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5679 Commits

Author SHA1 Message Date
Sandro
b7ec0afb59
Merge pull request #162205 from Stunkymonkey/treewide-vVersion 2022-02-28 14:26:16 +01:00
Felix Buehler
1573dbdcd0 treewide: fix versions starting with 'v' 2022-02-28 13:05:18 +01:00
Felix Buehler
fe7678ca81 raxml-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
Felix Buehler
13dca33cdc neuron-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
Bobby Rong
f35d1b8568
Merge pull request #160332 from florentc/tlaps 
tlaps: 1.4.3 -> 1.4.5
 2022-02-28 16:33:42 +08:00
Guillaume Girol
b9ecdae495
Merge pull request #161344 from ulrikstrid/ulrikstrid/tree-wide-native-inputs 
ocamlPackages tree-wide: Move buildInputs that should be nativeBuildInputs
 2022-02-27 19:49:07 +00:00
7c6f434c
da576d8a4a
Merge pull request #161876 from FRidh/sage-python 
Sage: make it possible to extend the Python runtime environment with additional packages
 2022-02-27 19:02:59 +00:00
Vincent Laporte
68e4b639a3
Merge pull request #161111 from ulrikstrid/ulrikstrid/coq-move-dune-to-native 
coq: Move dune, ocaml and findlib to nativeBuildInputs
 2022-02-26 08:54:53 +01:00
R. Ryantm
21a1125f37 gmsh: 4.9.4 -> 4.9.5 2022-02-25 14:21:11 -08:00
K900
cb2cfba6f7 treewide: switch all desktop file generators to new API 
Notably:
- remove explicit arguments that match the defaults
- convert everything to the right Nix types
 2022-02-25 13:40:38 -08:00
Frederik Rietdijk
330d9344d2 sage: make it possible not to rebuild sage-tests 
Requiring sage-tests as build input just so it gets build is a bit
unfortunatey but understandable. This commit introduces an option to not
add sage-tests as a dependency. This is preferred in case e.g. Python
packages are added to the environment.
 2022-02-25 21:27:14 +01:00
Frederik Rietdijk
7442533bf1 sage: support adding extra Python packages to environment 
mysage = sage.override { extraPythonPackages = ps: with ps; [ dask ]; };

Note that the sage-tests are executed again as well, which is not very nice.
 2022-02-25 21:18:23 +01:00
R. Ryantm
1e7c64aae1 bcftools: 1.14 -> 1.15 2022-02-25 11:12:05 -08:00
markuskowa
49186d631f
Merge pull request #161635 from r-ryantm/auto-update/jmol 
jmol: 14.32.21 -> 14.32.24
 2022-02-25 13:42:31 +01:00
Ulrik Strid
7e20e9039e coqPackages: tree-wide move packages to nativeBuildInputs and add strictDeps = true 
Co-authored-by: Vincent Laporte <vbgl@users.noreply.github.com>
 2022-02-25 07:54:17 +01:00
Vincent Laporte
056c34167d why3: 1.4.0 → 1.4.1 2022-02-25 06:00:09 +01:00
Justin Bedő
6b477d556d
Merge pull request #161695 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.26.10 -> 2.26.11
 2022-02-25 08:27:23 +11:00
R. Ryantm
d6a24fc108 cwltool: 3.1.20220217222804 -> 3.1.20220221074232 2022-02-24 15:52:49 -05:00
R. Ryantm
ce9d28cc49 picard-tools: 2.26.10 -> 2.26.11 2022-02-24 17:34:18 +00:00
Ulrik Strid
48df7cdbba coq: Move dune to nativeBuildInputs and add ocaml, findlib and menhir 2022-02-24 14:39:45 +01:00
Ulrik Strid
a13cdfe520 ocamlPackages tree-wide: Move buildInputs that should be nativeBuildInputs 
To keep this for the future we also strictDeps where possible, including for janePackages, topkg, oasis and ocamlbuild.
This makes some closures significantly smaller and makes cross compilation easier
 2022-02-24 14:39:27 +01:00
R. Ryantm
1b8518cadd jmol: 14.32.21 -> 14.32.24 2022-02-24 08:42:12 +00:00
Renaud
65ecaa9903
Merge pull request #150078 from r-ryantm/auto-update/gurobi 
gurobi: 9.1.2 -> 9.5.0
 2022-02-23 22:08:43 +01:00
Markus Kowalewski
469ae42107
gromacs: 2021.5 -> 2022 2022-02-23 14:47:26 +01:00
Renaud
a723c88d4e
Merge pull request #159967 from r-ryantm/auto-update/workcraft 
workcraft: 3.3.5 -> 3.3.6
 2022-02-23 13:30:39 +01:00
Renaud
359d63179e
Merge pull request #160360 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 3.22.0 -> 4.0.0
 2022-02-23 08:30:49 +01:00
Bobby Rong
93883402a4
Merge pull request #160594 from Cogitri/bada-bib 
bada-bib: 0.4.1 -> 0.5.1
 2022-02-22 12:10:40 +08:00
Wanja Zaeske
2d67cc2bf6 removing maintainer wucke13 from some packages 2022-02-21 22:58:18 +01:00
ajs124
55bf481a21
Merge pull request #159212 from helsinki-systems/init/febio-studio 
febio-studio: init at 1.6.1
 2022-02-21 17:24:33 +01:00
Scriptkiddi
4e60a4823b febio-studio: init at 1.6.1 2022-02-21 16:43:36 +01:00
Rasmus Thomsen
87c1d9f92c
bada-bib: 0.4.1 -> 0.5.1 2022-02-21 16:33:50 +01:00
R. Ryantm
c35aa0a0f3 cwltool: 3.1.20220217190813 -> 3.1.20220217222804 2022-02-21 01:31:33 -05:00
markuskowa
48ab0d0233
Merge pull request #160924 from qbg/submit/mathematica-13.0.1 
mathematica: 13.0.0 -> 13.0.1
 2022-02-20 10:23:22 +01:00
R. RyanTM
286ecff9e0
getdp: 3.3.0 -> 3.4.0 
(#150127)
 2022-02-19 22:41:33 +01:00
Mario Rodas
94723d21f9
Merge pull request #159540 from r-ryantm/auto-update/marvin 
marvin: 21.20.0 -> 22.3.0
 2022-02-19 15:59:08 -05:00
qbg
f4f52d9d70 mathematica: 13.0.0 -> 13.0.1 
https://wolfram.com/mathematica/quick-revision-history.html#v130
 2022-02-19 11:26:53 -06:00
Millian Poquet
bc2604732e simgrid: mark as broken on darwin 2022-02-19 10:05:17 +01:00
Millian Poquet
3f804f68bc simgrid: 3.28 -> 3.30 + python + clean 
- use latest SimGrid release
- enable the python binding (in new output "python")
- reviews from PR 141040 have been applied
 2022-02-19 10:05:12 +01:00
Ulrik Strid
4150bf02b5 coq: allow static linking by moving wrapGAppsHook to nativeBuildInputs 
Co-authored-by: Vincent Laporte <vbgl@users.noreply.github.com>
 2022-02-18 15:17:04 +01:00
Mario Rodas
947c98310c
Merge pull request #160545 from collares/lean-3.39.2 
lean: 3.39.1 -> 3.39.2
 2022-02-18 06:26:51 -05:00
R. Ryantm
b715fcd9d9 cwltool: 3.1.20220210171524 -> 3.1.20220217190813 2022-02-18 00:36:37 -05:00
Mauricio Collares
0c36a9cc35 lean: 3.39.1 -> 3.39.2 2022-02-17 23:42:05 -03:00
R. RyanTM
94f61e4c82
SPAdes: 3.15.3 -> 3.15.4 
(#158938)
 2022-02-18 00:55:34 +01:00
R. RyanTM
ac1c96ecec
colmap: 3.6 -> 3.7 
* colmap: 3.6 -> 3.7 (#159198)

* colmap: license is BSD-3-Clause

Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>
 2022-02-18 00:29:14 +01:00
Ben Wolsieffer
1382f006a9
qgroundcontrol: 4.1.4 -> 4.2.0 
* qgroundcontrol: 4.1.4 -> 4.2.0 (#159291)

QGroundControl now tries to download a prebuilt x86_64 .deb package for
the Airmap SDK, so we have to disable this feature. Previously, it was
disabled by default. I guess they were trying to make things easier for
users, but it seems pretty half-baked.

* qgroundcontrol: update homepage

The domain seems to have changed from .org to .com.
 2022-02-18 00:09:39 +01:00
Daniel Wheeler
4befe7a89f
snakemake: 6.10.0 -> 6.15.5 (#159026) 
Fetch from GitHub rather than PyPI so tests are included.
 2022-02-17 18:06:23 -05:00
ajs124
80160499bc
Merge pull request #160340 from helsinki-systems/tetgen 
tetgen: also install library and headers
 2022-02-17 01:57:18 +01:00
Scriptkiddi
c8fb08b1e4 tetgen: also install library and headers 2022-02-17 01:37:28 +01:00
R. Ryantm
581628a7f4 qalculate-gtk: 3.22.0 -> 4.0.0 2022-02-16 19:33:07 +00:00
Florent C
762faa21a2 tlaps: 1.4.3 -> 1.4.5 
This updates tlaps to the most recent stable version and fixes the
template for the url from which the sources are fetched. Previously, the
tarball was fetched from the "current" remote directory from which old
versions are eventually removed. The package was therefore broken.
It also adds myself (florentc) as a maintainer.
 2022-02-16 15:19:51 +01:00