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Author SHA1 Message Date
markuskowa 126e1f8fd0
Merge pull request #58538 from bzizou/stacks 
stacks: init at 2.3e
 2019-04-03 14:41:00 +02:00
Bruno Bzeznik e7899d2a00 stacks: init at 2.3e 2019-04-03 14:01:32 +02:00
R. RyanTM 882247fc3f quantum-espresso: 6.3 -> 6.4 
Semi-automatic update generated by
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based on information from
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 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
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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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 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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 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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 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 
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 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
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 2019-03-21 17:54:31 -07:00
R. RyanTM 6c14a2f3f8 eagle: 9.1.2 -> 9.3.1 
Semi-automatic update generated by
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 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
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 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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 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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 2019-03-03 20:49:36 +01:00
R. RyanTM 9989b7c8c4 igv: 2.4.17 -> 2.4.19 
Semi-automatic update generated by
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 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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 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 
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 2019-03-01 16:58:38 -08:00
R. RyanTM e869b87dbb clp: 1.16.11 -> 1.17.0 
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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 
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 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