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7863 Commits

Author SHA1 Message Date
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
R. Ryantm
54a5899734 minimap2: 2.24 -> 2.25 2023-04-29 21:45:58 +00:00
Weijia Wang
317f78618e
Merge pull request #228880 from r-ryantm/auto-update/sumo 
sumo: 1.16.0 -> 1.17.0
 2023-04-30 00:24:48 +03:00
Gaetan Lepage
608908ed7a lit: move to python-modules 2023-04-29 13:53:50 +02:00
R. Ryantm
ec75148ca2 sumo: 1.16.0 -> 1.17.0 2023-04-29 09:39:15 +00:00
R. Ryantm
395db2896e bedtools: 2.30.0 -> 2.31.0 2023-04-29 03:05:55 +00:00
Weijia Wang
8fcab98a40
Merge pull request #228633 from NixOS/revert-226351-pr/root7 
Revert "root: enable root7"
 2023-04-28 22:56:05 +03:00
Austin Seipp
5e871533c4 verilator: 5.006 -> 5.008 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2023-04-28 04:40:45 -05:00
Austin Seipp
6a086197c2 verilator: wrap with glibc LOCALE_ARCHIVE iff stdenv.isLinux 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2023-04-28 04:40:45 -05:00
Dmitry Kalinkin
9092b9b5df Revert "root: enable root7 (#226351)" 
This reverts commit cafa2f02fb.
 2023-04-27 22:23:56 -04:00
Dmitry Kalinkin
af661f3be7
Revert "root: fix build on aarch64-darwin" 2023-04-27 18:36:02 -04:00
Weijia Wang
36302a3056 root: fix build on aarch64-darwin 2023-04-27 23:22:33 +03:00
Weijia Wang
7b57f59155
Merge pull request #218968 from pmiddend/crystfel-aarch64 
CrystFEL: support aarch64-linux and HDF5 on Darwin
 2023-04-26 19:32:54 +03:00
Thomas Gerbet
af92bfe9b3 gerbv: 2.7.0 -> 2.9.6, switch to the maintained fork 
The current 2.7.0 has a bunch of known vulnerabilities
(CVE-2021-40391, CVE-2021-40393, CVE-2021-40394, CVE-2021-40400, CVE-2021-40401, CVE-2021-40402 and CVE-2021-40403)
and is not maintained upstream.

A forked repository exists and is maintained. Debian/Ubuntu, Fedora and Homebrew have switched to it.

Changelogs:
https://github.com/gerbv/gerbv/releases/tag/v2.9.6
https://github.com/gerbv/gerbv/releases/tag/v2.9.5
https://github.com/gerbv/gerbv/releases/tag/v2.9.4
https://github.com/gerbv/gerbv/releases/tag/v2.9.3
https://github.com/gerbv/gerbv/releases/tag/v2.9.2
https://github.com/gerbv/gerbv/releases/tag/v2.9.1
https://github.com/gerbv/gerbv/releases/tag/v2.9.0
https://github.com/gerbv/gerbv/releases/tag/v2.8.2
 2023-04-26 13:40:47 +02:00
Henner Zeller
e3032b1d78 surelog: 1.45 -> 1.57 
Also, no vendored dependencies anymore, so we can fetch git
without submodules and use the libraries provided from
nix (flatbuffers, uhdm, gtest, antlr).
 2023-04-26 01:47:32 -05:00
Henner Zeller
d2831ca5da uhdm: 1.45 -> 1.57 
Also no vendored dependencies anymore, capnproto is now directly
used from nix, no third_party/ submodules are needed anymore.
 2023-04-26 01:47:32 -05:00
Weijia Wang
df05dd61c9
Merge pull request #227939 from natsukium/bedops/darwin 
bedops: fix build on darwin
 2023-04-26 01:14:58 +03:00
Weijia Wang
1923403c55
Merge pull request #227712 from r-ryantm/auto-update/workcraft 
workcraft: 3.3.9 -> 3.4.0
 2023-04-26 00:24:21 +03:00
Anderson Torres
88d37af1e9 calc: use overlay-style overridable attributes 2023-04-25 18:17:30 -03:00
Anderson Torres
c3a3f7737a calc: realign lists 2023-04-25 18:17:30 -03:00
Anderson Torres
f4a6e456c1 calc: use hash instead of sha256 2023-04-25 18:17:30 -03:00
Anderson Torres
580519cfcd calc: rewrite the arguments attrset 2023-04-25 18:17:30 -03:00
Anderson Torres
2137fe7093 calc: remove references to pname 2023-04-25 18:17:30 -03:00
Anderson Torres
fc519cb40b calc: refactor meta 2023-04-25 18:17:30 -03:00
Anderson Torres
1ee74c1439 calc: add meta.changelog 2023-04-25 18:17:30 -03:00
Weijia Wang
b3962d303c
Merge pull request #227524 from r-ryantm/auto-update/celestia 
celestia: 1.6.2.2 -> 1.6.3
 2023-04-26 00:11:11 +03:00
Ben Darwin
3a39edac80 elmerfem: 9.0 -> unstable-2023-02-03 
vtk_8_withQt5 -> vtkWithQt5
 2023-04-24 21:47:01 -04:00
natsukium
8d40a0ecaa
bedops: fix build on darwin 2023-04-24 22:11:47 +09:00
markuskowa
167d970ba8
Merge pull request #227870 from markuskowa/upd-gromacs 
gromacs: 2023 -> 2023.1
 2023-04-24 11:33:16 +02:00
markuskowa
7677c610e1
Merge pull request #227874 from markuskowa/upd-octopus 
octopus: 12.1 -> 12.2
 2023-04-24 10:48:49 +02:00
Nick Cao
ab7c128e3c
Merge pull request #227207 from natsukium/kent/update 
kent: 404 -> 446
 2023-04-24 10:03:16 +08:00
Sandro
9bc9cfe51d
Merge pull request #222660 from natsukium/hh-suite/init 2023-04-23 23:42:38 +02:00
Markus Kowalewski
94add42651
octopus: 12.1 -> 12.2 2023-04-23 21:53:05 +02:00
Markus Kowalewski
6cc2ab022a
gromacs: 2023 -> 2023.1 2023-04-23 21:36:32 +02:00
R. Ryantm
8af51c3628 workcraft: 3.3.9 -> 3.4.0 2023-04-23 00:06:26 +00:00
Nick Cao
99c4e7b895
Merge pull request #227170 from jbedo/subread 
subread: 2.0.4 -> 2.0.5
 2023-04-22 11:05:37 +08:00
R. Ryantm
3a14846ec7 celestia: 1.6.2.2 -> 1.6.3 2023-04-22 00:23:56 +00:00
Robert Schütz
2362848adf truvari: add natsukium to maintainers 2023-04-21 13:43:26 -07:00
Robert Schütz
ea468d9691 truvari: 2.1.1 -> 4.0.0 
Diff: https://github.com/spiralgenetics/truvari/compare/v2.1.1...v4.0.0
 2023-04-21 13:43:26 -07:00
Weijia Wang
34880cf0dc
Merge pull request #227313 from r-ryantm/auto-update/jags 
jags: 4.3.1 -> 4.3.2
 2023-04-21 21:37:51 +03:00
Weijia Wang
482e796513
Merge pull request #227292 from r-ryantm/auto-update/tlaplus 
tlaplus: 1.7.2 -> 1.7.3
 2023-04-21 00:07:16 +03:00
Weijia Wang
7026ff1bd9
Merge pull request #226579 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.114 -> 3.3.115
 2023-04-20 21:54:13 +03:00
R. Ryantm
98a12d5f89 jags: 4.3.1 -> 4.3.2 2023-04-20 18:41:59 +00:00
R. Ryantm
3012b98a08 tlaplus: 1.7.2 -> 1.7.3 2023-04-20 15:51:31 +00:00
Felix Schröter
1843807ba3
sad: remove old, unmaintained package 
The package isn't maintained and hasn't been exposed for a while.
Meanwhile there's been added a new package with the same name.
This change doesn't touch the new package.
 2023-04-20 11:26:01 +02:00
Weijia Wang
7ea26cf753
Merge pull request #227027 from wegank/lablgl-fix 
ocamlPackages.lablgl: unbreak on darwin
 2023-04-20 10:17:15 +03:00
natsukium
23205d28d2
kent: add missing information to the meta 2023-04-20 16:06:09 +09:00
natsukium
5b62152599
kent: add runHooks 2023-04-20 16:06:08 +09:00
natsukium
1e68ff3ee9
kent: 404 -> 446 
https://github.com/ucscGenomeBrowser/kent/compare/v404_base...v446_base
 2023-04-20 16:05:44 +09:00
Weijia Wang
17148b8f7d
Merge pull request #226929 from cransom/pcb2gcode-darwin 
pcb2gcode: fix build on darwin
 2023-04-20 09:53:22 +03:00
Nick Cao
e6a95d9628
Merge pull request #227036 from natsukium/tandem-aligner/v0.1 
tandem-aligner: unstable-2022-09-17 -> 0.1
 2023-04-20 09:17:52 +08:00
Casey Ransom
3ed1e3b268 pcb2gcode: fix build on darwin 
This version bumps gerbv as well.
 2023-04-19 21:15:54 -04:00
Justin Bedo
718170ed41
subread: 2.0.4 -> 2.0.5 2023-04-20 10:25:20 +10:00
Robert Scott
d32a852d2a
Merge pull request #226329 from risicle/ris-streamlit-1.21.0 
streamlit: 1.18.1 -> 1.21.0
 2023-04-19 18:12:10 +01:00
Dmitry Kalinkin
cafa2f02fb
root: enable root7 (#226351) 2023-04-19 10:28:26 -04:00
natsukium
e201b1556f
tandem-aligner: add changelog to meta 2023-04-19 21:23:21 +09:00
natsukium
14d7a73714
tandem-aligner: unstable-2022-09-17 -> 0.1 
https://github.com/seryrzu/tandem_aligner/releases/tag/v0.1
 2023-04-19 21:22:18 +09:00
Weijia Wang
c2c0c070cf glsurf: update platforms 2023-04-19 12:01:16 +03:00
natsukium
a272606614
hh-suite: init at 3.3.0 2023-04-19 10:32:35 +09:00
Artturi
9a1f5d4248
Merge pull request #226889 from Artturin/fixlints2 2023-04-18 21:52:21 +03:00
Artturin
eac28f38d6 treewide: fix lints 
Arg to lib.optional is a list

build time tool in buildInputs

*Flags not a list

https://github.com/nix-community/nixpkgs-lint
 2023-04-18 20:20:56 +03:00
7c6f434c
0a187c56e3
Merge pull request #226628 from natsukium/jmol/update 
jmol: 16.1.3 -> 16.1.9
 2023-04-18 15:29:43 +00:00
Sandro
555daa9d33
Merge pull request #221957 from natsukium/dssp/update 
dssp: 4.0.5 -> 4.2.2.1
 2023-04-18 16:34:17 +02:00
Sandro
db3d1dbe79
Merge pull request #226042 from collares/ipywidgets805 
python3Packages.ipywidgets: 8.0.4 -> 8.0.6
 2023-04-18 16:25:27 +02:00
Doron Behar
0c57b3ac86
Merge pull request #226645 from alyaeanyx/qalculate-4.6.1 
libqalculate, qalculate-gtk, qalculate-qt: 4.6.0 -> 4.6.1
 2023-04-17 09:36:08 -07:00
Thomas Tuegel
ccf7156d8d
Merge pull request #217974 from pxrl/pxrl/z3 
z3: 4.8.15 -> 4.8.17
 2023-04-17 10:03:07 -05:00
alyaeanyx
834c6bf777 libqalculate, qalculate-gtk, qalculate-qt: 4.6.0 -> 4.6.1 2023-04-17 15:42:23 +02:00
Nick Cao
e94b6203c9
Merge pull request #226546 from returntoreality/kstars-update 
kstars: 3.6.3 -> 3.6.4
 2023-04-17 19:47:39 +08:00
natsukium
23e78ca2fc
jmol: 16.1.3 -> 16.1.9 2023-04-17 17:53:08 +09:00
R. Ryantm
c806a5c121 gtkwave: 3.3.114 -> 3.3.115 2023-04-17 03:29:10 +00:00
Weijia Wang
9e47fc8658
Merge pull request #226455 from wegank/nvc-bump 
nvc: 1.9.0 -> 1.9.1
 2023-04-16 19:01:18 +03:00
R. Ryantm
f30febf830 form: 4.3.0 -> 4.3.1 2023-04-16 11:18:22 -04:00
Weijia Wang
4825f97fce nvc: 1.9.0 -> 1.9.1 2023-04-16 15:11:11 +03:00
Atemu
445ef28548
Merge pull request #225748 from Atemu/buildFHSEnvBubblewrap-by-default 
buildFHSEnv: use bubblewrap by default
 2023-04-16 13:03:36 +02:00
Atemu
f63a12f296 tree-wide: buildFHSUserEnv -> buildFHSEnv 2023-04-16 10:15:13 +02:00
Bobby Rong
2abbfae038
Merge pull request #226353 from kindrowboat/fix-nasc 
nasc: fix compile failure
 2023-04-16 09:40:48 +08:00
Stef Dunlap
79c4e8aaa8 nasc: fix compile failure 
Fix inspired by AUR patch: https://aur.archlinux.org/packages/nasc#comment-879822
 2023-04-15 17:18:12 -04:00
Weijia Wang
ea734f4e9a
Merge pull request #224357 from wegank/sasview-fix 
sasview: fix build
 2023-04-15 20:35:49 +03:00
Evils
cce076bd24 kicad-unstable: 2023-03-29 -> 2023-04-14 
workaround for upstream issue 14346 no longer needed
 2023-04-15 12:32:23 +02:00
Evils
534f790a75 kicad: 7.0.1 -> 7.0.2 2023-04-15 12:32:23 +02:00
Robert Scott
a604287fbe streamlit: 1.18.1 -> 1.21.0 2023-04-15 11:23:01 +01:00
Nick Cao
25e21b34a9
Merge pull request #226208 from panicgh/dataexplorer 
dataexplorer: 3.7.4 -> 3.7.6
 2023-04-15 11:30:56 +08:00
Weijia Wang
b5eaa9ffd9 stellarium: update darwin patches 2023-04-15 03:10:34 +03:00
Nicolas Benes
1f8eeba04f dataexplorer: 3.7.4 -> 3.7.6 2023-04-15 00:47:26 +02:00
natsukium
62943901dd
dssp: 4.0.5 -> 4.2.2.1 
https://github.com/PDB-REDO/dssp/compare/v4.0.5...v4.2.2.1
 2023-04-14 11:35:48 +09:00
Mauricio Collares
058dc0f6df sage: replace ipywidgets workaround by update patches 2023-04-13 22:15:27 +02:00
7c6f434c
8f8acb2140
Merge pull request #225723 from r-ryantm/auto-update/opensmt 
opensmt: 2.4.3 -> 2.5.0
 2023-04-13 08:54:55 +00:00
Nick Cao
2833fc3981
Merge pull request #225841 from natsukium/mafft/update 
mafft: 7.515 -> 7.520
 2023-04-13 09:15:12 +08:00
Robert Scott
2107f7de60
Merge pull request #225865 from bzizou/samtools 
samtools: 1.13 -> 1.17
 2023-04-13 00:10:42 +01:00
Bruno Bzeznik
d69d242b7b Samtools: 1.13 -> 1.17 
Changelogs:
 - https://github.com/samtools/samtools/releases/tag/1.14
 - https://github.com/samtools/samtools/releases/tag/1.15
 - https://github.com/samtools/samtools/releases/tag/1.15.1
 - https://github.com/samtools/samtools/releases/tag/1.16
 - https://github.com/samtools/samtools/releases/tag/1.16.1
 - https://github.com/samtools/samtools/releases/tag/1.17
 2023-04-12 12:00:25 +02:00
Sandro
b0989ca61b
Merge pull request #222632 from panicgh/spdlog-upd 
tiledb: 2.3.3 -> 2.8.3, spdlog: 1.10.0 -> 1.11.0, spdlog_0: remove
 2023-04-12 10:57:23 +02:00
natsukium
f962206f94
mafft: 7.515 -> 7.520 
https://gitlab.com/sysimm/mafft/-/tags/v7.520
 2023-04-12 13:28:24 +09:00
Nick Cao
47f3cca66d
Merge pull request #225265 from NickCao/eigenmath 
eigenmath: unstable-2023-03-05 -> unstable-2023-04-07
 2023-04-12 11:45:15 +08:00
R. Ryantm
2ed32c48a5 primecount: 7.7 -> 7.8 2023-04-11 15:08:24 -03:00
R. Ryantm
84dbda044f opensmt: 2.4.3 -> 2.5.0 2023-04-11 10:26:10 +00:00
Sandro
23e55a367e
Merge pull request #223068 from MarcFontaine/master 2023-04-10 21:52:29 +02:00
Weijia Wang
282c22a4d2 nvc: 1.8.2 -> 1.9.0 2023-04-10 13:34:15 +03:00
Dmitry Kalinkin
df3bf8ff76
Merge pull request #218331 from xworld21/texlive-new-dependency-resolution 
texlive.combine: move dependencies to attribute tlDeps, resolve them …
 2023-04-09 23:59:45 -04:00
Sandro
08d2ac8dbc
Merge pull request #186127 from ShamrockLee/raspa2 2023-04-09 18:42:37 +02:00
Linus Karl
e7997ece6e kstars: 3.6.3 -> 3.6.4 
Changelog: 85dfd8fb6e/ChangeLog
 2023-04-08 22:03:04 +02:00
Nick Cao
027d18d6a7
eigenmath: enable tests 2023-04-08 23:19:59 +08:00
Nick Cao
16d7f06261
eigenmath: unstable-2023-03-05 -> unstable-2023-04-07 2023-04-08 15:00:16 +08:00
Nick Cao
6c38c33f01
eigenmath: add updateScript 2023-04-08 14:58:35 +08:00
github-actions[bot]
ee14a276ab
Merge master into haskell-updates 2023-04-07 00:11:54 +00:00
Justin Bedő
642ee2373c
Merge pull request #224827 from r-ryantm/auto-update/varscan 
varscan: 2.4.5 -> 2.4.6
 2023-04-06 22:51:16 +10:00
Nicolas Benes
3e886954ee spdlog: 1.10.0 -> 1.11.0 
Unpin from fmt_8.
 2023-04-06 07:25:19 +02:00
github-actions[bot]
6a7b8348a1
Merge master into haskell-updates 2023-04-06 00:11:55 +00:00
Sandro
5ea854454e
Merge pull request #224359 from hesiod/coin-utils 2023-04-06 01:08:07 +02:00
R. Ryantm
8fcdc3f62c varscan: 2.4.5 -> 2.4.6 2023-04-05 14:55:31 +00:00
Ellie Hermaszewska
bd54a9047d
tamarin-prover: Allow compiling with maude-3.3 2023-04-05 14:39:55 +08:00
Ryan Lahfa
ce35e61c3c
Merge pull request #221099 from evils/kicad 
kicad(-unstable): bump to latest version, cleanup and fixes
 2023-04-04 13:28:26 +02:00
Shamrock Lee
4e72d111e9 raspa: init at 2.0.47 and add tests 2023-04-03 20:53:23 +08:00
Weijia Wang
64a5b00d02
Merge pull request #224462 from wegank/scalp-mirror 
scalp: update mirror link
 2023-04-03 14:48:41 +03:00
Weijia Wang
4ad85a5c10 scalp: update mirror link 2023-04-03 14:16:03 +03:00
Tobias Markus
eae9398010 clp: Change license to epl20 2023-04-03 12:57:50 +02:00
Weijia Wang
150dcd7ce7
Merge pull request #224345 from natsukium/blast/darwin 
blast-bin: init at 2.13.0
 2023-04-03 09:59:08 +03:00
natsukium
cddb4a24ba
blast-bin: init at 2.13.0 2023-04-03 12:39:17 +09:00
Nick Cao
7613d23e78
Merge pull request #224414 from jbedo/last 
last: 1447 -> 1453
 2023-04-03 09:43:13 +08:00
Justin Bedo
e739dc5088
last: 1447 -> 1453 2023-04-03 08:38:27 +10:00
Vincenzo Mantova
acb02e2fab eukleides: move texlive dependencies to tlDeps 2023-04-02 13:00:52 +01:00
Tobias Markus
1718fc0b04 clp: 1.17.6 -> 1.17.7 2023-04-02 14:00:47 +02:00
Weijia Wang
4213fc7cde sasview: fix build 2023-04-02 15:00:07 +03:00
Vincenzo Mantova
6b2b9a0de3 eukleides: create pkgs fixpoint for texlive using mkDerivation 2023-04-02 12:58:47 +01:00
Nicolas Benes
c59f6c75b6 openroad: unstable-2022-07-19 -> unstable-2023-03-31 2023-04-02 05:44:19 +02:00
natsukium
5ac95120d5
pymol: remove broken mark for darwin 
The bug has been resolved by changing the backend to Qt
in this commit, ab3f0771a4.
 2023-04-01 20:41:01 +09:00
Michal Sojka
b1cb42d3b7 cppzmq: make zeromq propagatedBuildInput 
cppzmq is a header-only library. As such, it is not much useful
without zeromq, whose headers it includes. By having zeromq in
propagatedBuildInputs, we can simplify dependent expressions.

This change is motivated by
https://github.com/lopsided98/nix-ros-overlay/issues/255#issuecomment-1487590226.
The expressions in nix-ros-overlay are automatically generated and
since packages in other distributions where ROS runs need not to
explicitly depend on zeromq, the Nix expression should behave the
same. This way, nix-ros-overlay will not to have manually
patch/overlay the automatically generated expressions.
 2023-03-31 18:58:56 +02:00
Evils
23849267ee kicad-unstable: fix ngspice tests 2023-03-30 18:53:53 +02:00
MarcFontaine
2cfc128ca3
nanovna-saver: 0.5.4 -> 0.6.0 2023-03-30 10:58:55 +02:00
Evils
4f0de9463a kicad-unstable: 2023-02-14 -> 2023-03-29 
includes a fix for upstream issue 14346
  (attempting to installing pcbnew.py outside of $out)
 2023-03-30 09:22:08 +02:00
Nick Cao
2f73fede2a
calcmysky: unstable-2023-02-11 -> 0.3.0 
Diff: c5f2814528...v0.3.0
 2023-03-29 19:29:46 +08:00
Weijia Wang
626401c783
Merge pull request #220832 from wegank/glucose-bump 
glucose: 4.1 -> 4.2.1
 2023-03-29 09:13:21 +03:00
Weijia Wang
396b3b7271
Merge pull request #223075 from r-ryantm/auto-update/ginac 
ginac: 1.8.5 -> 1.8.6
 2023-03-29 00:27:26 +03:00
Mauricio Collares
a4f8bf2248
Merge pull request #223497 from r-ryantm/auto-update/primecount 
primecount: 7.6 -> 7.7
 2023-03-28 20:28:02 +02:00
Evils
7f3a08710a kicad: add requests runtime dependency 
required for some of the plugins
 2023-03-28 18:57:29 +02:00
Evils
d8020e1e17 kicad: remove withOCC and more cmakeFlags cleanup 
OCC is no longer optional
RPATH apparently no longer contains references to /build/
KICAD_SCRIPTING_WXPYTHON is ON by default

sort some of the options a bit

and remove stray lndir
 2023-03-28 18:57:29 +02:00
Evils
788df5456b kicad: 7.0.0 -> 7.0.1 
remove now integrated patches
 2023-03-28 18:57:29 +02:00
Weijia Wang
eac1ecb55a
Merge pull request #222531 from r-ryantm/auto-update/sumo 
sumo: 1.15.0 -> 1.16.0
 2023-03-28 16:47:07 +03:00
Nick Cao
98f3b08f58
Merge pull request #223453 from kilianar/stellarium-23.1 
stellarium: 1.2 -> 23.1
 2023-03-28 18:29:13 +08:00
Ali Caglayan
8fe1ea496b coq: 8.16.1 -> 8.17.0 
Signed-off-by: Ali Caglayan <alizter@gmail.com>
 2023-03-28 08:13:12 +02:00
R. Ryantm
3b3cc65701 primecount: 7.6 -> 7.7 2023-03-28 04:37:03 +00:00
kilianar
d19f5dedec stellarium: 1.2 -> 23.1 
https://github.com/Stellarium/stellarium/releases/tag/v23.1

Mitigates https://github.com/advisories/GHSA-7vmm-m8vp-g5h3
 2023-03-28 00:22:36 +02:00
kilianar
733e7c52c2 calcmysky: 0.2.1 -> unstable-203-02-11 2023-03-28 00:03:32 +02:00
Weijia Wang
c9d051b17d
Merge pull request #222979 from r-ryantm/auto-update/cvc5 
cvc5: 1.0.4 -> 1.0.5
 2023-03-27 09:36:32 +03:00
Sandro
c2ef479b62
Merge pull request #168773 from Leixb/megam-add-opt 2023-03-27 00:59:44 +02:00
Justin Bedő
c39e3d9b74
Merge pull request #221546 from NixOS/r-updates 
R: 4.2.2 -> 4.2.3
 2023-03-26 21:40:30 +00:00
github-actions[bot]
07fb9cae4e
Merge master into staging-next 2023-03-26 00:02:45 +00:00
Artturi
b213126ec0
Merge pull request #222766 from Artturin/fix-different-store 2023-03-25 22:17:07 +02:00
R. Ryantm
2cb2ee9630 ginac: 1.8.5 -> 1.8.6 2023-03-25 14:10:42 +00:00
R. Ryantm
bb270775f2 cvc5: 1.0.4 -> 1.0.5 2023-03-25 01:00:12 +00:00
github-actions[bot]
cead7e3e73
Merge master into staging-next 2023-03-25 00:02:20 +00:00
Weijia Wang
2ce97f2bf9
Merge pull request #222464 from r-ryantm/auto-update/diamond 
diamond: 2.1.5 -> 2.1.6
 2023-03-24 20:56:17 +02:00
Artturin
780669daf5 treewide: don't hardcode /nix/store (no rebuilds changes) 
improve experience for other store locations
 2023-03-24 20:11:33 +02:00
github-actions[bot]
adec6862c5
Merge master into staging-next 2023-03-24 18:01:06 +00:00
LeixB
d443805fe3
megam: add leixb as maintainer 2023-03-24 18:52:48 +01:00
LeixB
d85fae35d9
megam: add megam.opt binary 
- Add megam.opt (optimized native binary)
 2023-03-24 18:52:14 +01:00
Vladimír Čunát
1f1c1739d7
Merge #222442: R: override test for curl version 
...into staging-next
 2023-03-23 11:07:36 +01:00
R. Ryantm
d2bf9653de gretl: 2022c -> 2023a 2023-03-23 06:03:08 +00:00
github-actions[bot]
85f7b5276e
Merge master into staging-next 2023-03-22 18:01:11 +00:00
Luflosi
ddb714f68d
yices: fix typo in comment 2023-03-22 16:08:09 +01:00
Weijia Wang
120a484726
Merge pull request #220001 from wegank/isabelle-arm 
isabelle: add aarch64-linux support
 2023-03-22 16:15:34 +02:00
R. Ryantm
91c2c00aad sumo: 1.15.0 -> 1.16.0 2023-03-22 12:07:12 +00:00
github-actions[bot]
0537539006
Merge master into staging-next 2023-03-22 12:01:22 +00:00
Nick Cao
6c4095e7af
Merge pull request #222331 from r-ryantm/auto-update/seqkit 
seqkit: 2.3.1 -> 2.4.0
 2023-03-22 16:08:39 +08:00
R. Ryantm
4c2324cf14 diamond: 2.1.5 -> 2.1.6 2023-03-22 03:09:40 +00:00
MaxHearnden
bfbc0f56e5 override test for curl version 2023-03-21 22:50:14 +00:00
Vincent Laporte
48774c43cd
acgtk: use Dune 3 2023-03-21 13:05:53 +01:00
R. Ryantm
a6f33bd62f seqkit: 2.3.1 -> 2.4.0 2023-03-21 10:45:22 +00:00
R. Ryantm
4da1bc0bfa marvin: 22.13.0 -> 23.4.0 2023-03-21 07:22:28 +00:00