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8030 Commits

Author SHA1 Message Date
kilianar
24016b9633 stellarium: 23.1 -> 23.2 
https://github.com/Stellarium/stellarium/releases/tag/v23.2
 2023-07-03 14:04:41 +02:00
Weijia Wang
82d4f6b43d veryfasttree: fix build on darwin 2023-07-03 12:29:44 +03:00
Weijia Wang
d2eeccba40
Merge pull request #241086 from r-ryantm/auto-update/simgrid 
simgrid: 3.32 -> 3.34
 2023-07-03 10:38:49 +03:00
Nick Cao
8feaa9fe93
Merge pull request #241120 from jiegec/cbmc 
cbmc: 5.76.1 -> 5.86.0
 2023-07-03 13:58:03 +08:00
figsoda
5522188fc8
Merge pull request #241192 from tjni/snakemake 
snakemake: fix broken source hash
 2023-07-02 21:02:26 -04:00
Theodore Ni
1af33d4653
snakemake: fix broken source hash 2023-07-02 16:50:09 -07:00
Nick Cao
ab163c16ee
Merge pull request #241037 from NickCao/gprojector 
gprojector: 3.0.6 -> 3.1.0
 2023-07-03 06:20:55 +08:00
Martin Weinelt
5a193fb4dd
Merge pull request #232469 from natsukium/autodock-vina/init 
autodock-vina: init at 1.2.3
 2023-07-02 23:45:13 +02:00
Martin Weinelt
bb40b8c205
Merge pull request #235322 from natsukium/dssp/update 
dssp: 4.2.2.1 -> 4.3.1; libcifpp: 5.0.8 -> 5.1.0.1; libmcfp: 1.2.3 -> 1.2.4
 2023-07-02 23:12:49 +02:00
figsoda
50acc2d57a pkgs/applications: replace "${version}" with version 2023-07-02 14:39:50 -04:00
R. Ryantm
cb16c50571 veryfasttree: 3.1.1 -> 4.0 2023-07-02 15:55:36 +00:00
Jiajie Chen
2db283819e cbmc: 5.76.1 -> 5.86.0 2023-07-02 22:46:06 +08:00
R. Ryantm
1539e263f8 simgrid: 3.32 -> 3.34 2023-07-02 11:06:07 +00:00
Nick Cao
1693695975
gprojector: 3.0.6 -> 3.1.0 2023-07-02 13:06:15 +08:00
Doron Behar
48c25dcaf2 spdlog: reformat expression arguments, and comment about fmt_9 2023-07-01 16:59:49 +03:00
natsukium
7b49fced0f
dssp: fix format 
- add changelog to meta
- use finalAttrs
 2023-07-01 16:40:29 +09:00
natsukium
fba5a4d702
dssp: 4.2.2.1 -> 4.3.1 
Diff: https://github.com/PDB-REDO/dssp/compare/v4.2.2.1...v4.3.1
 2023-07-01 16:36:36 +09:00
Michael Gregson
9269d5823d tlaplus18: init at 1.8.0 
This is a pre-release of version 1.8 of TLA+. It adds, among other
things, a TLA+ REPL.

Release Notes: https://github.com/tlaplus/tlaplus/releases/tag/v1.8.0
 2023-06-30 16:09:41 -07:00
Théo Zimmermann
29cf8484ab
Merge pull request #240656 from vbgl/coq-8.17.1 
coq: 8.17.0 → 8.17.1
 2023-06-30 14:26:08 +02:00
Weijia Wang
3b743dd6b6
Merge pull request #240479 from r-ryantm/auto-update/gerbv 
gerbv: 2.9.7 -> 2.9.8
 2023-06-30 10:29:54 +03:00
Vincent Laporte
002ffb885a
coq: 8.17.0 → 8.17.1 2023-06-30 06:48:15 +02:00
R. Ryantm
c7231acb83 gerbv: 2.9.7 -> 2.9.8 2023-06-29 06:41:33 +00:00
Justin Bedő
296758401d
Merge pull request #239891 from NixOS/r-updates 
R updates
 2023-06-29 13:14:20 +10:00
Justin Bedő
2687680f22
Merge pull request #240318 from r-ryantm/auto-update/mosdepth 
mosdepth: 0.3.3 -> 0.3.4
 2023-06-29 09:52:34 +10:00
nviets
4bb4d449a7
snakemake: 7.25.3 -> 7.29.0 (#240263) 
Co-authored-by: nviets <nathan.viets@gmail.com>
 2023-06-28 17:09:10 +02:00
OTABI Tomoya
125bb92705
streamlit: 1.21.0 -> 1.24.0 (#240248) 
Diff: https://github.com/streamlit/streamlit/compare/1.21.0...1.24.0

Changelog: https://github.com/streamlit/streamlit/releases/tag/1.24.0
 2023-06-28 17:08:47 +02:00
Mario Rodas
e6a970aaba
Merge pull request #238994 from kilianar/geogebra 
geogebra: 5-0-745-0 -> 5-0-783-0, geogebra6: 6-0-745-0 -> 6-0-783-0
 2023-06-28 06:55:22 -05:00
R. Ryantm
abfcd95c63 mosdepth: 0.3.3 -> 0.3.4 2023-06-28 10:52:42 +00:00
R. Ryantm
75b8e7eb4b cryptominisat: 5.11.4 -> 5.11.11 2023-06-28 02:05:20 +00:00
kilianar
46f3360e1a geogebra6: 6-0-745-0 -> 6-0-785-0 2023-06-28 00:08:19 +02:00
kilianar
48a30529f7 geogebra: 5-0-745-0 -> 5-0-785-0 2023-06-28 00:08:19 +02:00
Sandro
6c112fb5de
Merge pull request #232600 from evils/kicad-unstable 2023-06-27 13:33:54 +02:00
Janik
77e5ce731b
Merge pull request #238964 from McSinyx/klee-3 2023-06-27 09:38:09 +02:00
Evils
ad19566aca kicad-unstable: 2023-04-14 -> 2023-06-24 
new qa_cli test needs pytest-image-diff
it also accesses $HOME, so setting that as well
and it checks for a valid commit
 which is exposed to the end-user via kicad-cli version --format=commit
 so i'm setting the placeholder to the actual commit used
  mostly to avoid doing a leaveDotGit and rewriting update.sh
 2023-06-27 08:27:47 +02:00
github-actions[bot]
4e9dcbbbc6
Merge master into staging-next 2023-06-26 18:01:29 +00:00
Janik
a2f36b2963
Merge pull request #231149 from mgregson/tlaplus-remove-unnecessary-jdk-dependency 2023-06-26 18:15:28 +02:00
github-actions[bot]
f04cfae48a
Merge master into staging-next 2023-06-26 12:01:27 +00:00
Mario Rodas
e0e4c97cd1
Merge pull request #239623 from marsam/update-z3 
z3: 4.11.0 -> 4.11.2, 4.12.1 -> 4.12.2
 2023-06-26 05:16:37 -05:00
Vladimír Čunát
24711148d4
openmvg: fixup build 
The build broke probably after cmake upgrade in b8ac5b6cfb,
but either way - this forcing of old C++ standard seemed bad.
https://hydra.nixos.org/build/225241222/nixlog/2/tail
 2023-06-26 11:28:12 +02:00
Justin Bedo
bd8f4a24e1
R: 4.3.0 -> 4.3.1 2023-06-26 16:47:23 +10:00
Weijia Wang
826bdb7214
Merge pull request #239691 from r-ryantm/auto-update/diamond 
diamond: 2.1.7 -> 2.1.8
 2023-06-26 07:46:03 +02:00
Weijia Wang
ca4181830d
Merge pull request #239646 from r-ryantm/auto-update/horizon-eda 
horizon-eda: 2.4.0 -> 2.5.0
 2023-06-26 07:41:37 +02:00
Weijia Wang
2b6acb1ae6
Merge pull request #239479 from r-ryantm/auto-update/qucs-s 
qucs-s: 1.0.2 -> 1.1.0
 2023-06-26 07:25:09 +02:00
Mario Rodas
27343d6e6b
Merge pull request #239795 from r-ryantm/auto-update/elan 
elan: 1.4.5 -> 1.4.6
 2023-06-25 14:10:25 -05:00
R. Ryantm
aa93209605 elan: 1.4.5 -> 1.4.6 2023-06-25 17:27:10 +00:00
R. Ryantm
fa6b5a3cb3 last: 1453 -> 1456 2023-06-25 11:01:07 -03:00
R. Ryantm
754d578555 diamond: 2.1.7 -> 2.1.8 2023-06-25 04:35:30 +00:00
R. Ryantm
0c7cacbac4 horizon-eda: 2.4.0 -> 2.5.0 2023-06-24 21:56:23 +00:00
Felix Buehler
f3719756b5 treewide: use optionalString instead of 'then ""' 2023-06-24 20:19:19 +02:00
Mario Rodas
b2aee9c18e
Merge pull request #230298 from jleightcap/jl/z3-4.12 
z3: 4.12.1
 2023-06-24 10:53:02 -05:00
Mario Rodas
cce7280539 z3_4_12: 4.12.1 -> 4.12.2 
https://github.com/Z3Prover/z3/releases/tag/z3-4.12.2
 2023-06-24 04:20:00 +00:00
Mario Rodas
f87301f5f1 z3_4_11: 4.11.0 -> 4.11.2 
https://github.com/Z3Prover/z3/releases/tag/z3-4.11.2
 2023-06-24 04:20:00 +00:00
Mario Rodas
2c0a8e5050 z3: add changelog to meta 2023-06-24 04:20:00 +00:00
R. Ryantm
296b322b40 qucs-s: 1.0.2 -> 1.1.0 2023-06-23 22:41:56 +00:00
Nick Cao
7d73228de8
eigenmath: unstable-2023-05-12 -> unstable-2023-06-16 
Diff: a6de473ad8...800adc5c0b
 2023-06-22 16:40:56 +08:00
Doron Behar
636000a5bb
Merge pull request #238771 from doronbehar/pkg/lammps-extras 
lammps-mpi: Use a generic extraBuildInputs instead of withMpi
 2023-06-22 06:50:03 +00:00
Doron Behar
4a64b8d9f3 lammps-mpi: Use a generic extraBuildInputs instead of withMpi 
Add support for `extraCmakeFlags` as well and add `pkg-config` to
`nativeBuildInputs`.
 2023-06-21 23:03:57 +03:00
Nguyễn Gia Phong
558af1d8a5
klee: 2.3 -> 3.0 2023-06-21 18:16:44 +09:00
R. Ryantm
6884e85326 verilator: 5.010 -> 5.012 2023-06-21 03:43:32 +00:00
Weijia Wang
dca415554f treewide: replace mavenfod with buildMavenPackage 2023-06-20 19:59:30 +03:00
Weijia Wang
40001fa439 treewide: remove mavenfod overrides 2023-06-20 19:54:51 +03:00
Weijia Wang
9ce0974026 gephi: convert to mavenfod 2023-06-20 15:04:49 +03:00
Tillerino
13dd515a92 maven: adjust hashes of pull-maven-dependencies derivations 
Since the newer Maven pulls different versions of its own dependencies,
the hashes of these derivations all changed.
 2023-06-20 13:15:27 +02:00
Weijia Wang
bac33585a7
Merge pull request #238709 from wegank/digital-mavenfod 
digital: convert to mavenfod
 2023-06-20 11:59:15 +03:00
Weijia Wang
06f73278ea digital: convert to mavenfod 2023-06-20 09:53:15 +03:00
Philipp Middendorf
8cff0900bc
crystfel: fix x86_64 hash (#238606) 2023-06-20 08:32:03 +02:00
Markus Kowalewski
a9d8ac0b1e
openmolcas: fix hash 2023-06-19 15:11:32 +02:00
Weijia Wang
799c5a8032
Merge pull request #238330 from figsoda/egglog 
egglog: unstable-2023-05-22 -> unstable-2023-06-11
 2023-06-18 02:07:56 +03:00
Weijia Wang
0de9ad3cc4
Merge pull request #238321 from markuskowa/upd-openmolcas 
openmolcas: 23.02 -> 23.06
 2023-06-18 02:03:59 +03:00
figsoda
70f33f2777 egglog: unstable-2023-05-22 -> unstable-2023-06-11 
Diff: 5242b50051...c7ef8b000c
 2023-06-17 17:33:00 -04:00
Markus Kowalewski
cb5504b21c
openmolcas: 23.02 -> 23.06 2023-06-17 22:38:08 +02:00
Mario Rodas
2bd4a56ee1
Merge pull request #237950 from bcdarwin/bppsuite-fix-homepage 
bppsuite: fix homepage
 2023-06-16 18:28:27 -05:00
figsoda
eaebbdf59a
Merge pull request #238092 from NickCao/calcmysky 
calcmysky: 0.3.0 -> 0.3.1
 2023-06-16 12:28:14 -04:00
Weijia Wang
e44c81a3b8
Merge pull request #229525 from lopsided98/mavproxy-update 
mavproxy, python3Packages.pymavlink: update
 2023-06-16 16:12:53 +03:00
Nick Cao
f9eed769ca
calcmysky: add stellarium to tests 2023-06-16 21:12:50 +08:00
Nick Cao
c196ad4df9
calcmysky: 0.3.0 -> 0.3.1 
Diff: https://github.com/10110111/CalcMySky/compare/refs/tags/v0.3.0...v0.3.1
 2023-06-16 21:11:04 +08:00
Pol Dellaiera
610f62011e
Merge pull request #237742 from natsukium/kalign/init 
kalign: init at 3.3.5
 2023-06-16 08:20:55 +02:00
Ben Wolsieffer
99002aba8e mavproxy: 1.8.60 -> 1.8.62 2023-06-15 17:36:54 -04:00
Ben Darwin
9120f78e06 bppsuite: fix homepage 
Old homepage is down, so point to GitHub instead.
 2023-06-15 12:18:11 -04:00
Weijia Wang
169cb59498 calc: replace util-linux with unixtools.col 2023-06-15 14:25:40 +03:00
Théo Zimmermann
2bdeec6f84 coq: use dune_3 
This is needed to build Coq dev and is compatible with all current releases of Coq that require Dune.
 2023-06-14 14:33:36 +02:00
natsukium
7b36afffd6
kalign: init at 3.3.5 2023-06-14 21:05:58 +09:00
Weijia Wang
3f3ca021b7
Merge pull request #237633 from wegank/gplates-python39 
gplates: drop python39
 2023-06-14 00:59:31 +03:00
natsukium
3d1b9f0819 macs2: rename from MACS2 2023-06-13 21:47:47 +00:00
natsukium
12cab182ae MACS2: 2.2.7.1 -> 2.2.8 
Diff: https://github.com/macs3-project/MACS/compare/v2.2.7.1...v2.2.8
changelog: https://github.com/macs3-project/MACS/releases/tag/v2.2.8
 2023-06-13 21:47:47 +00:00
Weijia Wang
28af3205bc gplates: drop python39 2023-06-14 00:18:09 +03:00
Nick Cao
80dcc617f1
Merge pull request #236565 from natsukium/aragorn/update 
aragorn: 1.2.38 -> 1.2.41
 2023-06-13 03:51:58 -06:00
toastal
8201afb77f ocamlPackages.mtime: create 1.x fork for compat 
Slapped mtime_1 affected ocamlPackages
 2023-06-13 13:14:38 +07:00
R. Ryantm
bc62c28b22 jmol: 16.1.9 -> 16.1.13 2023-06-09 20:47:32 +00:00
Pol Dellaiera
f03155fc9f
Merge pull request #218669 from avdv/gephi-0.10.1 
gephi: 0.9.6 -> 0.10.1
 2023-06-08 14:15:44 +02:00
natsukium
597e4e8652
aragorn: fix format 
- use finalAttrs instead of rec
- add runHook
 2023-06-08 18:42:29 +09:00
natsukium
bb317093e8
aragorn: 1.2.38 -> 1.2.41 
- change the source and homepage
- change the license
 2023-06-08 18:42:24 +09:00
Doron Behar
5e87e91405
Merge pull request #235853 from doronbehar/pkg/lammps 
lammps: stable_29Oct2020 -> 23Jun2022_update4
 2023-06-08 11:33:38 +03:00
natsukium
f2d7b3381b
cmtk: 3.3.1 -> 3.3.2 2023-06-08 15:34:29 +09:00
Claudio Bley
2c9092a377 gephi: 0.9.6 -> 0.10.1 
* gephi requires Java 11 to run according to https://gephi.org/users/requirements/
 2023-06-07 22:43:49 +02:00
Doron Behar
9c99223666 lammps: Add backwards compatible link to lmp_serial 2023-06-07 18:09:36 +03:00
Doron Behar
64bed841a9 lammps: mark as broken for 32 bit lapack & blas 2023-06-07 18:09:36 +03:00
R. Ryantm
ca10cb55d9 dataexplorer: 3.7.7 -> 3.7.8 2023-06-06 05:47:41 +00:00
figsoda
40fbe215ac
Merge pull request #235807 from figsoda/egglog 2023-06-05 12:27:03 -04:00
Weijia Wang
bff97d5215
Merge pull request #235727 from r-ryantm/auto-update/diamond 
diamond: 2.1.6 -> 2.1.7
 2023-06-04 19:10:45 +02:00
Justin Bedő
4ae814f720
Merge pull request #234958 from NixOS/r-updates 
R,rPackages: R 4.2.3 -> 4.3.0
 2023-06-04 21:23:50 +10:00
R. Ryantm
1f231abe57 fastp: 0.23.3 -> 0.23.4 2023-06-04 03:21:21 +00:00
Doron Behar
66c6053b10 lammps: 29Oct2020 -> 23Jun2022_update4 2023-06-04 01:29:54 +03:00
figsoda
1f3b4712f5 egglog: init at unstable-2023-05-22 
https://github.com/egraphs-good/egglog
 2023-06-03 14:11:55 -04:00
Doron Behar
4994570ab3 lammps: Add doronbehar as maintainer 2023-06-03 15:40:20 +03:00
Doron Behar
f204873aa8
Merge pull request #213235 from Stunkymonkey/mathematica-deprecate-phases 
mathematica{9,10,11}: deprecate phases
 2023-06-03 11:47:36 +03:00
R. Ryantm
33d8777af9 diamond: 2.1.6 -> 2.1.7 2023-06-03 08:46:43 +00:00
R. Ryantm
a9be9ddb0e calc: 2.14.1.5 -> 2.14.1.6 2023-06-02 23:42:17 +00:00
Felix Buehler
04512a32bf mathematica{9,10,11}: deprecate phases 2023-06-02 18:10:52 +02:00
Luflosi
30446d830a
boinc: 7.22.1 -> 7.22.2 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.22%2F7.22.2
 2023-06-01 22:37:28 +02:00
R. Ryantm
7c4e31bb4c igv: 2.16.0 -> 2.16.1 2023-05-31 13:33:15 +00:00
Fabian Affolter
1921b5e06d
Merge pull request #235127 from r-ryantm/auto-update/gerbv 
gerbv: 2.9.6 -> 2.9.7
 2023-05-31 12:32:39 +02:00
Fabian Affolter
083530b578
gerbv: equalize 2023-05-31 09:02:13 +02:00
Fabian Affolter
dd0a325d94
gerbv: specify license 2023-05-31 08:59:23 +02:00
R. Ryantm
da2658d2c9 gerbv: 2.9.6 -> 2.9.7 2023-05-31 04:45:46 +00:00
Vincent Laporte
3b666b41c3 alt-ergo: 2.4.2 → 2.4.3 2023-05-31 06:06:49 +02:00
Justin Bedo
b8a6381d6a
R: 4.2.3 -> 4.3.0 2023-05-30 16:23:47 +10:00
R. Ryantm
71a23afb45 iqtree: 2.2.2.4 -> 2.2.2.6 2023-05-30 01:13:17 +00:00
Weijia Wang
6b0f1241eb
Merge pull request #234658 from evils/kicad 
kicad: 7.0.4 -> 7.0.5
 2023-05-29 00:03:09 +03:00
Sandro
5cef1d6b2e
Merge pull request #231661 from fedeinthemix/wip-wolfram-engine 2023-05-28 20:02:32 +02:00
Evils
0ba170d016 kicad: 7.0.4 -> 7.0.5 
7.0.4 not officially released :(
https://www.kicad.org/blog/2023/05/KiCad-7.0.5-Release/
 2023-05-28 19:21:29 +02:00
figsoda
4e1b566701
Merge pull request #234572 from r-ryantm/auto-update/seqtk 
seqtk: 1.3 -> 1.4
 2023-05-28 10:03:37 -04:00
Andres Navarro
68e77505ae openbugs: init at 3.2.3 2023-05-28 12:58:37 +00:00
natsukium
d515191577
autodock-vina: init at 1.2.3 2023-05-28 16:17:36 +09:00
R. Ryantm
bebbc418d4 seqtk: 1.3 -> 1.4 2023-05-28 06:48:51 +00:00
Robert Scott
2c9bea0eaa sharpsat-td: patch with updated version of mpreal/mpfrc++ 
this version is needed for mpfr 4.2.0+ support

lesson - don't merge old PRs without re-testing them yourself
 2023-05-27 20:49:34 +01:00
Robert Scott
cfbb8e82c6
Merge pull request #178159 from risicle/ris-sharpsat-td 
sharpsat-td: init at unstable-2021-09-05
 2023-05-27 15:47:31 +01:00
Weijia Wang
5b61dd80b9
Merge pull request #234313 from r-ryantm/auto-update/opensmt 
opensmt: 2.5.0 -> 2.5.1
 2023-05-27 02:34:54 +03:00
R. Ryantm
b954ef286d opensmt: 2.5.0 -> 2.5.1 2023-05-26 22:27:08 +00:00
Silvan Mosberger
5c042401b4 flatcam: fix build 2023-05-26 21:05:49 +02:00
Samuel Ainsworth
bbdb8416a0
Merge pull request #233851 from ConnorBaker/feat/cudnn_8_9_1 
cudaPackages.cudnn: version bumps; remove patch from name
 2023-05-26 10:26:30 -07:00
Weijia Wang
8d1f69a0fc
Merge pull request #234100 from r-ryantm/auto-update/blast 
blast: 2.13.0 -> 2.14.0
 2023-05-26 11:23:55 +03:00
Weijia Wang
af29900c15
Merge pull request #228313 from LeSuisse/gerbv-2.9.6 
pcb2gcode: 2.4.0 -> 2.5.0, gerbv: 2.7.0 -> 2.9.6, switch to the maintained fork
 2023-05-26 09:28:40 +03:00
R. Ryantm
216e1726da blast: 2.13.0 -> 2.14.0 2023-05-26 00:23:49 +00:00
figsoda
8014b08ee0 treewide/applications: use top-level fetchPypi 2023-05-25 10:51:30 -04:00
Weijia Wang
25906f0ea1
Merge pull request #233893 from evils/kicad 
kicad: 7.0.2 -> 7.0.4
 2023-05-25 15:35:50 +03:00
Weijia Wang
8a7c32b8cb ngspice: 37 -> 40 2023-05-25 11:16:36 +03:00
Evils
1687e83a47 kicad: 7.0.2 -> 7.0.4 2023-05-25 00:06:01 +02:00
Connor Baker
222d966273 cudaPackages.cudnn: remove patch version from name to conform with cudaPackages standard 2023-05-24 12:56:22 -04:00
Weijia Wang
915219ace4
Merge pull request #192219 from r-ryantm/auto-update/marvin 
marvin: 22.13.0 -> 23.4.0
 2023-05-24 02:11:57 +03:00
OTABI Tomoya
bb820fbaf6
apbs: init at 3.4.1 (#230644) 
* apbs: init at 3.4.1

* Update pkgs/applications/science/chemistry/apbs/default.nix

---------

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2023-05-23 01:10:16 +02:00
Weijia Wang
87ab85b584
Merge pull request #233445 from kilianar/lean-3.51.0 
lean: 3.50.3 -> 3.51.0
 2023-05-23 01:27:11 +03:00
Weijia Wang
9845f9dade
Merge pull request #229602 from r-ryantm/auto-update/clp 
clp: 1.17.7 -> 1.17.8
 2023-05-23 01:16:56 +03:00
Mauricio Collares
f5373a830b
Merge pull request #233453 from collares/sage-platforms 
sage: add meta.platforms
 2023-05-22 20:58:34 +02:00
pennae
229321224a
Merge pull request #233441 from evils/kicad 
kicad: make KICAD7_TEMPLATE_DIR a single path
 2023-05-22 19:25:12 +02:00
Mauricio Collares
c88e999122 sage: add meta.platforms 2023-05-22 18:30:39 +02:00
kilianar
41f1482be7 lean: 3.50.3 -> 3.51.0 
https://github.com/leanprover-community/lean/releases/tag/v3.51.0
 2023-05-22 18:10:56 +02:00
Evils
e1a80940a5 kicad: make KICAD7_TEMPLATE_DIR a single path 
workaround for the upstream issue of not searching a : separated path
 2023-05-22 17:43:27 +02:00
Ryan Lahfa
b6beee67f0
Merge pull request #233336 from smancill/shogun-fix-build 
shogun: fix build
 2023-05-22 13:47:52 +02:00
Sandro
1e71d2aa88
Merge pull request #218014 from collares/singular431p3 2023-05-22 13:27:15 +02:00
Weijia Wang
6d71b5d6de iqtree: set platforms 2023-05-22 11:14:57 +03:00
R. Ryantm
b36979ec74 iqtree: 2.2.0.4 -> 2.2.2.4 2023-05-22 04:48:16 +00:00
Sebastián Mancilla
70b3662a67 shogun: disable broken test 
Shogun has been broken for a while [0].

Looks like the latest update to openblas, by f07a0615ea (openblas:
0.3.20 -> 0.3.21, 2022-08-10), broke the `libshogun-mathematics_lapack`
example. It calculates the eigenvectors for a matrix, but the assertions
now fail:

    compute_eigenvectors
    A=[
    [       -0.500000000000000111,  0.707106781186547351,   0.5],
    [       0.707106781186547351,   1.04083408558608426e-16,        0.707106781186547129],
    [       -0.499999999999999722,  -0.707106781186547462,  0.5]
    ]
    eigenvalues=[-1.41421356237309492,1.04083408558608426e-17,1.41421356237309492]
    terminate called after throwing an instance of 'shogun::ShogunException'

The darwin build output shows a bit more detail:

    assertion is_equal(A(0,0), 0.5, eps) failed in void test_ev()
    file /tmp/nix-build-shogun-6.1.4.drv-0/source/examples/undocumented/libshogun/mathematics_lapack.cpp
    line 49

Disable the test to fix the build, although the results seem "correct".
It appears that openblas now calculates values with slightly less
precision, thus the assertion fails due to the expected epsilon.

[0]: https://hydra.nixos.org/build/194671473
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
61fc2d2c89 shogun: disable tests that take too long 
The checkPhase may take from 30 minutes up to 2 hours and 30 minutes on
Hydra due to these tests:

    [...]
    311/375 Test #311: libshogun-evaluation_cross_validation_classification ............   Passed  247.33 sec
    312/375 Test #313: libshogun-evaluation_cross_validation_mkl_weight_storage ........   Passed  428.31 sec
    315/375 Test #312: libshogun-evaluation_cross_validation_locked_comparison .........   Passed  880.44 sec
    341/375 Test #316: libshogun-evaluation_cross_validation_regression ................   Passed  380.48 sec
    342/375 Test #343: libshogun-modelselection_grid_search_kernel .....................   Passed 4866.85 sec
    343/375 Test #344: libshogun-modelselection_grid_search_linear .....................   Passed  574.78 sec
    345/375 Test #342: libshogun-modelselection_combined_kernel_sub_parameters .........   Passed 5929.90 sec
    375/375 Test #346: libshogun-modelselection_grid_search_multiclass_svm .............   Passed 1826.27 sec
    [...]
    Total Test time (real) = 9046.65 sec
    checkPhase completed in 2 hours 30 minutes 47 seconds
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
5873454b52 shogun: fix compiler warnings 
Fix warnings related to virtual destruction. Kinda important to fix.
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
c812170c74 shogun: refactor derivation 2023-05-21 22:34:00 -04:00
Mauricio Collares
c13e4258f6 sageWithDoc: run src/doc/bootstrap script before docbuild 2023-05-21 22:37:53 +02:00
Mauricio Collares
0edaaae3ff sage: 9.8 -> 10.0 2023-05-21 16:28:24 +02:00
Mauricio Collares
19bf4ba0e0 giac, giac-with-xcas: 1.9.0-29 -> 1.9.0-43 2023-05-21 16:25:47 +02:00
Mauricio Collares
51541df982 singular: 4.3.1p2 -> 4.3.2p1 2023-05-20 16:02:19 +02:00
Mauricio Collares
57c940b93d pari: 2.15.2 -> 2.15.3 2023-05-20 16:02:18 +02:00
Mauricio Collares
d2814c733a maxima-ecl-5_45: remove 2023-05-20 16:02:17 +02:00
figsoda
98b9e41f61 pkgs: fix typos 2023-05-19 22:31:04 -04:00
Weijia Wang
3ff23faf74
Merge pull request #232767 from r-ryantm/auto-update/dataexplorer 
dataexplorer: 3.7.6 -> 3.7.7
 2023-05-20 00:35:21 +03:00
R. Ryantm
1be8707a2c dataexplorer: 3.7.6 -> 3.7.7 2023-05-19 06:08:59 +00:00
Nick Cao
3947c72691
Merge pull request #232547 from r-ryantm/auto-update/cytoscape 
cytoscape: 3.9.1 -> 3.10.0
 2023-05-18 21:28:10 -06:00
Sandro
d6c1f83e99
Merge pull request #232477 from fabaff/strictdoc-fix 
strictdoc: 0.0.26 -> 0.0.40
 2023-05-19 02:32:24 +02:00
R. Ryantm
1c6e2cfbea cytoscape: 3.9.1 -> 3.10.0 2023-05-18 03:01:55 +00:00
Weijia Wang
7c6ca2791b
Merge pull request #231635 from natsukium/bwa/build-on-aarch64 
bwa: 0.7.17 -> unstable-2022-09-23
 2023-05-18 01:10:14 +03:00
Weijia Wang
55e5de416f isabelle-components.isabelle-linter: add platforms 2023-05-17 23:01:48 +03:00
Fabian Affolter
5e342e2a4b strictdoc: 0.0.26 -> 0.0.40 2023-05-17 20:34:49 +02:00
Andreas Vollert
44110aeb11 isabelle-linter: unstable-2022-09-05 -> 1.2.1 2023-05-17 17:42:07 +02:00
Guillaume Maudoux
33399c9de8
Merge pull request #229008 from whonore/dafny-4 
dafny: 2.3.0 -> 4.0.0
 2023-05-17 09:53:06 +02:00
Weijia Wang
184ab791ab
Merge pull request #232217 from r-ryantm/auto-update/primesieve 
primesieve: 11.0 -> 11.1
 2023-05-16 23:49:19 +03:00
R. Ryantm
e72d3d4709 primesieve: 11.0 -> 11.1 2023-05-16 10:45:23 +00:00
Nick Cao
1385ce47b7
Merge pull request #232076 from nagy/betaflight 
betaflight-configurator: reduce size
 2023-05-16 03:23:18 -06:00
Martin Weinelt
177eb5dd49
Merge pull request #231826 from mweinelt/scikitimage-alias 
python310Packages.scikit-image: rename from scikitimage
 2023-05-16 01:53:43 +02:00
Daniel Nagy
66f045a65f
betaflight-configurator: reduce size 
This reduces the size of the output from 512.5M to 233.9M.
 2023-05-15 21:00:00 +02:00
Rabjerg
1784646fc1
fritzing: added meta.mainProgram (#232059) 2023-05-15 21:16:15 +03:00
Nick Cao
906c7dd78c
Merge pull request #231975 from jbedo/fastp 
fastp: 0.23.2 -> 0.23.3
 2023-05-15 05:11:28 -06:00
natsukium
04dd7f41e7
bwa: add runHook 2023-05-15 16:13:49 +09:00
natsukium
c85dced23e
bwa: update license 2023-05-15 16:13:49 +09:00
natsukium
01ddcaa879
bwa: 0.7.17 -> unstable-2022-09-23 
Diff: https://github.com/lh3/bwa/compare/v0.7.17...139f68fc4c3747813783a488aef2adc86626b01b
 2023-05-15 16:13:45 +09:00
Ryan Lahfa
308ee09f2f
Merge pull request #231598 from natsukium/truvari/disable-tests-darwin 
truvari: disable some tests on darwin
 2023-05-15 09:09:09 +02:00
Justin Bedo
60c69da248
fastp: 0.23.2 -> 0.23.3 2023-05-15 15:03:24 +10:00
natsukium
7edb72db10
truvari: add patches to fix truvari anno 2023-05-15 10:01:38 +09:00
Sandro
a94d6c485b
Merge pull request #231516 from benwbooth/jbrowse 
jbrowse: init at 2.5.0
 2023-05-14 23:09:10 +02:00
Martin Weinelt
cddb66d655
python310Packages.scikit-image: rename from scikitimage 
to match the pname and create an alias for the former name.
 2023-05-14 13:04:10 +02:00
R. Ryantm
95832c2802 antiprism: 0.29 -> 0.30 2023-05-13 13:57:15 -03:00
Federico Beffa
9dd76ff79c wolfram-engine: add 13.2.0 2023-05-13 14:46:07 +02:00
Nick Cao
8dd605f358
eigenmath: unstable-2023-04-07 -> unstable-2023-05-12 2023-05-13 10:39:50 +08:00
Nick Cao
bd73712425
Merge pull request #231413 from pmiddend/crystfel-dependencies-update 
crystfel: update dependencies
 2023-05-13 10:02:59 +08:00
Ben Booth
fed8eeba5c jbrowse: init at 2.5.0 2023-05-12 11:24:26 -07:00
Markus Kowalewski
ceca790324
wxmacmolplt: fix typo 2023-05-12 10:41:17 +02:00
Philipp Middendorf
05f9ddb8b5 crystfel: update dependencies 2023-05-12 07:41:39 +02:00
Jonas Heinrich
7c863a8a9f
Merge pull request #231063 from Luflosi/update/boinc 
boinc: 7.22.0 -> 7.22.1
 2023-05-11 01:27:04 +02:00
Jonas Heinrich
af6e6808ac
Merge pull request #231066 from jbedo/subread 
subread: 2.0.5 -> 2.0.6
 2023-05-11 01:22:34 +02:00
sternenseemann
bd8335552e Merge remote-tracking branch 'origin/master' into haskell-updates 2023-05-10 16:32:00 +02:00
sternenseemann
dd6a74bdbe tamarin-prover: allow maude 3.1.1 
See https://github.com/tamarin-prover/tamarin-prover/pull/544.

Added tamarin-prover to passthru.tests of maude to prevent future
regressions of this kind.
 2023-05-10 16:30:39 +02:00
Sandro
4c07adb240
Merge pull request #230773 from SuperSandro2000/labplot-nix-run 2023-05-10 14:33:02 +02:00
Justin Bedo
c7a6773f8e
subread: 2.0.5 -> 2.0.6 2023-05-10 22:30:35 +10:00
Luflosi
2654a46c01
boinc: 7.22.0 -> 7.22.1 
https://github.com/BOINC/boinc/releases/tag/client_release/7.22/7.22.1
 2023-05-10 12:56:39 +02:00
Michael Gregson
886fa6e8af add myself to the maintainers list 
This is my second patch to the tlaplus package and I agreed to add
myself as a maintainer on my next contribution.
 2023-05-10 01:30:45 -05:00
Michael Gregson
be76fb11c9 tlaplus: remove jdk dependency 
As of b5d3526, this package fetches a pre-compiled TLA+ distribution
instead of compiling from source.
 2023-05-10 01:19:15 -05:00
Weijia Wang
419d7f9c8d
Merge pull request #230753 from fetsorn/typos 
several typos
 2023-05-09 19:16:12 +03:00
fetsorn
f14fbf0278 siesta: fix typos 
"manualy" -> "manually"
"becuase" -> "because"
 2023-05-09 18:02:16 +04:00
Weijia Wang
32c81c727a
Merge pull request #230831 from wegank/root-python 
python311Packages.hepmc3: fix build
 2023-05-09 12:12:10 +03:00
Weijia Wang
d63d6cb660 python311Packages.hepmc3: fix build 2023-05-09 11:28:25 +03:00
Sandro Jäckel
e4d83f7129
labplot: fix nix run .#labplot 2023-05-08 23:40:59 +02:00
Sandro
05b1a97381
Merge pull request #179752 from hqurve/cantor 
init labplot, cantor and supporting libraries
 2023-05-08 21:28:08 +02:00
markuskowa
2b54d8d84b
Merge pull request #230671 from markuskowa/upd-nwchem 
nwchem: 7.0.2 -> 7.2.0
 2023-05-08 17:03:50 +02:00
hqurve
842704c7cf
labplot: init at 2.10.0 2023-05-08 14:40:27 +02:00
hqurve
547071ee63
sage: expose sage-with-env 2023-05-08 14:40:26 +02:00
Markus Kowalewski
d6b6fd9544
nwchem: enable new features (dftd3, libxc, plumed) 2023-05-08 14:24:07 +02:00
Renato Garcia
9d1a27e2fd
snakemake: 7.14.2 -> 7.25.3 (#230524) 2023-05-08 02:05:40 -04:00
Sandro
33f9eb206e
Merge pull request #223411 from apraga/kent-with-include 
Kent: add headers to the package
 2023-05-07 16:29:16 +02:00
Weijia Wang
9b3763d117
Merge pull request #230393 from r-ryantm/auto-update/_4ti2 
_4ti2: 1.6.9 -> 1.6.10
 2023-05-07 10:44:33 +03:00
Robert Scott
8f4308a432
Merge pull request #229364 from jleightcap/jl/verilog-12.0 
verilog: 11.0 -> 12.0
 2023-05-06 21:47:30 +01:00
R. Ryantm
b9216e3e4f _4ti2: 1.6.9 -> 1.6.10 2023-05-06 20:43:07 +00:00
Weijia Wang
589e345207
Merge pull request #230330 from r-ryantm/auto-update/gnuastro 
gnuastro: 0.19 -> 0.20
 2023-05-06 21:01:30 +03:00
Alexis Praga
e027a5d836 kent: package headers too. 
This is needed for perlPackages.BioBigFile.
Removing NIX_BUILD_TOP.
 2023-05-06 19:48:14 +02:00
Jack Leightcap
4fdd191d65
verilog-12.0: installCheckPhase on supported arch 
Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-06 13:06:47 -04:00
Jack Leightcap
03ad8569fd
verilog-12.0: temp disable regression test suite 
Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-06 12:35:27 -04:00
Ilya
32fc1ceac6
qucs-s: 0.0.22 -> 1.0.2 (#223378) 
* qucs-s: 0.0.22->1.0.1 (including Qt4=>Qt5)

* qucs-s: Qt5->Qt6

* qucs-s: add qtwayland input as recommended for Qt6

Co-authored-by: Tungsten842 <quantmint@protonmail.com>

* qucs-s 1.0.1->1.0.2

---------

Co-authored-by: Tungsten842 <quantmint@protonmail.com>
 2023-05-06 16:28:29 +02:00
R. Ryantm
7ef62c2132 gnuastro: 0.19 -> 0.20 2023-05-06 12:26:20 +00:00
Jack Leightcap
48ac8a3bac
z3: 4.12.1 
https://github.com/Z3Prover/z3/releases/tag/z3-4.12.1

declare most recent minor version.

Signed-off-by: Jack Leightcap <jack.leightcap@trailofbits.com>
 2023-05-06 04:48:46 -04:00
Markus Kowalewski
621e086136 nwchem: 7.0.2 -> 7.2.0 2023-05-05 12:43:59 +02:00
Weijia Wang
830fb9f17b
Merge pull request #229863 from r-ryantm/auto-update/sherpa 
sherpa: 2.2.14 -> 2.2.15
 2023-05-04 14:37:34 +03:00
R. Ryantm
48fe29f726 sherpa: 2.2.14 -> 2.2.15 2023-05-04 09:55:53 +00:00
R. Ryantm
be4b60bf4f minimap2: 2.25 -> 2.26 2023-05-03 19:38:48 +00:00
Jörg Thalheim
255c9a8b83
Merge pull request #229536 from lopsided98/mission-planner-update 
mission-planner: 1.3.76 -> 1.3.80
 2023-05-03 16:29:13 +01:00
R. Ryantm
b74708700e verilator: 5.008 -> 5.010 2023-05-03 07:37:25 -05:00
Sandro
93640c56d1
Merge pull request #227420 from GaetanLepage/torchbin-update 
python3Packages.torch-bin: 1.13.1 -> 2.0.0
 2023-05-03 09:58:56 +02:00
R. Ryantm
d18c6089de clp: 1.17.7 -> 1.17.8 2023-05-03 05:21:09 +00:00
Weijia Wang
2992b28922
Merge pull request #229494 from bcdarwin/update-ants 
ants: 2.4.3 -> 2.4.4
 2023-05-03 00:25:01 +03:00
Ben Wolsieffer
9034073d25 mission-planner: 1.3.76 -> 1.3.80 2023-05-02 15:48:27 -04:00
Ben Wolsieffer
329c8a2e63 mavproxy: 1.8.59 -> 1.8.60 2023-05-02 15:20:58 -04:00
Ben Darwin
cf573698b1 ants: 2.4.3 -> 2.4.4 2023-05-02 12:29:21 -04:00
Daniel Nagy
8372789e47
qgroundcontrol: 4.2.4 -> 4.2.6 
Diff: https://github.com/mavlink/qgroundcontrol/compare/v4.2.4...v4.2.6
 2023-05-02 16:45:00 +02:00
Weijia Wang
ea4289e1f9 nvc: 1.9.1 -> 1.9.2 2023-05-02 11:02:08 +03:00
Luflosi
e97667163e
verilog: 11.0 -> 12.0 
https://github.com/steveicarus/iverilog/releases/tag/v12_0

Bump `iverilog` to 12.0, fixing two build failures:

1. autoconf now picks up on the unwrapped `x86_64-unknown-gnu-gcc` in
   path that fails at configurePhase to link executables.
   See: https://github.com/NixOS/nixpkgs/issues/21751
   fix/hack: define the `{CC,CXX}_FOR_BUILD` variables.
2. buildPhase generates a `-Werror=format-security` error. Backport
   the the upstream patch that fixed the warning very shortly after the
   release was cut.

And in the process,

- use post-install tests from `.github/test.sh` and as a result,
  remove the now unneeded clone of `ivtest`
- un-pin the verilog autoconf version

Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-01 17:46:06 -04:00
Weijia Wang
f2bef820c8
Merge pull request #228994 from r-ryantm/auto-update/minimap2 
minimap2: 2.24 -> 2.25
 2023-05-01 07:13:09 +03:00
R. Ryantm
6300f3bfb2 elan: 1.4.2 -> 1.4.5 2023-04-30 15:35:03 +00:00
Weijia Wang
41bfa33de5
Merge pull request #229083 from sikmir/pulseview 
pulseview: enable on darwin
 2023-04-30 14:39:16 +03:00
Nikolay Korotkiy
11b65fea77
pulseview: enable on darwin 2023-04-30 14:34:10 +04:00
Nikolay Korotkiy
5b9065da7e
pulseview: refactor 
* Remove Qt's mkDerivation in favour of stdenv.mkDerivation to fix https://github.com/NixOS/nixpkgs/issues/180841
* Move qttools to nativeBuildInputs
 2023-04-30 14:33:24 +04:00
whonore
c0c08de5b4 dafny: remove unused deps 2023-04-29 19:13:11 -04:00
whonore
d4f814d956 dafny: move to separate file 2023-04-29 19:11:12 -04:00
figsoda
3dcff817ee
Merge pull request #228998 from r-ryantm/auto-update/rofi-calc 
rofi-calc: 2.1.0 -> 2.2.0
 2023-04-29 19:07:58 -04:00
R. Ryantm
168782c6c5 rofi-calc: 2.1.0 -> 2.2.0 2023-04-29 22:12:20 +00:00