pull request #71792 from FRidh/twisted 
python.pkgs.twisted: move twisted cache generation to postFixup
 2019-10-23 15:15:09 +02:00
Timo Kaufmann ed145e8f22 Merge pull request #71694 from r-ryantm/auto-update/nauty 
nauty: 26r11 -> 26r12
 2019-10-22 23:33:48 +02:00
Timo Kaufmann 79ee6d8284 Merge pull request #71026 from expipiplus1/joe-vim-plugs 
vimPlugins: add 10 plugins and update
 2019-10-12 15:33:26 +02:00
Timo Kaufmann 7a7e9c1b27 Merge pull request #64193 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
Timo Kaufmann b7e700b7ee Merge pull request #69803 from timokau/vimPlugins-2019-09-28 
vimPlugins: update
 2019-09-28 10:49:15 +00:00
Timo Kaufmann 10b241bfaa Merge pull request #69756 from r-ryantm/auto-update/python3.7-annoy 
python37Packages.annoy: 1.15.2 -> 1.16.0
 2019-09-28 09:32:00 +00:00
Timo Kaufmann 9c3452cbc3 vimPlugins: update 2019-09-28 11:13:13 +02:00
Timo Kaufmann 96466a57a9 Merge pull request #69690 from r-ryantm/auto-update/ntl 
ntl: 11.3.2 -> 11.3.4
 2019-09-28 08:24:44 +00:00
Timo Kaufmann 7cc78d4485 Merge pull request #67696 from eadwu/bcachefs/update-7 
bcachefs/update-7
 2019-09-28 08:22:24 +00:00
Timo Kaufmann 6cf6a22a9f Merge pull request #69412 from timokau/fflas-ffpack-avx 
fflas-ffpack: disable all avx versions by default
 2019-09-27 10:20:35 +00:00
Timo Kaufmann 6181a20ab2 Merge pull request #69609 from r-ryantm/auto-update/jmol 
jmol: 14.29.49 -> 14.29.53
 2019-09-27 09:22:11 +00:00
Timo Kaufmann 4a863fa567 Merge pull request #69519 from r-ryantm/auto-update/eclib 
eclib: 20190226 -> 20190909
 2019-09-26 17:27:41 +00:00
Timo Kaufmann 1366266a11 Merge pull request #69409 from timokau/home-manager-2019-09-20 
home-manager: 2019-09-04 -> 2019-09-20
 2019-09-25 12:24:38 +00:00
Timo Kaufmann 030d44f693 fflas-ffpack_1: remove 
No longer used in nixpkgs, so we can clean it up.
 2019-09-25 11:38:33 +02:00
Timo Kaufmann cc625cfba4 fflas-ffpack: add timokau as a maintainer 
I'm interested in this package as a dependency of sage and therefore
would like ofBorg to notify me on changes.
 2019-09-25 11:29:19 +02:00
Timo Kaufmann 47bdb5f2ee fflas-ffpack: disable all avx versions by default 
To fix a transient failure on hydra. See
https://github.com/linbox-team/fflas-ffpack/issues/284 for more details.
 2019-09-25 11:22:38 +02:00
Timo Kaufmann d7d54ac28a home-manager: 2019-09-04 -> 2019-09-20 2019-09-25 10:56:53 +02:00
Timo Kaufmann 78741fc409 sage: 8.9.rc0 -> 8.9.rc1 2019-09-25 10:19:04 +02:00