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Author SHA1 Message Date
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
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
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 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