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2623 Commits

Author SHA1 Message Date
R. RyanTM
882247fc3f quantum-espresso: 6.3 -> 6.4 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/quantum-espresso/versions
 2019-04-02 15:30:36 -07:00
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
Sébastien Maret
806a3fa2e6
gildas: 20190301_b -> 20190401_a 2019-04-02 09:04:39 +02:00
R. RyanTM
5f4e5553bc jmol: 14.29.31 -> 14.29.32 (#58698) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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 2019-04-01 20:12:53 +00:00
John Ericson
4ccb74011f Merge commit '18aa59b0f26fc707e7313f8467e67159e61600c2' from master into staging 
There was one conflict in the NixOS manual; I checked that it still
built after resolving it.
 2019-04-01 00:40:03 -04:00
markuskowa
c637aeff19
Merge pull request #58541 from luispedro/add_megahit 
megahit: init at 1.1.4
 2019-03-31 12:51:59 +02:00
Luis Pedro Coelho
bf48451959 megahit: init at 1.1.4 
This is widely used in bioinformatics for assembling genomes &
metagenomes
 2019-03-31 05:56:14 +02:00
Dmitry Kalinkin
ea757ac59f
Merge pull request #58108 from veprbl/pr/root5_fix 
root5: fix build
 2019-03-30 22:36:23 -04:00
R. RyanTM
893abe12e8 bowtie2: 2.3.4.3 -> 2.3.5 (#58014) 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/bowtie2/versions
 2019-03-31 00:37:38 +01:00
Silvan Mosberger
aadb1cbe26
Merge pull request #58494 from markuskowa/upd-octopus 
octopus: 8.3 -> 8.4
 2019-03-29 20:43:28 +01:00
markuskowa
7701fd7603
Merge pull request #58097 from r-ryantm/auto-update/ginac 
ginac: 1.7.4 -> 1.7.5
 2019-03-29 20:27:39 +01:00
Silvan Mosberger
030b845413
Merge pull request #58492 from markuskowa/upd-molden 
molden: 5.9.3 -> 5.9.5
 2019-03-29 20:16:08 +01:00
geistesk
5e6273df68 stellarium: 0.18.3 -> 0.19.0 2019-03-28 21:21:54 +01:00
markuskowa
403aa2dfed
Merge pull request #58180 from luzpaz/gmsh4.2.2 
gmsh 4.2.1->4.2.2
 2019-03-28 18:11:58 +01:00
Markus Kowalewski
3c19324e2a
octopus: 8.3 -> 8.4 2019-03-28 18:00:41 +01:00
Markus Kowalewski
6ea9c0243b
molden: 5.9.3 -> 5.9.5 2019-03-28 17:39:15 +01:00
R. RyanTM
2ce544a8b1 minimap2: 2.15 -> 2.16 (#57319) 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/minimap2/versions
 2019-03-27 23:25:52 +01:00
R. RyanTM
1b73fd1954 paml: 4.9h -> 4.9i (#57354) 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/paml/versions
 2019-03-27 15:44:21 +01:00
Bruno Bzeznik
00431493c0 itsx: init at 1.1.1 2019-03-26 15:52:35 +01:00
Joachim F
c9cd1356ea
Merge pull request #56522 from bzizou/messer-slim 
messer-slim: init at 3.2.1
 2019-03-26 00:42:58 +00:00
Gabriel Ebner
4446452347
Merge pull request #58163 from dtzWill/update/qalculate-3 
libqalculate,qalculate-gtk: 2.9.0 -> 3.0.0
 2019-03-23 18:50:24 +01:00
luz.paz
13158c692c gmsh 4.2.1->4.2.2 2019-03-23 12:51:12 -04:00
markuskowa
b10799905c
Merge pull request #58162 from r-ryantm/auto-update/gromacs 
gromacs: 2019 -> 2019.1
 2019-03-23 12:29:48 +01:00
Frederik Rietdijk
23e431387b Merge staging-next into staging 2019-03-23 09:20:09 +01:00
Will Dietz
24484b216a qalculate-gtk: 2.9.0 -> 3.0.0 
http://qalculate.github.io/news.html
 2019-03-23 01:09:17 -05:00
R. RyanTM
c70807aa13 gromacs: 2019 -> 2019.1 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/gromacs/versions
 2019-03-22 22:05:26 -07:00
Gabriel Ebner
11318d1ba2 elan: 0.7.4 -> 0.7.5 2019-03-22 11:16:44 +01:00
Jörg Thalheim
70d6db9097
Merge pull request #58065 from r-ryantm/auto-update/eagle 
eagle: 9.1.2 -> 9.3.1
 2019-03-22 07:22:58 +00:00
Wael M. Nasreddine
5af0780492
Merge remote-tracking branch 'origin/master' into staging 
* origin/master: (693 commits)
  buildGoModule: use go_1_12 instead of go_1_11 (#58103)
  gitAndTools.lab: 0.15.2 -> 0.15.3 (#58091)
  signal-desktop: 1.22.0 -> 1.23.0
  added missing semicolon to documentation
  terminus_font_ttf: 4.46.0 -> 4.47.0
  buildGoModule: remove SSL env vars in favor of cacert in buildInputs (#58071)
  dav1d: init at 0.2.1
  dropbox-cli: 2018.11.28 -> 2019.02.14
  atlassian-confluence: 6.14.1 -> 6.14.2
  maintainers: update email for dywedir
  python.pkgs.hglib: use patch to specify hg path (#57926)
  chkrootkit: 0.52 -> 0.53
  radare2-cutter: 1.7.2 -> 1.8.0
  autorandr: 1.7 -> 1.8
  pythonPackages.pyhepmc: fix build
  llvm-polly/clang-polly: use latest llvm
  apulse: 0.1.11.1 -> 0.1.12, cleanup
  factorio: experimental 0.17.14 → 0.17.16 (#58000)
  sequeler: 0.6.7 -> 0.6.8
  nasc: 0.5.1 -> 0.5.2
  ...
 2019-03-21 21:01:25 -07:00
R. RyanTM
34cba0b001 ginac: 1.7.4 -> 1.7.5 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
 2019-03-21 17:54:31 -07:00
R. RyanTM
6c14a2f3f8 eagle: 9.1.2 -> 9.3.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eagle/versions
 2019-03-21 10:40:06 -07:00
worldofpeace
0353967957 nasc: 0.5.1 -> 0.5.2 
Main improvment is that libqalculatenasc.so is now properly linked

Changelog: https://github.com/parnold-x/nasc/compare/0.5.1...0.5.2
 2019-03-20 23:10:33 -04:00
Gabriel Ebner
52c3ee6c4d elan: 0.7.2 -> 0.7.4 2019-03-20 13:33:24 +01:00
Dmitry Kalinkin
c36f841ec7
root5: fix build 2019-03-20 00:26:13 -04:00
Timo Kaufmann
5fc5881221
sage: backport bugfix (#57794) 2019-03-17 14:36:01 +00:00
Timo Kaufmann
8fc3c033cb
pynac: 0.7.23 -> 0.7.24 (#57791) 
Apparently some python3 related fixes: https://trac.sagemath.org/ticket/27241

Also switch to using pname.
 2019-03-17 14:35:28 +00:00
Stephen
a14a7d958f labelimg: fix build (#57714) 
for #56826 see https://hydra.nixos.org/build/90477186/nixlog/2
 2019-03-15 20:50:03 +01:00
Dmitry Kalinkin
d5f97ae600
Merge pull request #57650 from stephengroat/patch-4 
apmplanner2: fix build
 2019-03-14 15:28:57 -04:00
Alex Branham
1e354a7e40 R: 3.5.2 -> 3.5.3 
Closes https://github.com/NixOS/nixpkgs/pull/57400.
 2019-03-14 19:50:37 +01:00
Stephen
08e4d7cf69 apmplanner2: fix build 
see ArduPilot/apm_planner#1166
 2019-03-14 11:23:20 -07:00
Gabriel Ebner
be261a1ede isabelle: refactor 
Fixes #33337
 2019-03-14 11:48:30 +01:00
Gabriel Ebner
308456a7a7
Merge pull request #57567 from gebner/isabelle-2018 
isabelle: 2017 -> 2018
 2019-03-14 11:25:02 +01:00
Gabriel Ebner
c7f43de43c isabelle: 2017 -> 2018 2019-03-12 14:32:48 +01:00
Sébastien Maret
6f81adb7ee
gildas: 20190301_a -> 20190301_b 2019-03-11 21:43:41 +01:00
Matthew Bauer
37eba81c7b
Merge pull request #56391 from matthewbauer/cmake-treewide 
Add more CMake flags
 2019-03-11 12:43:46 -04:00
Matthew Bauer
6ed49262f5 treewide: remove BUILD_TESTING flag 
This is now set by CMake
 2019-03-11 10:11:28 -04:00
worldofpeace
988ed26778
Merge pull request #57363 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.25 -> 2.18.27
 2019-03-11 07:13:20 -04:00
R. RyanTM
70815de29c picard-tools: 2.18.25 -> 2.18.27 
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
 2019-03-11 03:37:34 -07:00
Peter Hoeg
136126ceae
Merge pull request #56498 from ariutta/patch-1 
cytoscape: bump 3.6.1 -> 3.7.1
 2019-03-11 11:20:50 +08:00
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
3b7fb15182
Merge pull request #57126 from timokau/sage-maxima-downgrade 
sage: downgrade maxima to 5.41
 2019-03-09 20:05:01 +00:00
Timo Kaufmann
23908a0ee3 sage: downgrade maxima to 5.41 
See discussion at
82254747af.
 2019-03-09 17:23:57 +01:00
Silvan Mosberger
8ca1c925c6
sad: Fix build 2019-03-09 01:07:18 +01:00
luz.paz
77cb537712 gmsh: 4.1.5 -> 4.2.1 2019-03-08 05:24:15 -05:00
Timo Kaufmann
e2b287b32a maxima: remove ecl known-failures patch 
It doesn't apply anymore since the recent update. Since the testsuite is
completely disabled now, there is little point in rebasing it.
 2019-03-07 16:08:10 +01:00
Ryan Mulligan
5896677b47
Merge pull request #56956 from smaret/gildas 
gildas: 20190201_b -> 20190301_a
 2019-03-06 19:28:41 -08:00
Sébastien Maret
880d0ac9f0
gildas: 20190201_b -> 20190301_a 2019-03-06 13:56:17 +01:00
Jörg Thalheim
9b57d852af
Merge pull request #56905 from timokau/pari-fix 
pari: fix off-by-one error
 2019-03-06 11:00:07 +00:00
Jan Tojnar
d3ff902e94
webkit: move to aliases 2019-03-06 00:20:55 +01:00
Timo Kaufmann
a648b8c714 pari: fix off-by-one error 
Done by applying upstream patch. Will be included in the next release.

Upstream: https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2117
 2019-03-05 21:50:44 +01:00
Timo Kaufmann
00fa98f012 pari: add timokau as maintainer 
I'm mostly interested in this package because it is a dependency of
sage. I'd like to be notified on changes (which ofBorg will do when I'm
listed as a maintainer).
 2019-03-05 20:23:04 +01:00
Timo Kaufmann
5a23cb575e pari: slight refactoring 
Use pname, one line per argument.
 2019-03-05 20:21:26 +01:00
Peter Simons
1c6a193b3e wxmaxima: update to version 19.03.0 2019-03-05 12:53:05 +01:00
Peter Simons
82254747af maxima: update to version 5.42.2 2019-03-05 12:53:04 +01:00
Dmitry Kalinkin
aa4f5cc4a3
simgrid: Fix the upstream project URL 
Closes: #56849
 2019-03-04 16:42:46 -05:00
R. RyanTM
27e05d81a5 star: 2.7.0a -> 2.7.0c 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/star/versions
 2019-03-03 20:55:25 +01:00
R. RyanTM
6a987f5730 form: 4.2.0 -> 4.2.1 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/form/versions
 2019-03-03 20:49:36 +01:00
R. RyanTM
9989b7c8c4 igv: 2.4.17 -> 2.4.19 
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
 2019-03-03 20:48:52 +01:00
Timo Kaufmann
37182b20a6
Merge pull request #56781 from timokau/sage-python-upgrade-fixes 
Sage python upgrade fixes
 2019-03-03 20:48:10 +01:00
R. RyanTM
2d20e8c5f2 gtkwave: 3.3.98 -> 3.3.99 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/gtkwave/versions
 2019-03-03 17:13:47 +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
R. RyanTM
4f1c44906c cryptominisat: 5.6.6 -> 5.6.8 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/cryptominisat/versions
 2019-03-01 16:58:38 -08:00
R. RyanTM
e869b87dbb clp: 1.16.11 -> 1.17.0 
Semi-automatic update generated by
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based on information from
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 2019-03-01 16:08:32 -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