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340 Commits

Author SHA1 Message Date
R. Ryantm
5ba5ff1a84 cytoscape: 3.8.2 -> 3.9.0 2021-10-29 09:08:26 +00:00
Dmitry Kalinkin
49d19b7945
snakemake: 6.7.0 -> 6.10.0 2021-10-24 17:49:14 -04:00
Vladimir Korolev
72d4a1f13d openmodelica: v1.17.0 -> v1.18.0, add balodja to openmodelica maintainers 2021-10-02 12:39:57 +03:00
Robert Schütz
98c8fc6fd0 gplates: 2.2.0 -> 2.3.0 2021-09-26 23:11:29 -07:00
Dmitry Kalinkin
84f408f206
Merge pull request #136016 from veprbl/pr/root_6_24_04 
root: 6.24.02 -> 6.24.06
 2021-09-15 11:35:07 -04:00
Dmitry Kalinkin
0ec2acf51f
root: build with -Dimt=ON 2021-09-03 12:41:16 -04:00
Dmitry Kalinkin
95b2d74bc5
root: re-enable unvendored LLVM 2021-09-03 12:41:16 -04:00
Dmitry Kalinkin
aedfb59c87
root: 6.24.02 -> 6.24.06 2021-09-03 12:41:04 -04:00
Dmitry Kalinkin
0a312a356c
root5: fix for gcc10 2021-09-01 07:14:56 -04:00
Dmitry Kalinkin
b8c5c06aab
snakemake: 6.6.1 -> 6.7.0 2021-08-28 02:18:38 -04:00
Dmitry Kalinkin
e51edc1e64
Merge pull request #130903 from veprbl/pr/cwltool 
cwltool: init at 3.1.20210628163208
 2021-08-08 11:15:33 -04:00
Ben Siraphob
0f34985134
Merge pull request #122828 from balodja/openmodelica 2021-07-25 09:24:25 +07:00
Vladimir Korolev
5c8561f11a openmodelica: 1.9.3 -> 1.17.0 with lots of changes 
Co-authored-by: Jaakko Luttinen <jaakko.luttinen@iki.fi>

Most of changes are:
* separate packages for different openmodelica components,
* qt4 -> qt5,
* patches to instruct the OMEdit wrapper with stdenv executables
  location,
* adoption of #89731 and #109595,
* openblas -> blas, lapack according to #83888,
* parallel building,
* getting rid of spurious build phases,
* correct the license,
* cross-compilation,
* forcing compiler to clang++ according to OM build recommendations,
* drop of pangox_compat according to #75909 and #76412,
* better dependencies, and more.
 2021-07-24 20:29:26 +03:00
Dmitry Kalinkin
3f24366cda
cwltool: init at 3.1.20210628163208 2021-07-21 22:11:17 -04:00
Sandro
d06f7e07a6
Merge pull request #130925 from SuperSandro2000/python-aliases 2021-07-22 03:21:11 +02:00
Sandro Jäckel
b4099137b1
pythonPackages: deprecate ConfigArgParse alias 2021-07-21 13:32:54 +02:00
Sandro
aee461ddb4
toil: update homepage 2021-07-21 13:28:37 +02:00
Dmitry Kalinkin
866fe59150
toil: init at 5.4.0 2021-07-20 22:18:08 -04:00
Dmitry Kalinkin
3a79b1fece
snakemake: 6.5.3 -> 6.6.1 2021-07-19 16:22:36 -04:00
Dmitry Kalinkin
a93f2af20b
snakemake: add missing optional dependenices 
These are needed to generate reports
 2021-07-19 16:19:27 -04:00
Millian Poquet
c6f34aeaef simgrid: compile tests in parallel 2021-07-19 14:05:17 +02:00
Millian Poquet
c4ec6ffb78 simgrid: fix paths in smpicc/smpicxx 2021-07-19 14:04:57 +02:00
Millian Poquet
33f915f241 simgrid: propagate boost 
Since SimGrid include files directly include boost files,
most SimGrid users need boost as well.
 2021-07-19 14:03:50 +02:00
Millian Poquet
2d05c2d535 simgrid: 3.27 -> 3.28 2021-07-19 14:01:30 +02:00
Felix Buehler
82cb33a0ae treewide: remove meta.version 2021-07-18 00:07:38 +02:00
Dmitry Kalinkin
1cbb9c64d1
root,root5: apply nixpkgs-fmt 2021-07-14 16:23:09 -04:00
Dmitry Kalinkin
62ab958fb0
root: 6.24.00 -> 6.24.02 2021-07-14 14:58:15 -04:00
Dmitry Kalinkin
45bed6d99f
snakemake: 6.5.0 -> 6.5.3 2021-07-11 10:40:09 -04:00
Andrew Childs
55dcd99859 root: use pure CoreSymbolication on Darwin 
The current build works by linking against CoreSymbolication in
/System/Library/PrivateFrameworks. This is impure and doesn't work in
newer versions of macOS.

See https://github.com/NixOS/nixpkgs/issues/128576
 2021-06-29 11:00:05 +09:00
Dmitry Kalinkin
e3678ae8a6
snakemake: 6.0.5 -> 6.5.0 2021-06-24 11:36:26 -04:00
Sandro
47480918a5
Merge pull request #125802 from yipengsun/root-6-24-00 2021-06-09 15:42:05 +02:00
Yipeng Sun
ffced8d681 root: 6.22.08 -> 6.24.00 
We switched to the bundled llvm-clang combo because to use the llvm
provided in nixpkgs, clang also needs to be patched and built
externally, which is too much trouble.
 2021-06-09 14:06:13 +02:00
Sandro
c037394f5f
Merge pull request #117606 from bgamari/graphia 2021-06-05 16:31:10 +02:00
Ben Gamari
dcfaa98677 graphia: init at 2.2 
Graphia is a relatively new tool for graph visualisation and analysis,
in the same vain as gephi.
 2021-06-02 09:07:32 -04:00
Sandro Jäckel
d6ff646b3f pythonPackages.smart_open: rename to smart-open 2021-05-22 15:02:50 -07:00
Stéphan Kochen
7e9451ffb3
rink: fix darwin build (#123501) 2021-05-18 10:34:25 -04:00
Jonathan Ringer
1d85caaa26 root: fix build 2021-05-08 01:29:18 -07:00
V
5a835e6e92 rink: 0.6.0 -> 0.6.1 2021-05-01 10:46:51 +02:00
Fabian Affolter
e4149e6e0b
rink: specify license 2021-04-11 23:18:32 +02:00
R. RyanTM
12518ff683 rink: 0.5.1 -> 0.6.0 2021-04-11 14:49:45 +00:00
Dmitry Kalinkin
1d93243467
root: 6.22.06 -> 6.22.08 2021-04-06 02:41:06 -04:00
Sandro Jäckel
3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Millian Poquet
99a5de6ebc simgrid: 3.26 -> 3.27 2021-03-29 21:20:27 +02:00
Dmitry Kalinkin
8887f4655e
snakemake: 5.28.0 -> 6.0.5 2021-03-26 18:32:26 -04:00
Ben Siraphob
e03c068af5 treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
Sandro Jäckel
6ad10c3bcd
treewide: Remove doBuild cause it does not exist 2021-02-02 14:46:06 +01:00
Pavol Rusnak
a6ce00c50c
treewide: remove stdenv where not needed 2021-01-25 18:31:47 +01:00
Jonathan Ringer
9bb3fccb5b treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 
continuation of #109595

pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.

python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
 2021-01-19 01:16:25 -08:00
Ben Siraphob
badf51221d treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
Profpatsch
4a7f99d55d treewide: with stdenv.lib; in meta -> with lib; 
Part of: https://github.com/NixOS/nixpkgs/issues/108938

meta = with stdenv.lib;

is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.

This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.

The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
 2021-01-11 10:38:22 +01:00