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7717 Commits

Author SHA1 Message Date
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
github-actions[bot]
bb48723d63
Merge master into staging-next 2023-03-21 00:02:39 +00:00
Vincent Laporte
e12230e716
why3: 1.5.1 → 1.6.0; ocamlPackages.lambdapi: 2.2.1 → 2.3.1 (#220986) 
why3: 1.5.1 → 1.6.0
ocamlPackages.lambdapi: 2.2.1 → 2.3.1

Co-authored-by: Weijia Wang <9713184+wegank@users.noreply.github.com>
 2023-03-20 20:45:47 +01:00
Martin Weinelt
9959ec97f8
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
- pkgs/development/python-modules/wxPython/4.0.nix
- pkgs/development/python-modules/wxPython/4.1.nix
 2023-03-20 15:07:36 +01:00
Weijia Wang
802b7ac3e7
Merge pull request #221743 from r-ryantm/auto-update/gatk 
gatk: 4.3.0.0 -> 4.4.0.0
 2023-03-20 14:33:37 +02:00
github-actions[bot]
96f7385465
Merge master into staging-next 2023-03-20 00:02:29 +00:00
Mauricio Collares
bd3de7859d
Merge pull request #221718 from wegank/sage-fix 
sage: add libpng to sagelib, import package update patches
 2023-03-19 19:31:02 +01:00
github-actions[bot]
84c97a9e91
Merge master into staging-next 2023-03-19 18:00:59 +00:00
Weijia Wang
2572ddc706
Merge pull request #221977 from wegank/mavproxy-wx 
mavproxy: migrate to wxPython_4_2
 2023-03-19 20:00:39 +02:00
Weijia Wang
a1e27cf0e9 sage: add libpng to sagelib 2023-03-19 19:33:36 +02:00
Mauricio Collares
c13d98c7bf sage: import python package upgrade fixes 2023-03-19 19:32:56 +02:00
natsukium
21affa5ff1
trf: init at 4.09.1 2023-03-19 22:25:42 +09:00
Weijia Wang
4fe9738427 mavproxy: migrate to wxPython_4_2 2023-03-19 10:29:51 +02:00
github-actions[bot]
c70342c89c
Merge master into staging-next 2023-03-19 00:02:27 +00:00
Weijia Wang
7574e25ef3
Merge pull request #221864 from natsukium/mafft/update 
mafft: 7.508 -> 7.515
 2023-03-19 00:03:19 +02:00
Weijia Wang
8da8071e37 glucose: 4.1 -> 4.2.1 2023-03-18 22:17:16 +02:00
github-actions[bot]
403b148aa5
Merge master into staging-next 2023-03-18 18:01:02 +00:00
Weijia Wang
0ddc01c569 glucose: refactor 2023-03-18 19:00:45 +02:00
natsukium
f3b75ef3ce
mafft: 7.508 -> 7.515 2023-03-19 00:42:29 +09:00
Weijia Wang
f15cf7e6af
Merge pull request #221809 from wegank/nest-bump 
nest: 3.3 -> 3.4
 2023-03-18 17:17:18 +02:00
github-actions[bot]
a912b83051
Merge master into staging-next 2023-03-18 12:01:30 +00:00
Weijia Wang
b45fe715d9
Merge pull request #217922 from r-ryantm/auto-update/openboardview 
openboardview: 9.0.3 -> 9.95.0
 2023-03-18 13:00:52 +02:00
Fabian Affolter
109f8ccdfe
nest: specify license 2023-03-18 11:23:52 +01:00
Fabian Affolter
c7ec291235
nest: add changelog to meta 2023-03-18 11:23:06 +01:00
Weijia Wang
ea847dd1a0 nest: 3.3 -> 3.4 2023-03-18 12:13:46 +02:00
R. Ryantm
0d44f838ca gatk: 4.3.0.0 -> 4.4.0.0 2023-03-18 01:10:14 +00:00
K900
a5a292c7a8 treewide: clear out remaining qt5 conditionals 2023-03-18 02:10:20 +03:00
github-actions[bot]
d761f69867
Merge master into staging-next 2023-03-17 17:57:00 +00:00
Markus Kowalewski
545b5d04f4
openmolcas: 22.10 -> 23.02 2023-03-17 13:33:41 +01:00
github-actions[bot]
2394986204
Merge master into staging-next 2023-03-17 12:01:17 +00:00
Weijia Wang
9c8a92bcde
Merge pull request #205310 from r-ryantm/auto-update/sumo 
sumo: 1.9.2 -> 1.15.0
 2023-03-17 12:56:48 +02:00
github-actions[bot]
f5629a4518
Merge master into staging-next 2023-03-17 06:01:16 +00:00
Weijia Wang
854414836c
Merge pull request #221529 from wegank/qalculate-qt-darwin 
qalculate-qt: add darwin support
 2023-03-17 07:47:56 +02:00
Justin Bedő
bf32c70253
Merge pull request #221559 from r-ryantm/auto-update/subread 
subread: 2.0.3 -> 2.0.4
 2023-03-17 01:57:57 +00:00
github-actions[bot]
6746017444
Merge master into staging-next 2023-03-17 00:02:33 +00:00
R. Ryantm
2a35b86739 subread: 2.0.3 -> 2.0.4 2023-03-16 23:09:44 +00:00
markuskowa
0fea9287f4
Merge pull request #221301 from sheepforce/plumed 
plumed: init at 2.8.2
 2023-03-16 20:43:54 +01:00
Weijia Wang
5c214fb163 qalculate-qt: add darwin support 2023-03-16 21:31:51 +02:00
github-actions[bot]
455127ad5e
Merge master into staging-next 2023-03-16 18:01:20 +00:00
Weijia Wang
183c970c9a
Merge pull request #221403 from r-ryantm/auto-update/gama 
gama: 2.23 -> 2.24
 2023-03-16 18:03:12 +02:00
Weijia Wang
de6210e074
Merge pull request #217539 from GenericNerdyUsername/horizon-occ 
horizon-eda: switch from OCE to OCC
 2023-03-16 17:20:47 +02:00
Bernardo Meurer
6e55733359
Merge pull request #219747 from Stunkymonkey/deprecate-isNull 2023-03-16 11:10:22 -03:00
Phillip Seeber
09b52c631a cp2k: enable plumed plugin 
cp2k: enable plumed plugin


cp2k: use mpicxx to figure out link lines
 2023-03-16 14:30:27 +01:00
github-actions[bot]
80a0ae17b5
Merge master into staging-next 2023-03-16 12:01:29 +00:00
Vladimír Čunát
0f9354bfee
Merge #218309: ffmpeg: ffmpeg_4 → ffmpeg_5 
...into staging
 2023-03-16 11:11:31 +01:00
Weijia Wang
b3e468975f
Merge pull request #221402 from r-ryantm/auto-update/uarmsolver 
uarmsolver: 0.2.4 -> 0.2.5
 2023-03-16 09:09:24 +02:00