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8923 Commits

Author SHA1 Message Date
Weijia Wang
0d335e0d7d
Merge pull request #278776 from TomaSajt/trimmomatic 
trimmomatic: make deterministic and clean up
 2024-01-11 20:33:56 +01:00
R. Ryantm
6ae414b6de gtkwave: 3.3.117 -> 3.3.118 2024-01-11 19:30:32 +01:00
github-actions[bot]
28d4a2210a
Merge master into staging-next 2024-01-11 06:01:20 +00:00
R. Ryantm
2202d5c909 primesieve: 11.1 -> 11.2 2024-01-11 05:36:25 +00:00
Someone
e529aea84f
Merge pull request #274319 from ConnorBaker/feat/cudaPackages-all-packages-eval 
tree-wide: cudaPackages attributes should not cause default eval to fail
 2024-01-11 04:32:59 +00:00
Felix Buehler
a69b0e8a68 python311Packages.sip4: rename from sip_4 2024-01-10 22:50:20 +01:00
Felix Buehler
f5888649c0 python311Packages.pyqt5-sip: rename from pyqt5_sip 2024-01-10 22:49:05 +01:00
github-actions[bot]
769e5f5d37
Merge master into staging-next 2024-01-10 18:01:17 +00:00
Weijia Wang
485a574457
Merge pull request #280055 from rafaelrc7/mathematica/14.0.0 
mathematica: 13.3.1 -> 14.0.0
 2024-01-10 18:54:41 +01:00
rafaelrc7
b4521d10d5
mathematica: 13.3.1 -> 14.0.0 2024-01-10 12:19:37 -03:00
github-actions[bot]
d9ad8d1e35
Merge master into staging-next 2024-01-10 06:01:12 +00:00
anna
4c3dbc1a11
magic-vlsi: remove anna328p from maintainers 2024-01-09 21:34:27 -08:00
Vincent Laporte
2225c6a883 iprover: 3.1 → 3.8.1 2024-01-10 06:33:50 +01:00
Connor Baker
9bebd9e72d tree-wide: cudaPackages should not break default eval 
cudaPackages: guard expressions against null values
 2024-01-10 01:15:01 +00:00
github-actions[bot]
122355be99
Merge master into staging-next 2024-01-10 00:02:18 +00:00
K900
838aefefc3 Merge remote-tracking branch 'origin/master' into staging-next 2024-01-09 22:42:37 +03:00
R. Ryantm
b6839c45e5 magic-vlsi: 8.3.454 -> 8.3.456 2024-01-09 17:36:06 +00:00
Phillip Seeber
24d7e572bf cp2k: 2023.2 -> 2024.1 
cp2k: fix hdf5 includes
 2024-01-09 16:44:06 +01:00
markuskowa
250bf92b66
Merge pull request #279827 from markuskowa/fix-cp2k-cuda 
cp2k: fix CUDA support
 2024-01-09 16:20:42 +01:00
Peder Bergebakken Sundt
c3db3ff73d
Merge pull request #255271 from evils/kicad-testing 
kicad-testing: init at 7.0-2024-01-07
 2024-01-09 15:57:48 +01:00
Markus Kowalewski
930e7fe5d1 cp2k: fix CUDA support 
Note, that it currently does not build with cufft support.
Any attempt to build it cufft suport results in missing symbols from
CP2K itself.
 2024-01-09 14:17:19 +01:00
K900
bff9ee8862 Merge remote-tracking branch 'origin/master' into staging-next 2024-01-09 13:03:34 +03:00
Robert Scott
d2415e5194
Merge pull request #279239 from LeSuisse/dcmtk-3.6.8 
dcmtk: 3.6.7 -> 3.6.8
 2024-01-08 19:36:33 +00:00
Evils
e3eb5b9e9d kicad: update.sh: use created_at date 2024-01-08 07:57:24 +01:00
Evils
3aaab6bc2a kicad.passthru.updateScript: fix integration 
accept UPDATE_NIX_PNAME
output JSON
handle the -small packages

not sure why i thought i couldn't call it for each pname...

and some cleanup
 2024-01-08 07:57:24 +01:00
Evils
e0fe5cf69f kicad-testing: init at 7.0-2024-01-07 
update update.sh to include it in versions.nix

sort the package inputs a bit
 2024-01-08 07:57:03 +01:00
R. Ryantm
b3249dde09 igv: 2.16.2 -> 2.17.0 2024-01-08 05:30:06 +00:00
K900
9e0000be28 Merge branch 'master' into staging-next 2024-01-08 00:51:35 +03:00
Felix Buehler
2adcc8846a python311Packages.wxpython: rename from wxPython_4_2 2024-01-07 21:16:47 +01:00
github-actions[bot]
f85fe5fc29
Merge master into staging-next 2024-01-07 18:00:54 +00:00
Dmitry Kalinkin
be5b82b259
Merge pull request #275882 from veprbl/pr/snakemake_8_0_1 
snakemake: 7.32.4 -> 8.0.1
 2024-01-07 11:03:10 -05:00
R. Ryantm
a373789932 rink: 0.6.3 -> 0.7.0 2024-01-07 14:39:33 +00:00
Vladimír Čunát
0dc45cc1ed
Merge #278132: gmsh: pull gcc-13 build fix from upstream 
...into staging-next
 2024-01-07 07:51:57 +01:00
Martin Weinelt
1442bd4bc7
Merge remote-tracking branch 'origin/master' into staging-next 2024-01-07 05:01:18 +01:00
R. Ryantm
8a8c1f22a3 verilator: 5.018 -> 5.020 2024-01-06 20:39:51 -06:00
Weijia Wang
a1648566d0
Merge pull request #278952 from wegank/gtksheet-init 
lepton-eda: 1.9.17-20211219 -> 1.9.18-20220529
 2024-01-07 01:51:06 +01:00
Martin Weinelt
0161570089
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
-	pkgs/development/python-modules/archspec/default.nix
 2024-01-07 01:31:56 +01:00
Thomas Gerbet
d99ca3f1cd dcmtk: 3.6.7 -> 3.6.8 
Fixes CVE-2022-43272.

Changes:
https://github.com/DCMTK/dcmtk/compare/DCMTK-3.6.7...DCMTK-3.6.8
 2024-01-06 23:03:08 +01:00
Felix Buehler
63f5f08857 python311Packages.zope-*: rename from zope_* 2024-01-06 21:04:16 +01:00
Martin Weinelt
eba4d277a0 Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
-	pkgs/development/python-modules/sabctools/default.nix
 2024-01-06 04:51:01 +01:00
Weijia Wang
b813f7f148 lepton-eda: 1.9.17-20211219 -> 1.9.18-20220529 2024-01-05 17:36:26 +01:00
R. Ryantm
9ed34e2ec3 nvc: 1.11.1 -> 1.11.2 2024-01-05 08:38:36 +00:00
R. Ryantm
ee887b1a8a gwyddion: 2.64 -> 2.65 2024-01-05 05:30:02 +00:00
github-actions[bot]
1e290d634f
Merge master into staging-next 2024-01-05 00:02:27 +00:00
Weijia Wang
864ba7fd57
Merge pull request #277673 from r-ryantm/auto-update/phd2 
phd2: 2.6.12 -> 2.6.13
 2024-01-05 00:59:42 +01:00
TomaSajt
51b6d44f8b
trimmomatic: make deterministic and clean up 2024-01-04 21:45:11 +01:00
Weijia Wang
7fabb43469
Merge pull request #278422 from r-ryantm/auto-update/dataexplorer 
dataexplorer: 3.8.0 -> 3.8.3
 2024-01-04 21:13:06 +01:00
github-actions[bot]
065e28482b
Merge master into staging-next 2024-01-04 18:00:54 +00:00
Nick Cao
6a98d1fe8b
Merge pull request #278630 from r-ryantm/auto-update/wxmacmolplt 
wxmacmolplt: 7.7.2 -> 7.7.3
 2024-01-04 11:08:27 -05:00
Vladimír Čunát
8a839514de
Merge branch 'master' into staging-next 2024-01-04 15:07:44 +01:00
Weijia Wang
516a83e137
Merge pull request #277269 from r-ryantm/auto-update/tulip 
tulip: 5.7.2 -> 5.7.3
 2024-01-04 13:15:06 +01:00
Weijia Wang
6ebf3f2c5c
Merge pull request #278628 from r-ryantm/auto-update/uarmsolver 
uarmsolver: 0.2.5 -> 0.2.6
 2024-01-04 13:11:15 +01:00
R. Ryantm
babf9e08bf wxmacmolplt: 7.7.2 -> 7.7.3 2024-01-04 05:15:19 +00:00
R. Ryantm
f1e6479489 uarmsolver: 0.2.5 -> 0.2.6 2024-01-04 05:06:17 +00:00
Weijia Wang
553ccf3dfe tulip: fix build on darwin 2024-01-03 22:16:58 +01:00
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