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8637 Commits

Author SHA1 Message Date
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