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2551 Commits

Author SHA1 Message Date
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
R. RyanTM
4f1c44906c cryptominisat: 5.6.6 -> 5.6.8 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/cryptominisat/versions
 2019-03-01 16:58:38 -08:00
Frederik Rietdijk
2fcb11a244 Merge staging-next into master 2019-03-01 09:06:20 +01:00
Bruno Bzeznik
598f11862c messer-slim: init at 3.2.1 2019-02-28 15:11:18 +01:00
Anders Riutta
c792fd107b
cytoscape: bump 3.6.1 -> 3.7.1 
Needed to update URL, because `wget "http://chianti.ucsd.edu/cytoscape-3.7.1/cytoscape-3.7.1.tar.gz"` returns `404`.
 2019-02-27 16:40:50 -08:00
John Ericson
8293ab8461
Merge pull request #56408 from Mic92/runtime-shell 
treewide: use runtimeShell instead of stdenv.shell whenever possible
 2019-02-26 18:04:27 -05:00
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
Merlin Göttlinger
5781856630 clprover: init at 1.0.3 (#56403) 
* clprover: init at 1.0.3
 2019-02-26 12:36:04 +00:00
Vincent Laporte
4266523c14 why3: 1.1.1 -> 1.2.0 2019-02-25 10:09:15 +01:00
Sophie Taylor
59338fb99d Fix sc2-headless map hash (#56320) 2019-02-25 01:08:12 +01:00
Vladimír Čunát
71f4ba29a3
Merge branch 'master' into staging-next 
Hydra nixpkgs: ?compare=1506218
 2019-02-22 17:51:01 +01:00
markuskowa
0b00338eb9
Merge pull request #56178 from luzpaz/gmsh-4.1.5 
gmsh: 4.1.3 -> 4.1.5
 2019-02-22 11:26:15 +01:00
Sophie Taylor
c736f9693d Added maps to sc2-headless 2019-02-22 09:01:00 +00:00
luz.paz
add7b20858 gmsh: 4.1.3 -> 4.1.5 2019-02-21 22:55:48 -05:00
Frederik Rietdijk
5871da418f Merge staging into python-unstable 2019-02-21 08:02:10 +01:00
Frederik Rietdijk
e2cd07b997 Merge staging-next into staging 2019-02-21 07:54:33 +01:00
Matthew Bauer
b1bbd94bb6 Merge remote-tracking branch 'NixOS/master' into staging 2019-02-18 20:36:48 -05:00
Ryan Mulligan
f56693f25a
Merge pull request #55052 from smaret/gildas-update 
gildas: 20190101_b -> 20190201_b
 2019-02-17 06:46:15 -08:00
Frederik Rietdijk
04f051d79f spyder: 3.2.8 -> 3.3.3 2019-02-17 14:40:54 +01:00
Frederik Rietdijk
4b2336ea28 python.pkgs.caffe: fix build, closes #8749 2019-02-17 10:13:22 +01:00
Gabriel Ebner
7cbc76a3e6 Merge branch 'auto-update/qalculate-gtk' 2019-02-16 17:25:47 +01:00
Frederik Rietdijk
fd48a94b62 Merge staging-next into staging 2019-02-16 09:30:46 +01:00
Frederik Rietdijk
6fe10d2779 Merge master into staging-next 2019-02-16 09:29:54 +01:00
R. RyanTM
ef405c5b67 qalculate-gtk: 2.8.2 -> 2.9.0 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/qalculate-gtk/versions
 2019-02-15 11:39:04 -08:00
Sébastien Maret
a69d2c2e69
gildas: 20190201_a -> 20190201_b 2019-02-15 13:27:57 +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
Samuel W. Flint
52a7c4e30e z3: Patch file to get rid of python error 
See #55591, Z3Prover/z3#2131
 2019-02-14 10:11:15 -06:00
Frederik Rietdijk
a25d48cd4f Merge master into staging 2019-02-14 11:35:50 +01:00
Jan Tojnar
606ceda352
gnome3: stop using aliases 2019-02-14 02:31:15 +01:00
Michael Bishop
ac29d96d25
Merge pull request #55629 from spacekitteh/patch-30 
Add maps to SC2
 2019-02-13 19:13:14 -04:00
Michael Raskin
8384cfe455
Merge pull request #55129 from oxij/tree/move-defaults-to-package-files 
all-packages.nix: move defaults to package files
 2019-02-13 20:04:08 +00:00
Frederik Rietdijk
7257dedd7c Merge master into staging-next 2019-02-13 12:33:29 +01:00
Sophie Taylor
744e344171
Update maps.nix 2019-02-13 08:53:32 +10:00
Sophie Taylor
ce1eb1ea79 Update and rename maps.nix to maps-replays.nix 2019-02-12 10:41:41 +00:00
Sarah Brofeldt
c0cfe9bf50
Merge pull request #54991 from FlorianFranzen/sc2-headless 
sc2-headless: 3.17 -> 4.7.1
 2019-02-12 09:42:56 +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
Florian Franzen
f470720aa8 Merge branch 'staging-next' into staging 2019-02-10 14:37:31 +01:00
Matthew Bauer
5c09d977c7 Merge remote-tracking branch 'origin/master' into staging 2019-02-09 12:14:06 -05:00
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
tbenst
1cb81a69a0 cmtk: init at 3.3.1 (#54016) 
* cmtk: init at 3.3.1
 2019-02-08 17:41:14 -05:00
Will Dietz
dcfce974d9
Merge pull request #55077 from m-labs/for-upstream 
rink: init at 0.4.4
 2019-02-07 09:47:46 -06:00
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
markuskowa
0496c08afd
Merge pull request #55298 from r-ryantm/auto-update/igv 
igv: 2.4.16 -> 2.4.17
 2019-02-06 12:50:24 +01:00
Markus Kowalewski
64e9f2ad65
jmol: remove redundant name attribute 
version and pname are alrady present
 2019-02-06 12:25:25 +01:00
R. RyanTM
a1360faba7 jmol: 14.29.29 -> 14.29.31 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/jmol/versions
 2019-02-05 20:33:46 -08:00
R. RyanTM
da628f0cbd igv: 2.4.16 -> 2.4.17 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
 2019-02-05 20:06:55 -08:00
markuskowa
9703765556 molden: 5.8.2 -> 5.9.3 (#55044) 2019-02-05 23:57:29 +02:00
markuskowa
5c7edec7a3
Merge pull request #55152 from r-ryantm/auto-update/star 
star: 2.6.1d -> 2.7.0a
 2019-02-04 22:53:49 +01:00
R. RyanTM
b015c68def verilator: 4.008 -> 4.010 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/verilator/versions
 2019-02-04 11:54:29 -06:00
R. RyanTM
e27eaf6111 star: 2.6.1d -> 2.7.0a 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
 2019-02-03 17:20:27 -08:00
Jan Malakhovski
c7675be3c1 sc2-headless: move defaults to package file 2019-02-03 15:33:29 +00:00
Vladimír Čunát
32767d139f
Merge branch 'staging-next' 
This round is without the systemd CVE,
as we don't have binaries for that yet.
BTW, I just ignore darwin binaries these days,
as I'd have to wait for weeks for them.
 2019-02-20 09:38:45 +01:00
Michael Raskin
446520bb9b
Merge pull request #56026 from oxij/tree/move-defaults-to-package-files-half-cuda 
all-packages.nix: move defaults to package files continues^2
 2019-02-19 21:54:02 +00:00
Vincent Laporte
e4035c3e0e
Merge pull request #55633 from vbgl/alt-ergo-2.3.0 
alt-ergo: 2.2.0 -> 2.3.0
 2019-02-19 09:53:57 +01:00
Frederik Rietdijk
815b77cbe6 Merge master into staging-next 2019-02-18 14:18:04 +01:00
Vladimír Čunát
f7f1a2f54e
Merge branch 'master' into staging-next 
A mass darwin rebuild from master (#55784).
 2019-02-17 08:05:24 +01:00
Vincent Laporte
e4a8af06d1
alt-ergo: 2.2.0 -> 2.3.0 2019-02-12 09:19:06 +00:00
Jan Malakhovski
4bc66b1994 cntk: move defaults to package file 2019-02-03 15:32:16 +00:00
Jan Malakhovski
31aa884b7f caffe: move defaults to package file 2019-02-03 15:32:15 +00:00
Jan Malakhovski
49148a3ea2 mxnet: move defaults to package file 2019-02-03 15:32:14 +00:00
Jan Malakhovski
88ca6dd78a cplex: move defaults to package file 2019-02-03 15:30:47 +00:00
Jan Malakhovski
ec2452dac1 scilab: move defaults to package file 2019-02-03 15:30:45 +00:00
Sebastien Bourdeauducq
3b03b901fb rink: init at 0.4.4 2019-02-03 13:29:18 +08:00
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
Sébastien Maret
cb72eec530
gildas: 20190101_b -> 20190201_a 2019-02-01 16:29:30 +01:00
Vladimír Čunát
8ba516664b
Merge branch 'staging-next' into staging 2019-02-01 09:42:53 +01:00
Florian Franzen
337babae4c sc2-headless: 3.17 -> 4.7.1 2019-01-31 15:21:58 +01:00
markuskowa
e27e114803
Merge pull request #53677 from jbedo/snpeff-4.3T 
snpeff: 4.3q -> 4.3t
 2019-01-31 10:36:32 +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
Justin Bedo
75dd587793
snpeff: 4.3q -> 4.3t 2019-01-31 15:15:05 +11:00
markuskowa
ca13dc163b
Merge pull request #49871 from wucke13/getdp 
getdp: init at 3.0.4
 2019-01-31 00:43:08 +01:00
markuskowa
a98cebbc35
Merge pull request #54828 from r-ryantm/auto-update/gmsh 
gmsh: 4.1.0 -> 4.1.3
 2019-01-29 12:39:06 +01:00
Sébastien Maret
d5f4b2b63e gildas: 20181201_a -> 20190101_b 2019-01-29 11:00:45 +00:00
R. RyanTM
2b39f17d08 minimap2: 2.14 -> 2.15 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
 2019-01-28 20:01:47 +00:00
R. RyanTM
2b03ef0521 gmsh: 4.1.0 -> 4.1.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions
 2019-01-28 10:33:36 -08:00
R. RyanTM
00cdff318a picard-tools: 2.18.23 -> 2.18.25 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-01-28 17:17:30 +00:00
wucke13
4f40b5e00e getdp: init at 3.0.4 2019-01-28 16:45:13 +01:00
Dmitry Kalinkin
b8d6cc8157
Merge pull request #54520 from veprbl/pr/sherpa_2.2.6 
sherpa: 2.2.5 -> 2.2.6
 2019-01-27 22:01:53 -05:00
Matthew Bauer
92f0f8dd68 Merge remote-tracking branch 'NixOS/master' into staging 2019-01-27 00:01:13 -05:00
Michael Raskin
cc74c0399e leo3: init at 1.2 2019-01-27 01:57:11 +01:00
Artemis Tosini
51a2a08d6e
mathematica: 11.2.0 -> 11.3.0 
Note that this only affects the English version, as I do not have access
to the hash for the Japanese version.
 2019-01-25 15:29:02 +00:00
Dmitry Kalinkin
d28bce307e
sherpa: 2.2.5 -> 2.2.6 2019-01-24 18:46:15 -05:00
worldofpeace
78da8d668b pantheon: init a 5.0 2019-01-24 20:54:14 +00:00
Vincent Laporte
b76961124d coq_8_9: 8.9+beta1 -> 8.9.0 2019-01-24 09:08:51 +00:00
Michael Raskin
ebb370f680 z3-tptp: init 
Z3 ships a TPTP-supporting wrapper as an example; allow building it
 2019-01-22 16:51:18 +01:00
Vladimír Čunát
3fe32b675e
Merge branch 'master' into staging 2019-01-22 15:59:42 +01:00
Dmitry Kalinkin
958201a98f
Merge pull request #48675 from veprbl/pr/xfitter_fix 
xfitter: runtime fixes
 2019-01-20 20:00:02 -05:00
Mario Rodas
9a18d9356d
lean: 3.4.1 -> 3.4.2 2019-01-20 06:46:37 -05:00
Austin Seipp
5069fa0a30 nixpkgs: remove sapic-0.9 
SAPIC is bundled with Tamarin and doesn't have separate releases
anymore; add an appropriate 'throw' clause to the alias so people know
where to find it.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-01-19 18:54:38 -06:00
Austin Seipp
fc159594a7 tamarin-prover: 1.4.0 -> 1.4.1, bundled sapic 
With this, we can drop the old 1.4.0 patches for 8.4 support, since
those are now upstream.

Furthermore, SAPIC Is now bundled inside Tamarin, so we can drop the
external dependency. (This includes a patch that compiles SAPIC to
native code, much like the original, to reduce closure size.)

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-01-19 18:54:38 -06:00
Dmitry Kalinkin
0f3758b5e6
Merge pull request #53839 from fusion809/marvin 
marvin: init at 19.1.0
 2019-01-19 15:50:49 -05:00
Frederik Rietdijk
d531da6f8a
Merge pull request #54094 from rnhmjoj/shell 
treewide: use ${stdenv.shell} instead of /bin/sh where possible
 2019-01-19 14:15:51 +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
markuskowa
4545aaa671
Merge pull request #54209 from r-ryantm/auto-update/gmsh 
gmsh: 4.0.7 -> 4.1.0
 2019-01-18 11:40:48 +01:00
worldofpeace
ce69fadb36
Merge pull request #54153 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.21 -> 2.18.23
 2019-01-18 01:51:04 +00:00
R. RyanTM
55ea7b1bbe gmsh: 4.0.7 -> 4.1.0 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions
 2019-01-17 12:55:54 -08:00
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