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Author SHA1 Message Date
Austin Seipp b0fea1dc9c
verilog: 2018.12.15 -> 2019.03.27, parallel build 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-04-22 14:27:45 -05:00
Austin Seipp fe8eb566b5
symbiyosys: 2019.03.28 -> 2019.04.18 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-04-22 14:27:45 -05:00
Daniel Schaefer bac4d95aa2 treewide: Change URLs to HTTPS 
Lots of URLs were HTTP redirect to HTTPS. Changed those and checked them
if there's actual content. Inspired by
https://github.com/NixOS/nixpkgs/issues/60004
 2019-04-22 10:19:54 +02:00
Timo Kaufmann 512097dece
Merge pull request #59921 from timokau/gap-update 
gap: 4.10.0 -> 4.10.1
 2019-04-20 13:17:04 +02:00
R. RyanTM 0dc3184871 picard-tools: 2.18.27 -> 2.19.0 (#59634) 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-04-20 13:15:40 +02:00
Timo Kaufmann 9c7f774a39 gap: mark as broken on darwin 
Has been failing to build for a while.
 2019-04-20 12:36:11 +02:00
Timo Kaufmann af6739fdd7 gap: 4.10.0 -> 4.10.1 2019-04-20 09:54:27 +02:00
Aaron Andersen 77dbfa3a55
Merge pull request #53803 from jfrankenau/init-groove 
groove: init at 5.7.4
 2019-04-19 20:27:18 -04:00
Aaron Andersen 11cf1a282d
Merge pull request #58377 from bzizou/exonerate 
exonerate: init at 2.4.0
 2019-04-19 13:25:49 -04:00
Mario Rodas f84a7b3828
Merge pull request #59834 from luispedro/add_prodigal 
Prodigal: init at 2.6.3
 2019-04-19 09:50:03 -05:00
Bruno Bzeznik 6a8c9bff8f exonerate: init at 2.4.0 2019-04-19 14:58:57 +02:00
Bruno Bzeznik 90b4796c60 sumatools: init at 1.0.34 2019-04-19 14:43:40 +02:00
Johannes Frankenau e7f021ca93 groove: init at 5.7.4 2019-04-19 13:34:30 +02:00
Luis Pedro Coelho 3fc55eec05 Prodigal: init at 2.6.3 2019-04-19 08:38:14 +02:00
Timo Kaufmann 49b8efcb84 sage: 8.6 -> 8.7 
https://groups.google.com/forum/#!topic/sage-release/3m8PV9JkFro
 2019-04-17 22:44:32 +02:00
Timo Kaufmann e0e5445667 sage: fix another transient sig_on bug 
Caused a test failure on hydra, backporting upstream fix.
 2019-04-17 19:58:07 +02:00
R. RyanTM d11731130d star: 2.7.0c -> 2.7.0f 
Semi-automatic update generated by
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 2019-04-16 18:30:49 +02:00
Michael Raskin 3d3a415f24 petrinizer: init at 0.9.1.1 2019-04-16 15:11:03 +02:00
Austin Seipp bb27856a5c
Merge pull request #59522 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.99 -> 3.3.100
 2019-04-16 02:12:25 -05:00
Matthew Bauer f475aeaf29
Merge pull request #59535 from matthewbauer/homepage-fixes 
treewide: update homepages to https where available
 2019-04-15 20:47:30 -04:00
Matthew Bauer 290a5d916e treewide: update homepages to https where available 
Based on "problems" from repology:

https://repology.org/repository/nix_unstable/problems

Mostly simple changes to reflect redirects.
 2019-04-15 10:10:05 -04:00
R. RyanTM c906798997 jmol: 14.29.32 -> 14.29.36 (#59546) 
Semi-automatic update generated by
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 2019-04-15 12:02:41 +02:00
Austin Seipp a5add1e623
symbiyosys: 2018.12.09 -> 2019.03.28 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-04-15 00:17:54 -05:00
Luis Pedro Coelho 13a1f2c296 eggnog-mapper: init at 1.0.3 (#58905) 2019-04-14 17:22:47 -07:00
R. RyanTM 8a4ad20ed0 gtkwave: 3.3.99 -> 3.3.100 
Semi-automatic update generated by
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 2019-04-14 14:47:32 -07:00
R. RyanTM 00d17e36ea gmsh: 4.2.2 -> 4.2.3 
Semi-automatic update generated by
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based on information from
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 2019-04-14 13:15:32 -07:00
Timo Kaufmann 62c288ec20
python.pkgs.sympy: 1.3 -> 1.4 (#59482) 2019-04-14 17:52:03 +02:00
Michael Raskin 796050fedd openmvs: mark as broken 2019-04-14 17:45:21 +02:00
R. RyanTM c3a9b4e1fd eagle: 9.3.1 -> 9.3.2 
Semi-automatic update generated by
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 2019-04-14 07:47:26 -07:00
markuskowa 87f595a1f0
Merge pull request #56615 from r-ryantm/auto-update/clp 
clp: 1.16.11 -> 1.17.0
 2019-04-14 12:05:32 +02:00
Markus Kowalewski 19dfffff3c
clp: restrict to x86_64-linux + darwin 2019-04-14 00:17:25 +02:00
Markus Kowalewski e879991e1b
clp: 1.17.0 -> 1.17.11 2019-04-14 00:04:06 +02:00
Joe Hermaszewski 0e2d27f5af fped: init at 2017-05-11 2019-04-13 13:36:46 +08:00
Julien Dehos a13f5d0da1 mxnet: fix cuda support enabled build (#48781) 2019-04-12 10:31:22 +00:00
Frederik Rietdijk 993e2b4ec2
Merge pull request #59098 from NixOS/staging-next 
Staging next
 2019-04-11 18:23:14 +02:00
Frederik Rietdijk 230c67f43b Merge master into staging-next 2019-04-11 07:50:23 +02:00
Dmitry Kalinkin c321b64b3f
snakemake: 5.2.2 -> 5.4.4 2019-04-10 14:18:26 -04:00
xeji cc118b4426
Merge pull request #58676 from smaret/gildas-update 
gildas: update to 20190401_a
 2019-04-10 14:30:50 +02:00
Frederik Rietdijk d108b49168 Merge master into staging-next 2019-04-09 16:38:35 +02:00
Vladimír Čunát f7ddff5c6d
R: fix regression from commit cbade453 #58989 
Normally the directory is created in fixup phase.
 2019-04-07 17:38:45 +02:00
Frederik Rietdijk 7f7da0a16f Merge master into staging-next 2019-04-07 15:14:52 +02:00
rhokue cbade453ac R: explicitly declare which as a run-time dependency 
Fixes https://github.com/NixOS/nixpkgs/issues/58963.
Closes https://github.com/NixOS/nixpkgs/pull/58989.
 2019-04-07 11:12:43 +02:00
Frederik Rietdijk 4a125f6b20 Merge master into staging-next 2019-04-07 08:33:41 +02:00
Timo Kaufmann ceede33ddf
python.pkgs.cypari2: 2.0.3 -> 2.1.0 (#59085) 2019-04-06 21:46:13 +00:00
Pascal Wittmann cfb6ade58c
Merge pull request #58931 from bzizou/migrate 
migrate: init at 3.7.2
 2019-04-06 14:23:50 +02:00
Vincent Laporte 50a03f8632 hol_light: 2018-09-30 -> 2019-03-27 2019-04-06 11:03:29 +02:00
Timo Kaufmann 6662fbc822
Merge pull request #58961 from timokau/nauty-features 
nauty: disable cpu feature detection
 2019-04-05 13:12:05 +00:00
Jan Tojnar cb1a20499a
Merge branch 'master' into staging 2019-04-05 11:37:15 +02:00
Bruno Bzeznik 0b03f44c2f migrate: init at 3.7.2 2019-04-05 09:01:36 +02:00
Timo Kaufmann 7f22a42976 nauty: disable cpu feature detection 2019-04-04 14:54:55 +02:00
Timo Kaufmann 15045e6233 nauty: add timokau as a maintainer 
I'm interested in this package as a sage dependency.
 2019-04-04 14:54:31 +02:00
Timo Kaufmann 5880c449dd nauty: small refactoring 2019-04-04 14:54:05 +02:00
R. RyanTM 9f68f2a7dc verilator: 4.010 -> 4.012 
Semi-automatic update generated by
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 2019-04-03 13:43:11 -05:00
markuskowa e2ce5fd7fe
Merge pull request #58860 from r-ryantm/auto-update/quantum-espresso 
quantum-espresso: 6.3 -> 6.4
 2019-04-03 15:42:40 +02:00
Markus Kowalewski c109aaa5cb
quantum-espresso: remove outdated makefile fix 2019-04-03 15:00:17 +02:00
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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 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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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
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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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based on information from
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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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based on information from
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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
Bruno Bzeznik 6858d0fd62 clustal-omega: init at 1.2.4 2019-03-26 15:45:59 +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
Dmitry Kalinkin 9ba406ff1c
kicad: replace with3DPackages option with an override 2019-03-24 01:37:47 -04:00
Dmitry Kalinkin d0fc807347
kicad: make module list overridable 
This moves module definition into passthru. Otherwise building kicad
would still require all modules to be built first even if they are not
used.

Also this drops preferLocalBuild from packages3d. hydraPlatforms should
do what we need to. preferLocalBuild would addtitionaly disable remote
builders, which is probably not what we want.
 2019-03-24 01:37:46 -04:00
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
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based on information from
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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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based on information from
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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
Thibaut Marty 2f5439a950 kicad: fix #49089 by adding libraries files 
This splits the KiCad package in several derivations:
- original package (main KiCad package)
- internationalization package
- templates
- schematic symbols libraries
- PCB footprints libraries
- 3D models libraries

From these derivations, 2 packages are exposed in top level:
- `kicad` (main KiCad package + all libraries except 3D models)
- `kicad-with-3dpackages` (kicad + all libraries)

The 3D models can also be installed separately with `kicad.packages3d`.
This prevents a new compilation of KiCad, but the user must set the
`KISYS3DMOD` environment variable or option accordingly.
 2019-03-14 21:07:38 +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
https://github.com/ryantm/nixpkgs-update tools. This update was made
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
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
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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 
Semi-automatic update generated by
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 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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 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
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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
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
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based on information from
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 2019-02-05 20:33:46 -08:00
R. RyanTM da628f0cbd igv: 2.4.16 -> 2.4.17 
Semi-automatic update generated by
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based on information from
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 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
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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
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based on information from
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 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
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based on information from
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 2019-01-28 20:01:47 +00:00
R. RyanTM 2b03ef0521 gmsh: 4.1.0 -> 4.1.3 
Semi-automatic update generated by
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based on information from
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 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
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 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
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based on information from
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 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
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
R. RyanTM b2a7ef628a picard-tools: 2.18.21 -> 2.18.23 
Semi-automatic update generated by
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based on information from
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 2019-01-16 21:43:19 -08:00
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
rnhmjoj bcf54ce5bb
treewide: use ${stdenv.shell} instead of /bin/sh where possible 2019-01-16 20:37:15 +01:00
Gabriel Ebner 49db581e8c elan: 0.7.1 -> 0.7.2 2019-01-15 10:05:45 +01:00
Brenton Horne 6be5e679b1 marvin: init at 19.1.0 
Also adding myself (fusion809) as a maintainer.
The marvin Nix file in this commit is largely thanks to @msteen.
 2019-01-15 00:23:38 +10:00
Johannes Frankenau bebf305c1b gurobi: 8.0.1 -> 8.1 (#53884) 2019-01-13 23:22:55 +01:00
R. RyanTM 26b492b207 minimap2: 2.10 -> 2.14 (#52845) 
Semi-automatic update generated by
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 2019-01-13 22:34:45 +01:00
Vladimír Čunát bde8efe792
Merge branch 'master' into staging-next 
A couple thousand rebuilds have accumulated on master.
 2019-01-12 12:19:34 +01:00
Dmitry Kalinkin 73625f2522 root5: mark as broken on Linux 2019-01-11 20:45:37 -05:00
Dmitry Kalinkin 0c9335fb1c root, root5: fix build on darwin 2019-01-11 20:45:37 -05:00
tbenst d34f2b9b96 bftools: init at 5.9.2 (#53769) 2019-01-10 18:28:28 -05:00
markuskowa b70a4b2b98
Merge pull request #53478 from bgamari/bump-ngspice 
ngspice: 29 -> 30
 2019-01-10 20:17:54 +01:00
Vladimír Čunát 287144e342
Merge branch 'master' into staging-next 2019-01-10 13:07:21 +01:00
Austin Seipp c10650760d yices: s/fetchurl/fetchFromGitHub/ 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-01-08 19:15:24 -06:00
Austin Seipp 38aa0a3df4 z3: 4.8.3 -> 4.8.4 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-01-08 19:15:24 -06:00