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8918 Commits

Author SHA1 Message Date
Weijia Wang
ac32817df9
Merge pull request #277227 from r-ryantm/auto-update/cvc5 
cvc5: 1.0.9 -> 1.1.0
 2024-01-03 19:34:52 +01:00
github-actions[bot]
307002948d
Merge master into staging-next 2024-01-03 18:00:57 +00:00
Weijia Wang
a9c97eaee7
Merge pull request #276101 from r-ryantm/auto-update/delly 
delly: 1.1.8 -> 1.2.6
 2024-01-03 18:29:26 +01:00
Weijia Wang
2f787a3dfe
Merge pull request #274004 from r-ryantm/auto-update/celestia 
celestia: 1.6.3 -> 1.6.4
 2024-01-03 16:30:30 +01:00
Weijia Wang
aa604af269
Merge pull request #273163 from r-ryantm/auto-update/qgroundcontrol 
qgroundcontrol: 4.2.9 -> 4.3.0
 2024-01-03 15:47:07 +01:00
Weijia Wang
b9384442f0
Merge pull request #272422 from r-ryantm/auto-update/gretl 
gretl: 2023b -> 2023c
 2024-01-03 14:40:11 +01:00
R. Ryantm
025e631d48 dataexplorer: 3.8.0 -> 3.8.3 2024-01-03 06:00:29 +00:00
Weijia Wang
eb5334c27d Merge branch 'master' into staging-next 2024-01-03 03:22:40 +01:00
Weijia Wang
ec07157196
Merge pull request #275873 from fedeinthemix/wip-xyce-7.8 
xyce: 7.7.0 -> 7.8.0
 2024-01-03 02:18:54 +01:00
Mauricio Collares
24954c2e73
Merge pull request #278257 from nevivurn/fix/sage-ecl 
sage: import 10.2.beta3 patches
 2024-01-02 13:18:11 -03:00
Yongun Seong
2c045c7890
sage: import 10.2.beta3 patches 
- fix for ecl >= 23.9.9
- fix for python >= 3.11
 2024-01-02 23:04:53 +09:00
R. Ryantm
61721a17e7 pspp: 1.6.2 -> 2.0.0 2024-01-02 06:35:29 +00:00
Sergei Trofimovich
775c761fd8 gmsh: pull gcc-13 build fix from upstream 
Without the change `gmsh` build fails in `staging-next` as:

    /build/gmsh-4.11.1-source/src/mesh/meshGFacePack.cpp:209:7: error: 'uint32_t' was not declared in this scope
      209 |   for(uint32_t j = 0; j < 6; j++) {
          |       ^~~~~~~~
    /build/gmsh-4.11.1-source/src/mesh/meshGFacePack.cpp:16:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
       15 | #include "robustPredicates.h"
      +++ |+#include <cstdint>
 2024-01-01 20:30:30 +00:00
github-actions[bot]
e61ae81f8f
Merge master into staging-next 2024-01-01 00:02:16 +00:00
R. Ryantm
e79af9e68d eigenmath: unstable-2023-12-12 -> unstable-2023-12-31 2023-12-31 20:08:50 +00:00
github-actions[bot]
65cbf5e637
Merge master into staging-next 2023-12-31 18:01:09 +00:00
Lucas Van Laer
696735c9d2 z3_4_12: 4.12.2 -> 4.12.4 2023-12-31 14:12:54 +01:00
Jan Tojnar
80020c7db4 Merge branch 'master' into staging-next 
; Conflicts:
;	pkgs/development/lua-modules/generated-packages.nix
;	pkgs/development/lua-modules/overrides.nix
 2023-12-31 02:31:32 +01:00
R. Ryantm
2aa11b0ee6 phd2: 2.6.12 -> 2.6.13 2023-12-30 07:01:45 +00:00
Mario Rodas
d22c786ac9
Merge pull request #276424 from kilianar/stellarium-23.4 
stellarium: 23.3 -> 23.4
 2023-12-29 14:13:31 -05:00
github-actions[bot]
f50aae4fb1
Merge master into staging-next 2023-12-29 18:00:57 +00:00
Bobby Rong
c198051feb
Merge pull request #277435 from trofi/picoscope.rules-fix-eval 
picoscope: fix `rules` eval
 2023-12-29 21:40:07 +08:00
github-actions[bot]
bd7fd36fe2
Merge master into staging-next 2023-12-29 00:01:57 +00:00
Sergei Trofimovich
41941e7cf3 picoscope: fix rules eval 
Without the change `picoscope.rules` failed to evaluate due to wrong
attribute path:

    $ nix build --no-link -f. picoscope.rules
    error: attribute 'writeTextDir' missing
              116|   # users.users.you.extraGroups = [ "pico" ];
              117|   passthru.rules = lib.writeTextDir "lib/udev/rules.d/95-pico.rules" ''
                 |                    ^
 2023-12-28 23:20:14 +00:00
Nick Cao
684dbecf47
Merge pull request #277028 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.453 -> 8.3.454
 2023-12-28 13:37:37 -05:00
R. Ryantm
c777f0bfa7 tulip: 5.7.2 -> 5.7.3 2023-12-28 07:46:06 +00:00
R. Ryantm
feadff003e cvc5: 1.0.9 -> 1.1.0 2023-12-28 02:05:44 +00:00
github-actions[bot]
308ac97674
Merge master into staging-next 2023-12-27 06:00:55 +00:00
Fabián Heredia Montiel
48d1e73d8b
Merge pull request #276854 from r-ryantm/auto-update/cadical 
cadical: 1.9.1 -> 1.9.3
 2023-12-26 23:29:49 -06:00
R. Ryantm
4d2e0e140d magic-vlsi: 8.3.453 -> 8.3.454 2023-12-27 03:17:28 +00:00
github-actions[bot]
d37b121146
Merge master into staging-next 2023-12-27 00:02:11 +00:00
Mario Rodas
1c0dab4a37
Merge pull request #276940 from tejing1/cleanup-lean4 
lean4: clean up colliding files
 2023-12-26 17:49:35 -05:00
Jeff Huffman
b3a184a4aa
lean4: clean up colliding files 2023-12-26 16:13:31 -05:00
Mario Rodas
126fcb5e99
Merge pull request #275586 from r-ryantm/auto-update/cvc5 
cvc5: 1.0.8 -> 1.0.9
 2023-12-26 16:02:43 -05:00
github-actions[bot]
d4086e3e8b
Merge master into staging-next 2023-12-26 12:01:11 +00:00
R. Ryantm
c4a88ae424 cadical: 1.9.1 -> 1.9.3 2023-12-26 05:17:29 +00:00
R. Ryantm
4c5759ed4a wxmaxima: 23.11.0 -> 23.12.0 2023-12-26 02:24:50 +00:00
github-actions[bot]
f6ece27ed4
Merge master into staging-next 2023-12-25 18:00:59 +00:00
Jan Tojnar
2ac16accc0 Merge branch 'master' into staging-next 
Conflicts:
	pkgs/development/python-modules/hahomematic/default.nix
 2023-12-25 16:54:44 +01:00
Doron Behar
a90c911ba6
Revert "gwyddion: mark as broken" 2023-12-25 14:19:34 +00:00
Markus Kowalewski
2058c3a373 lammps: fix homepage and license 2023-12-24 23:05:00 +01:00
Jan Tojnar
8fcbb0c6ed Merge branch 'master' into staging-next 
Conflicts:
- pkgs/development/python-modules/boto3-stubs/default.nix
- pkgs/development/python-modules/openllm-core/default.nix
  Between 0.4.22 → 0.4.34 (a82245bd3d)
  and 0.4.22 -> 0.4.41 (72c55ce6a6)
  Does not build, not pre-merge either.
 2023-12-24 14:33:18 +01:00
kilianar
ec2daea6e2 stellarium: 23.3 -> 23.4 
https://github.com/Stellarium/stellarium/releases/tag/v23.4
 2023-12-24 10:08:44 +01:00
Fabián Heredia Montiel
8f080df5b7
Merge pull request #276231 from r-ryantm/auto-update/samtools 
samtools: 1.18 -> 1.19
 2023-12-24 01:50:02 -06:00
Martin Weinelt
a3e53d17b6 Merge remote-tracking branch 'origin/master' into staging-next 2023-12-24 02:39:15 +01:00
Nick Cao
c66be39e13
Merge pull request #276240 from r-ryantm/auto-update/seqkit 
seqkit: 2.6.0 -> 2.6.1
 2023-12-23 10:53:39 -05:00
Nick Cao
e5e39db8d3
Merge pull request #276190 from r-ryantm/auto-update/qtrvsim 
qtrvsim: 0.9.5 -> 0.9.6
 2023-12-23 10:47:30 -05:00
Andreas Rammhold
d7821df52c
Merge pull request #275710 from andir/xflr5-fetchsvn 
xflr5: use fetchsvn instead of fetchzip
 2023-12-23 13:43:36 +01:00
R. Ryantm
02ddd820f8 seqkit: 2.6.0 -> 2.6.1 2023-12-23 08:17:11 +00:00
R. Ryantm
d4211ea181 samtools: 1.18 -> 1.19 2023-12-23 06:46:26 +00:00
github-actions[bot]
4690ffb5b2
Merge master into staging-next 2023-12-23 06:00:57 +00:00
R. Ryantm
541e9020e9 qtrvsim: 0.9.5 -> 0.9.6 2023-12-23 03:21:44 +00:00
R. Ryantm
eb84f26482 delly: 1.1.8 -> 1.2.6 2023-12-22 18:36:25 +00:00
R. Ryantm
5098005a85 lean4: 4.3.0 -> 4.4.0 2023-12-22 06:12:02 +00:00
Dmitry Kalinkin
7ff81781f2 snakemake: 7.32.4 -> 8.0.1 2023-12-21 14:32:05 -05:00
Federico Beffa
a596167020 xyce: 7.7.0 -> 7.8.0 2023-12-21 19:37:28 +01:00
github-actions[bot]
459873d8d6
Merge master into staging-next 2023-12-21 06:01:01 +00:00
OTABI Tomoya
9db0d0a0ec
Merge pull request #274810 from r-ryantm/auto-update/messer-slim 
messer-slim: 4.0.1 -> 4.1
 2023-12-21 10:58:25 +09:00
github-actions[bot]
63203647a1
Merge master into staging-next 2023-12-21 00:02:16 +00:00
Guillaume Maudoux
26241b6458
Merge pull request #274496 from whonore/update-dafny-4.4.0 
dafny: 4.3.0 -> 4.4.0
 2023-12-20 23:29:29 +01:00
Martin Weinelt
431215ad32
fasttext: 0.9.2 -> 0.9.2-unstable-2023-11-28 
Fixes the build with GCC 13.
 2023-12-20 20:46:24 +01:00
Martin Weinelt
8056f9250c
treewide: remove redundant SETUPTOOLS_SCM_PRETEND_VERSION usage 
The setuptools-scm packages gained a setup hook, that sets it to the
derivation version automatically, so setting it to that manually has
become redundant.

This also affects downstream consumers of setuptools-scm, like hatch-vcs
or flit-scm.
 2023-12-20 20:16:39 +01:00
Andreas Rammhold
9eb6350536 xflr5: use fetchsvn instead of fetchzip 
The Sourceforge ZIP URLs aren't stable. They (sometimes?) disappear
and throw 404. Probably until someone requests the file to be
generated from the UI. This made the build of xflr5 fail. By using the
SVN checkout we should be on the safer side.
 2023-12-20 20:04:46 +01:00
Vincent Laporte
b0d34692a2
Merge pull request #275608 from proux01/coq_8_19 
coq_8_19: init at 8.19+rc1
 2023-12-20 11:06:56 +01:00
R. Ryantm
b297165efd cvc5: 1.0.8 -> 1.0.9 2023-12-20 08:10:00 +00:00
Justin Bedő
7dcf6462dd
Merge pull request #275350 from r-ryantm/auto-update/last 
last: 1518 -> 1519
 2023-12-20 10:04:19 +11:00
Pierre Roux
d77d8f69f7 coq_8_19: init at 8.19+rc1 2023-12-19 14:41:20 +01:00
R. Ryantm
0ecf097e92 last: 1518 -> 1519 2023-12-19 07:59:25 +00:00
OTABI Tomoya
bda147b4f6
Merge pull request #273915 from r-ryantm/auto-update/bcftools 
bcftools: 1.18 -> 1.19
 2023-12-19 15:57:58 +09:00
OTABI Tomoya
b04bd65c5b
Merge pull request #274736 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.449 -> 8.3.453
 2023-12-19 15:51:26 +09:00
Emily
17e365438e
Merge pull request #274363 from r-ryantm/auto-update/gatk 
gatk: 4.4.0.0 -> 4.5.0.0
 2023-12-18 18:46:35 +01:00
Vincent Laporte
1791eeb7bd cgal: default to version 5 2023-12-18 18:18:00 +01:00
Phillip Seeber
1d2d308e2e avogadro2: 1.97.0 -> 1.98.1 2023-12-18 14:21:12 +01:00
R. Ryantm
8a034b1227 nnpdf: 4.0.6 -> 4.0.7 2023-12-18 04:59:18 -05:00
Doron Behar
b4f9bed389
Merge pull request #274646 from r-ryantm/auto-update/lammps-mpi 
lammps-mpi: 2Aug2023_update1 -> 2Aug2023_update2
 2023-12-18 08:49:41 +00:00
Peder Bergebakken Sundt
13d052ddce
Merge pull request #272697 from fedeinthemix/wip-xyce-7.7 
xyce: 7.6.0 -> 7.7.0
 2023-12-17 21:55:30 +01:00
Weijia Wang
050c97ef96
Merge pull request #273352 from wegank/dl-poly-gcc 
dl-poly-classic-mpi: fix build with gcc 11+
 2023-12-17 19:17:39 +01:00
Federico Beffa
344d4e77da xyce: 7.6.0 -> 7.7.0 2023-12-17 18:48:06 +01:00
Samuel Ainsworth
701617bf45
Merge pull request #274699 from tmplt/feat/mujoco-3.1.0 
mujoco: 3.0.1 -> 3.1.0
 2023-12-17 12:14:06 -05:00
Weijia Wang
2a3d4f9afe alt-ergo: fix build on darwin 2023-12-17 16:12:48 +01:00
R. Ryantm
232b3c6fb6 jmol: 16.1.45 -> 16.1.47 2023-12-17 16:11:46 +01:00
Nick Cao
d319012df5
Merge pull request #274921 from r-ryantm/auto-update/nvc 
nvc: 1.11.0 -> 1.11.1
 2023-12-17 10:10:04 -05:00
Dmitry Kalinkin
d245890087
root: 6.28.10 -> 6.30.02 (#274348) 2023-12-17 05:20:40 -05:00
R. Ryantm
4af519af84 nvc: 1.11.0 -> 1.11.1 2023-12-17 07:23:15 +00:00
R. Ryantm
dfa0eb5286 messer-slim: 4.0.1 -> 4.1 2023-12-16 20:13:33 +00:00
R. Ryantm
e5f5f16f4b magic-vlsi: 8.3.449 -> 8.3.453 2023-12-16 14:26:08 +00:00
Viktor Sonesten
b5aa9eaa9c mujoco: 3.0.1 -> 3.1.0 2023-12-16 11:30:45 +01:00
R. Ryantm
bebc9fc5db lammps-mpi: 2Aug2023_update1 -> 2Aug2023_update2 2023-12-16 06:40:55 +00:00
whonore
9e1d149f05 dafny: 4.3.0 -> 4.4.0 2023-12-15 15:48:44 -05:00
Nick Cao
4d9f672c6c
Merge pull request #274370 from r-ryantm/auto-update/cadical 
cadical: 1.9.0 -> 1.9.1
 2023-12-15 10:11:20 -05:00
Dmitry Kalinkin
d4af6e420f
root: build with root7 and webgui (#272723) 2023-12-15 08:43:44 -05:00
R. Ryantm
a1e9171ca3 cadical: 1.9.0 -> 1.9.1 2023-12-15 05:27:39 +00:00
R. Ryantm
c618d890bc gatk: 4.4.0.0 -> 4.5.0.0 2023-12-15 04:20:42 +00:00
R. Ryantm
a365120b26 eigenmath: unstable-2023-12-11 -> unstable-2023-12-12 2023-12-14 13:59:07 +00:00
Federico Beffa
1ff13b86c8 fasthenry: init at 3.0.1 2023-12-13 17:48:20 +01:00
R. Ryantm
0d31c8b213 celestia: 1.6.3 -> 1.6.4 2023-12-13 15:52:46 +00:00
R. Ryantm
bb215123da bcftools: 1.18 -> 1.19 2023-12-13 06:48:21 +00:00
Dmitry Kalinkin
1a5412e140
toil: 5.7.1 -> 5.12.0 (#273274) 2023-12-12 16:04:33 -05:00
Weijia Wang
9a67c36f6d
Merge pull request #273382 from wegank/strelka-aarch64 
strelka: add aarch64-linux support
 2023-12-12 01:51:59 +01:00
OTABI Tomoya
bea3c001fd
Merge pull request #273485 from r-ryantm/auto-update/kalign 
kalign: 3.3.5 -> 3.4.0
 2023-12-12 08:56:04 +09:00
Nick Cao
7c71bd5224
Merge pull request #273629 from r-ryantm/auto-update/eigenmath 
eigenmath: unstable-2023-11-17 -> unstable-2023-12-11
 2023-12-11 17:57:54 -05:00
R. Ryantm
35c04706b1 eigenmath: unstable-2023-11-17 -> unstable-2023-12-11 2023-12-11 20:20:25 +00:00
Weijia Wang
bf4d34ba62 dl-poly-classic-mpi: fix build with gcc 11+ 2023-12-11 19:01:06 +01:00
Weijia Wang
b7081671e3
Merge pull request #273100 from r-ryantm/auto-update/calc 
calc: 2.15.0.1 -> 2.15.0.2
 2023-12-11 15:02:47 +01:00
Weijia Wang
3ce2a25e50 strelka: add aarch64-linux support 2023-12-11 13:37:17 +01:00
R. Ryantm
0cd6e601a6 kalign: 3.3.5 -> 3.4.0 2023-12-11 06:26:11 +00:00
Aaron Jheng
930b7d743f
poretools: mark as broken 2023-12-11 04:28:39 +00:00
Sergei Trofimovich
a92211886b strelka: fix build on gcc-12 
Without the change build fails as:

    src/c++/lib/calibration/IndelErrorModel.hh💯33: error: 'numeric_limits' is not a member of 'std'
      100 |     double logErrorRate = -std::numeric_limits<double>::infinity();
          |                                 ^~~~~~~~~~~~~~
 2023-12-10 17:44:19 +01:00
Weijia Wang
64891e361b
Merge pull request #243497 from jvanbruegge/isabelle-2023 
isabelle: 2022 -> 2023
 2023-12-10 14:07:23 +01:00
Weijia Wang
e87c4b32ee
Merge pull request #273265 from aaronjheng/gwyddion 
gwyddion: mark as broken
 2023-12-10 13:20:33 +01:00
Doron Behar
29d6c96900
Merge pull request #271142 from alyaeanyx/qalculate-4.9.0 
{libqalculate, qalculate-gtk, qalculate-qt}: 4.8.1 -> 4.9.0
 2023-12-10 11:11:37 +00:00
Aaron Jheng
b5b4d4e373
gwyddion: mark as broken 2023-12-10 03:32:47 +00:00
OTABI Tomoya
b9cb1d8d5f
Merge pull request #271924 from stepbrobd/z3-solver 
python3Packages.z3-solver: rename from z3
 2023-12-10 12:28:16 +09:00
Dmitry Kalinkin
b9c3a2f996
Merge pull request #272727 from NixOS/pr/root_6_28_10 
root: 6.28.08 -> 6.28.10
 2023-12-09 21:39:07 -05:00
Jan van Brügge
3e90293669 isabelle-linter: 1.2.1 -> 2023-1.0.0 2023-12-10 02:27:06 +01:00
R. Ryantm
f32aee4e1b eprover: 3.0 -> 3.0.03 2023-12-09 18:57:23 +00:00
R. Ryantm
c7fc09f681 qgroundcontrol: 4.2.9 -> 4.3.0 2023-12-09 16:27:13 +00:00
R. Ryantm
2010a2f7e2 calc: 2.15.0.1 -> 2.15.0.2 2023-12-09 09:24:28 +00:00
Weijia Wang
195821f0e8
Merge pull request #272707 from wegank/nvc-bump 
nvc: 1.10.4 -> 1.11.0
 2023-12-08 16:17:57 +01:00
Connor Baker
855a7ba029 caffe: fix eval when CUDNN is not available 2023-12-07 21:02:12 +00:00
alyaeanyx
08cdc6a005 qalculate-{gtk, qt}: add meta.mainProgram 2023-12-07 20:19:52 +01:00
Dmitry Kalinkin
190cb5fc41 root: 6.28.08 -> 6.28.10 2023-12-07 12:36:03 -05:00
Weijia Wang
4598bad931 nvc: 1.10.4 -> 1.11.0 2023-12-07 16:48:30 +01:00
Yifei Sun
3d0affa9c9
python3Packages.z3-solver: rename from z3 2023-12-06 12:30:03 -05:00
R. Ryantm
dc68acff61 gretl: 2023b -> 2023c 2023-12-06 07:34:23 +00:00
Rick van Schijndel
ba75066821
Merge pull request #271362 from pbsds/rm-dead-patches 
treewide: remove unreferenced patch files
 2023-12-06 03:28:15 +01:00
Justin Bedő
65238bae4c
Merge pull request #272274 from r-ryantm/auto-update/last 
last: 1499 -> 1518
 2023-12-06 09:40:13 +11:00
Connor Baker
ec3c8084ec
Merge pull request #272063 from SomeoneSerge/fix/cuda-upkeep 
cudaPackages: drop some runfile dependencies and fix a few builds
 2023-12-05 14:40:13 -05:00
Weijia Wang
7a5f0e9467 clp: unbreak on aarch64-linux 2023-12-05 16:54:45 +01:00
R. Ryantm
5d669c5d95 last: 1499 -> 1518 2023-12-05 14:44:08 +00:00
markuskowa
566008762b
Merge pull request #270650 from sheepforce/quantum-espresso 
quantum-espresso: 6.6 -> 7.2
 2023-12-05 14:06:34 +01:00
Weijia Wang
8c59802efd
Merge pull request #272185 from wegank/cbc-clang 
cbc: fix build with clang 16
 2023-12-05 11:48:51 +01:00
Weijia Wang
3b03119bcf
Merge pull request #263288 from r-ryantm/auto-update/cryptominisat 
cryptominisat: 5.11.14 -> 5.11.15
 2023-12-05 10:46:20 +01:00
Jonas Chevalier
80d540bd31
fahclient: wrap in FHS (#271994) 
Folding@home downloads arbitrary binaries that it runs and that have the
wrong loader.

Fixes https://github.com/NixOS/nixpkgs/pull/246832#issuecomment-1837625014
 2023-12-05 10:04:09 +01:00
Weijia Wang
999811113f cbc: fix build with clang 16 2023-12-05 08:07:55 +01:00
Peder Bergebakken Sundt
87639758aa
Merge pull request #266961 from mayl/openems 
openems: unstable-2020-02-15 -> 0.0.36
 2023-12-05 02:38:30 +01:00
Larry May
d7632d8a73 csxcad: unstable-2022-05-18 -> v0.6.3 2023-12-04 16:14:13 -05:00
Someone Serge
31f1b517cd
gromacs: drop cudatoolkit.run 2023-12-04 20:24:32 +00:00
sternenseemann
8c59811e4e root5: broken with clang 
Seems like any clang version > 5 doesn't work. Since root >= 6.0 is
available from nixpkgs, I think it is reasonable to mark it as broken
for now. Maybe someone can figure out if it is possible to backport a
fix from root >= 6.0.
 2023-12-04 19:43:08 +01:00
Phillip Seeber
50fc2bfb8b quantum-espresso: 6.6 -> 7.2 2023-12-04 17:08:07 +01:00
Larry May
4803b4b517 openems: unstable-2020-02-15 -> v0.0.36 2023-12-04 10:14:48 -05:00
Weijia Wang
e420273763
Merge pull request #266665 from r-ryantm/auto-update/seqkit 
seqkit: 2.5.1 -> 2.6.0
 2023-12-04 02:43:42 +01:00
Weijia Wang
4a0d12f347
Merge pull request #266351 from r-ryantm/auto-update/sumo 
sumo: 1.18.0 -> 1.19.0
 2023-12-04 02:41:11 +01:00
Weijia Wang
e4a901b362
Merge pull request #264994 from r-ryantm/auto-update/kallisto 
kallisto: 0.50.0 -> 0.50.1
 2023-12-04 01:43:00 +01:00
K900
00639571f8
Merge pull request #271540 from SuperSandro2000/kde-mirror 
treewide: use kde mirror everywhere
 2023-12-03 10:39:25 +03:00
Samuel Ainsworth
d71187cf33
Merge pull request #266099 from tmplt/feat/mujoco-3.0.0 
mujoco: 2.3.7 -> 3.0.1, add Python bindings
 2023-12-02 15:47:04 -08:00
Sandro Jäckel
aa15f5066d
treewide: use kde mirror everywhere, don't use pname in download urls 2023-12-02 17:14:24 +01:00
Peder Bergebakken Sundt
5c2f149bab
Merge pull request #271114 from vbgl/why3-1.7.0 
why3: 1.6.0 → 1.7.0
 2023-12-02 10:48:36 +01:00
Emily Trau
e8ba25580a
Merge pull request #270695 from r-ryantm/auto-update/simgrid 
simgrid: 3.34 -> 3.35
 2023-12-02 13:04:42 +11:00
Doron Behar
0a862713eb
Merge pull request #269053 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 23.10.0 -> 23.11.0
 2023-12-01 11:09:48 +00:00
Peder Bergebakken Sundt
f41aba3739 treewide: remove unreferenced patch files 
Found with `fd \\.patch$ pkgs/ -x bash -c 'rg -F "{/}" pkgs/ -q || echo {}'`
 2023-12-01 06:11:20 +01:00
Doron Behar
df20638983
Merge pull request #186462 from apraga/bio-bigfile-1.07 
bio-bigfile: init 1.07
 2023-11-30 13:39:01 +00:00
alyaeanyx
90a5c36a85 {libqalculate, qalculate-gtk}: change sha256 attribute to hash 2023-11-30 09:48:44 +01:00
alyaeanyx
016d7891e9 {libqalculate, qalculate-gtk, qalculate-qt}: 4.8.1 -> 4.9.0 2023-11-30 09:05:31 +01:00
Mario Rodas
c462586977
Merge pull request #271084 from marsam/update-lean4 
lean4: 4.2.0 -> 4.3.0
 2023-11-30 02:30:54 -05:00
Vincent Laporte
ef6c49fa50
why3: 1.6.0 → 1.7.0 2023-11-30 05:41:54 +01:00
Vincent Laporte
556712bb7c acgtk: 1.5.4 → 2.0.0 2023-11-30 05:37:04 +01:00
Henner Zeller
409e9d1a30 surelog: 1.76 -> 1.80 2023-11-29 13:18:33 -06:00
Henner Zeller
39dd77fde8 uhdm: 1.77 -> 1.80 2023-11-29 13:18:33 -06:00
Emily Trau
7b642cf00b
Merge pull request #270312 from rafaelrc7/update-mathematica 
mathematica: 13.3.0 -> 13.3.1
 2023-11-29 18:26:20 +11:00
Mario Rodas
cbcf0e94ac lean4: 4.2.0 -> 4.3.0 
Diff: https://github.com/leanprover/lean4/compare/v4.2.0...v4.3.0

Changelog: https://github.com/leanprover/lean4/blob/v4.3.0/RELEASES.md
 2023-11-29 04:20:00 +00:00
R. Ryantm
fc9bec86de simgrid: 3.34 -> 3.35 2023-11-28 16:59:53 +00:00
Emery Hemingway
0f089515b1 mosdepth: build with a lockfile 2023-11-28 16:48:10 +02:00
markuskowa
537453f5fd
Merge pull request #267703 from zimbatm/gromacs-plumed 
gromacs: add the plumed patches
 2023-11-28 09:07:16 +01:00
Pol Dellaiera
bc513821fd
Merge pull request #269115 from r-ryantm/auto-update/phd2 
phd2: 2.6.11 -> 2.6.12
 2023-11-27 21:11:38 +01:00
rafaelrc7
0bd493d85d
mathematica: add rafaelrc to maintainers 2023-11-27 17:10:58 -03:00
Jonas Chevalier
a403a118d1
fahclient: 7.6.21 -> 8.1.18 (#246832) 
Rebuild from source
 2023-11-27 14:20:58 +01:00
rafaelrc7
cc1b0c4091
mathematica: 13.3.0 -> 13.3.1 2023-11-26 19:43:17 -03:00
Stian Lågstad
54f913f862 igv: Fix missing wrapGAppsHook causing causing GLib-GIO-ERROR 
Fixes https://github.com/NixOS/nixpkgs/issues/270226
 2023-11-26 19:57:18 +01:00
MarcFontaine
2459917e66 xearth: improve meta.license 2023-11-26 18:32:06 +01:00
Robert Scott
ba608c6c07
Merge pull request #269034 from a-n-n-a-l-e-e/lp_solver-fix 
lp_solve: ignore implicit int warnings
 2023-11-26 16:41:43 +00:00
R. Ryantm
ec60dd7600 magic-vlsi: 8.3.447 -> 8.3.449 2023-11-25 22:13:26 -03:00
Peder Bergebakken Sundt
c612fc6155
Merge pull request #258205 from evils/kicad 
kicad: 7.0.7 -> 7.0.9
 2023-11-26 01:13:04 +01:00
Pierre Bourdon
f4db50bafb
Merge pull request #269700 from NixOS/pr/root_warning_fix 
root: fix excessive build log size
 2023-11-25 10:38:13 +01:00
OTABI Tomoya
09fecf05a2
Merge pull request #269640 from natsukium/dssp/update 
dssp: 4.4.4.1 -> 4.4.5
 2023-11-25 18:35:26 +09:00
Dmitry Kalinkin
8ae6154b2b root: fix excessive build log size 2023-11-24 14:33:55 -05:00
natsukium
87a4074d00
dssp: 4.4.4.1 -> 4.4.5 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.4.1...v4.4.5

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.5
 2023-11-24 22:34:06 +09:00
Mario Rodas
b9a67f7317 lean4: fix build on darwin 2023-11-23 04:20:00 +00:00
R. Ryantm
9191cc9865 jmol: 16.1.43 -> 16.1.45 2023-11-22 08:17:54 -08:00
R. Ryantm
c8208d43fd gama: 2.26 -> 2.27 2023-11-22 08:06:27 -08:00
Emily Trau
d68237057b
Merge pull request #268779 from NixOS/update-xflr5 
xflr5: 6.47 -> 6.61
 2023-11-23 01:08:48 +11:00
R. Ryantm
2f143de8fd phd2: 2.6.11 -> 2.6.12 2023-11-22 05:33:54 +00:00
annalee
540ea20215
lp_solve: ignore implicit int warnings, add x64 darwin ldflags 
the configuration code generates small c programs with a main function
sans return type specifer. this causes clang builds to fail. add
'-Wno-error=implicit-int' to fix the build.

add -headerpad_max_install_names to env.NIX_LDFLAGS for x64 darwin
 2023-11-22 03:28:26 +00:00
Alexis Praga
75fc8ae0f4 perlPackages.BioBigFile: Addressing reviewer change 2023-11-21 23:16:39 +01:00
Alexis Praga
cc4bd30387 perlPackages.BioBigfile: init at 1.07 
Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d836 : packaging kent header
- 2b2c6f4c28 : enabling patches in kent
 2023-11-21 23:16:12 +01:00
R. Ryantm
110e47b449 wxmaxima: 23.10.0 -> 23.11.0 2023-11-21 21:10:32 +00:00
R. Ryantm
f23cd2617d cadical: 1.8.0 -> 1.9.0 2023-11-21 17:11:06 +00:00
Andreas Rammhold
9808815f41 xflr5: 6.47 -> 6.61 
This updates to the latest version. Unfortunately the project stopped
publishing source tarballs in the way we used to consume them. We've
to retrieve a source snapshot from sourceforge's SVN service instead.
The alternative would be a subversion checkout which I don't think is
any better or worse.
 2023-11-20 18:45:41 +01:00
ajs124
f1f62c94f6
Merge pull request #267114 from katexochen/maintainers/jfrankenau 
maintainers: remove jfrankenau
 2023-11-20 12:26:57 +01:00
Vincent Laporte
181a9fe1ea easycrypt: fix runtest command 
The `ec-runtest` program is still available as a separate
easycrypt-runtest package, but the `easycrypt runtest` command now also
works out-of-the-box.
 2023-11-20 09:04:33 +01:00
Paul Meyer
2c97a5caa7 maintainers: remove jfrankenau 
due to inactivity.
 2023-11-20 08:44:58 +01:00
Vincent Laporte
4800982f99 hol_light: 2023-07-21 → 2023-11-03 2023-11-20 07:03:45 +01:00
R. Ryantm
bac54b6e1b eigenmath: unstable-2023-10-26 -> unstable-2023-11-17 2023-11-18 21:18:16 +00:00
TelepathicWalrus
88387cffd2 update sources 2023-11-18 11:37:58 +00:00
Adam Joseph
c7e0f6b905 treewide: s_targetPlatform_hostPlatform_ in non-compiler packages 
stdenv.targetPlatform really shouldn't be used by software that
doesn't generate or manipulate binaries.  I reviewed all uses of
targetPlatform outside of pkgs/development/compilers and pkgs/stdenv
and replaced those which weren't involved in something which fits
these criteria.
 2023-11-17 08:07:34 +00:00
annalee
38eccd74c3
eprover: update hash - target modified inplace 
the last commit was Wed Nov 15 13:09:21 2023 +0000 but the target, E.tgz
was modified at 2023-11-15 23:29 (assuming utc)
https://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_3.0/
 2023-11-17 04:12:46 +00:00
Viktor Sonesten
dd6fa9c2e6 mujoco: 3.0.0 -> 3.0.1 2023-11-16 19:09:22 +01:00
github-actions[bot]
dba5c9ef4e
Merge master into staging-next 2023-11-16 18:01:17 +00:00
Jeremy Fleischman
d0bec347c4 kicadAddons.kikit,kicadAddons.kikit-library: init at 1.3.0 
Create a new kicadAddons package set, and a mechanism to override
kicad to bundle addons.

Co-authored-by: Rohit <rohitsutradhar311@gmail.com>
Co-authored-by: Jeremy Fleischman <jeremyfleischman@gmail.com>
Co-authored-by: Shahar "Dawn" Or <mightyiampresence@gmail.com>
Co-authored-by: Alejandro Sanchez Medina <alejandrosanchzmedina@gmail.com>
Co-authored-by: Matúš Ferech <matus.ferech@gmail.com>
 2023-11-16 21:24:05 +07:00
Vladimír Čunát
0fe5300699
Merge branch 'master' into staging-next 2023-11-16 09:49:24 +01:00
7c6f434c
91c993afb9
Merge pull request #267664 from r-ryantm/auto-update/eprover 
eprover: 2.6 -> 3.0
 2023-11-15 23:52:24 +00:00
Alex Martens
0e1c4b8429 verilator: 5.016 -> 5.018 2023-11-15 14:54:37 -06:00
zimbatm
21c4107d3e gromacs: add the plumed patches 
plumed 2.9.0 only supports gromacs-2023 so I had to downgrade the
package as well.
 2023-11-15 18:28:24 +01:00
Nick Cao
4211246b55
Merge pull request #267679 from r-ryantm/auto-update/picard-tools 
picard-tools: 3.1.0 -> 3.1.1
 2023-11-15 11:08:55 -05:00
R. Ryantm
282aede4e4 picard-tools: 3.1.0 -> 3.1.1 2023-11-15 14:35:32 +00:00
R. Ryantm
e13386b72e eprover: 2.6 -> 3.0 2023-11-15 13:09:21 +00:00
Vladimír Čunát
c46eae0f35
Merge branch 'master' into staging-next 2023-11-15 07:33:10 +01:00
Mario Rodas
5268a6e24b
Merge pull request #267372 from cu1ch3n/update-abella 
abella: 2.0.7 -> 2.0.8
 2023-11-14 19:02:22 -05:00
github-actions[bot]
6cc772a6fa
Merge master into staging-next 2023-11-14 18:01:11 +00:00
Madoura
9709e96e1e
treewide: make 'gpuBackend' use 'config.(cuda|rocm)Support' 2023-11-14 08:44:42 -06:00
Chen
109bef7af3 abella: 2.0.7 -> 2.0.8 2023-11-14 13:38:26 +08:00
github-actions[bot]
772c3bbbf5
Merge master into staging-next 2023-11-14 00:02:14 +00:00
Pascal Bach
f524257148
Merge pull request #266008 from r-ryantm/auto-update/dsview 
dsview: 1.3.0 -> 1.3.1
 2023-11-13 22:16:44 +01:00
Fabián Heredia Montiel
884449105e Merge remote-tracking branch 'origin/master' into staging-next 2023-11-13 14:31:51 -06:00
Artturi
b5bd1053d2
Merge pull request #266273 from evils/xnec2c 2023-11-13 21:17:11 +02:00
Uri Shaked
4335400d78 magic-vlsi: 8.3.446 -> 8.3.447 2023-11-13 11:30:40 +02:00
Alexis Praga
2b2c6f4c28 kent: enable patches if needed. 
This is required by BioBigFile, which needs an older Kent version.
 2023-11-12 21:46:39 +01:00
Weijia Wang
74d102ce50 Merge branch 'master' into staging-next 2023-11-12 19:45:20 +01:00
Uri Shaked
ac5c40ee45 magic-vlsi: 8.3.277 -> 8.3.446 2023-11-12 12:01:48 -06:00
Viktor Sonesten
290bc1fbe0 mujoco: 2.3.7 -> 3.0.0, add Python bindings 
https://mujoco.readthedocs.io/en/stable/changelog.html#version-3-0-0-october-18-2023

Fixes #262698
Fixes #262629
Fixes #262593

Co-authored-by: Silvio Traversaro <silvio@traversaro.it>
 2023-11-12 11:45:20 +01:00
github-actions[bot]
eb26e06e9b
Merge master into staging-next 2023-11-12 06:01:07 +00:00
Pierre Bourdon
4098144884
Merge pull request #266486 from Luflosi/update/yosys 
yosys: 0.34 -> 0.35
 2023-11-12 03:24:48 +01:00
github-actions[bot]
9776723357
Merge master into staging-next 2023-11-11 18:00:58 +00:00
Anthony Roussel
e30f48be94
treewide: fix redirected and broken URLs 
Using the script in maintainers/scripts/update-redirected-urls.sh
 2023-11-11 10:49:01 +01:00
Weijia Wang
d8ebb73023 Merge branch 'master' into staging-next 2023-11-10 16:25:02 +01:00
7c6f434c
5c93b37109
Merge pull request #264760 from r-ryantm/auto-update/R 
R: 4.3.1 -> 4.3.2
 2023-11-10 15:12:42 +00:00
Alyssa Ross
afabc4a15d
Merge remote-tracking branch 'origin/master' into HEAD 
Conflicts:
	pkgs/development/libraries/SDL2/default.nix
 2023-11-10 15:18:19 +01:00
R. Ryantm
a7b54e1136 seqkit: 2.5.1 -> 2.6.0 2023-11-10 12:50:42 +00:00
Renato Garcia
3c87cb32f0
snakemake: 7.29.0 -> 7.32.4 (#266543) 2023-11-10 06:48:45 -05:00
github-actions[bot]
b55905ceb6
Merge master into staging-next 2023-11-10 06:01:22 +00:00
Silvan Mosberger
fb2e311d1e root5: Fix build with Python 3.11 
Was broken since the Python update from https://github.com/NixOS/nixpkgs/pull/251878

This should fix the apfelgrid and applgrid builds, not tested yet
 2023-11-09 19:01:58 +01:00
github-actions[bot]
e112f9b8bb
Merge master into staging-next 2023-11-09 18:00:56 +00:00
R. Ryantm
70bc041b9c bedtools: 2.31.0 -> 2.31.1 2023-11-09 06:18:08 +00:00
R. Ryantm
8f0fc5a2eb sumo: 1.18.0 -> 1.19.0 2023-11-08 23:02:41 +00:00
Luflosi
783a01c64e
abc-verifier: unstable-2023-09-13 -> unstable-2023-10-13 2023-11-08 15:21:35 +01:00
Luflosi
9882bdee1e
abc-verifier: cleanup 
- Move each function argument into its own line
- Use `finalAttrs` instead of the `rec` keyword to properly handle overriding
- Run the `preInstall` and `postInstall` hooks in the `installPhase`
- Use `install` instead of `mkdir -p` and `mv` to be more concise
 2023-11-08 15:21:34 +01:00
Luflosi
0942f79dda
abc-verifier: add Luflosi as maintainer 2023-11-08 15:21:31 +01:00
Evils
47a196d1f8 xnec2c: add wrapGAppsHook 2023-11-08 14:47:04 +01:00
github-actions[bot]
263a89fa08
Merge master into staging-next 2023-11-08 12:01:20 +00:00
Weijia Wang
67fc292e5a
Merge pull request #266136 from wegank/stellarium-fix 
stellarium: fix version
 2023-11-08 12:12:26 +01:00
Adam Joseph
ba2ed469c2
Merge branch 'master' into staging-next 2023-11-08 06:15:46 +00:00
Justin Bedő
5cd7971391
Merge pull request #264872 from r-ryantm/auto-update/last 
last: 1471 -> 1499
 2023-11-08 09:21:48 +11:00
Artturi
d24da52844
Merge pull request #265764 from amjoseph-nixpkgs/pr/pythonForBuild 2023-11-08 00:13:25 +02:00
Weijia Wang
73698c7c06 stellarium: fix version 2023-11-07 21:23:26 +01:00
github-actions[bot]
bed56440cb
Merge master into staging-next 2023-11-07 12:00:57 +00:00
R. Ryantm
6ff2f664cd polymake: 4.10 -> 4.11 2023-11-07 10:26:26 +00:00
Weijia Wang
1136113354
Merge pull request #265975 from wegank/readstat-clang-16 
readstat: fix build with clang 16
 2023-11-07 09:22:07 +01:00
R. Ryantm
71e8d7a47b dsview: 1.3.0 -> 1.3.1 2023-11-07 07:00:00 +00:00
Weijia Wang
311c0ae699 Merge branch 'master' into staging-next 2023-11-07 03:22:29 +01:00
Weijia Wang
c97fbef1f3
Merge pull request #265981 from wegank/root-patches-drop 
root: drop patches
 2023-11-07 03:20:41 +01:00