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2073 commits

Author SHA1 Message Date
Chris Ostrouchov
a2bc529f22
siesta: init at 4.0.2 2018-09-14 15:40:25 -04:00
Chris Ostrouchov
2c7295ebe0
quantum-espresso: init at 6.3 2018-09-14 15:40:14 -04:00
Maximilian Bosch
2cfc0bb7ee tamarin-prover: fix ghc 8.4 build (#46597) 
See https://hydra.nixos.org/build/81125645

`tamarin-prover' upstream has a patch to fix GHC 8.4 compilation (and
uses stack lts-12.1 now), but it's not released yet:

a08f6e4007

The build is divided in several derivations, therefore the patch had to
be splitted and rebased for `lib/term', `lib/theory' and `lib/utils' to
ensure that the patch applies properly during the `patchPhase'.

Addresses #45960
 2018-09-13 14:11:09 +02:00
Markus J. Ankenbrand
e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
R. RyanTM
e94947af0a gromacs: 2018.2 -> 2018.3 (#46275) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
gromacs
 2018-09-12 23:07:27 +02:00
R. RyanTM
c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
star
 2018-09-12 22:49:12 +02:00
Matthew Bauer
40d19d8e7c
Merge pull request #45102 from jbedo/hisat2 
hisat2: init 2.1.0
 2018-09-10 15:11:58 -05:00
Matthew Bauer
05d379f3cf
Merge pull request #46211 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.11 -> 2.18.12
 2018-09-10 14:58:59 -05:00
Silvan Mosberger
10a412f251
almonds: update license 2018-09-09 02:04:34 +02:00
Markus Kowalewski
70e254d6bd
root: add license 2018-09-08 14:51:28 +02:00
Markus Kowalewski
1cff2dd135
pynac: add license 2018-09-08 14:48:19 +02:00
Markus Kowalewski
258c202565
prooftree: add license 2018-09-08 14:44:43 +02:00
Markus Kowalewski
2ed07fdb2b
drgeo: add license + homepage 2018-09-08 14:42:12 +02:00
Timo Kaufmann
db784d883c sage: re-add pkg-config aliases 
Those were removed because they were added to openblas itself. There was
an error with that however and it will take some time until the fix
makes its way through staging. For the time being, reverting this part
of 26d5d030fe will fix the sage build.
This commit should be reverted once
408eacbc89 is in master.
 2018-09-07 21:55:41 +02:00
Timo Kaufmann
7521f2863d sage: fix numpy and scipy integration 2018-09-07 18:36:52 +02:00
Timo Kaufmann
759e495881
Merge pull request #46268 from r-ryantm/auto-update/jmol 
jmol: 14.29.17 -> 14.29.19
 2018-09-07 11:32:26 +02:00
R. RyanTM
baf51804f0 jmol: 14.29.17 -> 14.29.19 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
jmol
 2018-09-06 19:54:40 -07:00
R. RyanTM
f72cba212c picard-tools: 2.18.11 -> 2.18.12 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
 2018-09-06 14:22:26 -07:00
Profpatsch
3e45b61a99 lib/trivial: add a few examples of usage of assertMsg/assertOneOf 2018-09-06 18:14:27 +02:00
Sebastien Maret
5b58c6ac76 gildas: add alternative url for the source code (#46145) 
For each new release, the upstream developers of Gildas move the
source code of the previous release to a different directory. Add this
directory to the list of url to avoid build failure at each new
release.
 2018-09-06 15:10:21 +01:00
Renato Garcia
318c9296fa snakemake: add maintainers (#46117) 2018-09-05 21:46:17 +02:00
xeji
bf2a90298a
Merge pull request #46053 from danieldk/mxnet-fixes 
pythonPackages.mxnet: fix build
 2018-09-05 16:07:56 +02:00
Sebastien Maret
b76cf0b54c gildas: ignore clang warnings for unused command line arguments 
See #46044
 2018-09-05 12:17:05 +02:00
Daniël de Kok
590ce7d1ae mxnet: fix library dependencies. 
- mxnet now builds the open source MKL DNN library. However, this
  was not included with the build.
- mxnet builds its own OpenMP library, even when OpenMP is provided
  by the system. This leads to problems, so remove the included
  OpenMP implementation:

  https://github.com/apache/incubator-mxnet/pull/12160
 2018-09-04 20:27:25 +02:00
Sebastien Maret
3bc898035d gildas: fix makefile rule 2018-09-04 16:05:44 +02:00
Daniël de Kok
93a5947158 mxnet: 1.1.0 -> 1.2.1 (#46026) 
Update and fix the build:

- Perl is a build-time requirement.
- Fix hardcoded /bin/bash invocation.
 2018-09-04 11:37:54 +02:00
Ryan Mulligan
7b54a50e97
Merge pull request #45730 from Helkafen/snakemake 
snakemake: init at 5.2.2
 2018-09-02 07:54:13 -07:00
xeji
a3434cf4e5
Merge pull request #45921 from markuskowa/homepages 
Cleanup homepage links
 2018-09-02 08:39:30 +02:00
Markus Kowalewski
ee54f1f817
plm: remove dead homepage link, mark as broken 2018-09-02 01:46:25 +02:00
Markus Kowalewski
5cf25dded7
symmetrica: update homepage 2018-09-02 01:46:25 +02:00
Markus Kowalewski
c184150a22
jags: update homepage + fix license 2018-09-02 01:46:18 +02:00
Markus Kowalewski
e5974ddaec
jonprl: update homepage 2018-09-02 00:36:01 +02:00
Vladimír Čunát
342d3db703
Merge branch 'staging-next' 
The failure diff seems good-enough on Hydra now.
 2018-09-01 17:02:15 +02:00
Sebastian Meric de Bellefon
93ce77af40 python.pkgs.snakemake: init at 5.2.2 2018-09-01 09:18:19 -04:00
Gabriel Ebner
da3326902a vampire: fix nondeterministic hash 
Probably related to #8567
 2018-09-01 15:03:31 +02:00
R. RyanTM
7fdaf76869 verilator: 3.924 -> 3.926 (#45797) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
verilator
 2018-09-01 12:14:00 +02:00
Robert Schütz
93550cbddf Merge branch 'master' into staging-next 2018-08-31 17:32:48 +02:00
John Ericson
2c2f1e37d4 reewide: Purge all uses stdenv.system and top-level system 
It is deprecated and will be removed after 18.09.
 2018-08-30 17:20:32 -04:00
Frederik Rietdijk
6038628ea5 Merge master into staging-next 2018-08-29 20:54:55 +02:00
R. RyanTM
e301589013 gmsh: 3.0.6 -> 4.0.0 (#45592) 
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.
 2018-08-27 16:06:28 +02:00
Frederik Rietdijk
7945295410 Merge master into staging 2018-08-27 08:21:50 +02:00
Timo Kaufmann
c614c15f93
Merge pull request #45257 from timokau/openblas-pc 
openblas: add pkg-config aliases
 2018-08-26 20:13:19 +02:00
Timo Kaufmann
0e4160a3a1 pythonPackages.sympy: 1.1.1 -> 1.2 2018-08-26 19:56:44 +02:00
Frederik Rietdijk
c71942eb7e
Merge pull request #44752 from costrouc/costrouc/lammps-update 
material science packages (init and update): lammps, python - ase, pymatgen-lammps, lammps-cython, dftfit
 2018-08-25 19:03:36 +02:00
wucke13
b7e695461e apmplanner2: fixed wrong path in .desktop file 
The `apmplanner2.desktop` file defaults to `/usr/share/...` regardless which out
prefix is given to make. So I chose to fix it manually.
 2018-08-25 00:39:58 +02:00
Vladimír Čunát
7db611f2af
Merge branch 'staging' 
Includes libX11 security update.
 2018-08-24 09:19:43 +02:00
Bignaux Ronan
70d5f16898 astrolabe-generator: init at 3.3 (#45429) 2018-08-23 22:35:05 +02:00
Joachim F
0d80f9659c
Merge pull request #45305 from wucke13/apmplanner2 
apmplanner2: init at 2.0.26
 2018-08-23 14:07:45 +00:00
Matthew Bauer
f7bc33abf0 Revert "treewide: fixup breakage due to absolute compiler path" 
This reverts commit d0888d1503.
 2018-08-22 01:14:53 +02:00
xeji
6216f5da04
Merge pull request #45263 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.1 -> 2.3.4.2
 2018-08-21 19:51:36 +02:00