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5949 Commits

Author SHA1 Message Date
Jakub Dupak
b72a99d718 QtRVSim: 0.9.1 -> 0.9.2 2022-03-14 22:04:17 +02:00
Alyssa Ross
d7e181ff83
Merge remote-tracking branch 'nixpkgs/staging-next' into staging 
Conflicts:
	pkgs/development/compilers/ocaml/4.12.nix
	pkgs/development/python-modules/oci/default.nix
	pkgs/tools/admin/bubblewrap/default.nix
 2022-03-14 12:33:16 +00:00
github-actions[bot]
0ed928e4ab
Merge master into staging-next 2022-03-14 12:01:26 +00:00
Mauricio Collares
5240cbc0d8 sage: adapt tachyon interface for 0.99.3 2022-03-13 16:53:22 -03:00
R. Ryantm
6d61669d69 jmol: 14.32.30 -> 14.32.33 2022-03-13 16:20:57 +00:00
github-actions[bot]
1630ab9b47
Merge master into staging-next 2022-03-13 06:05:11 +00:00
Jakub Dupak
d09489e5f1
QtRvSim: init at 0.9.1 (#163128) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-03-13 03:08:40 +01:00
github-actions[bot]
6f7d104254
Merge master into staging-next 2022-03-13 00:02:14 +00:00
Sandro
529b89d755
Merge pull request #161434 from collares/lean-3.40.0 2022-03-12 23:43:20 +01:00
Sandro
8057801ad7
Merge pull request #163849 from fedeinthemix/add-xschem-2 2022-03-12 22:32:08 +01:00
R. Ryantm
29d7a27d9f opensmt: 2.2.0 -> 2.3.0 2022-03-12 17:44:51 +00:00
Federico Beffa
5d702c6b23 gaw: init at version 20200922 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-03-12 17:50:10 +01:00
Federico Beffa
a40de4b146 xschem: init at version 3.0.0 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-03-12 17:49:48 +01:00
github-actions[bot]
a9a2d9475d
Merge staging-next into staging 2022-03-11 18:01:59 +00:00
github-actions[bot]
7573d7fe79
Merge master into staging-next 2022-03-11 18:01:20 +00:00
Renaud
28721c55c5
Merge pull request #160342 from Luflosi/update/yosys 
yosys: 0.12+54 -> 0.15
 2022-03-11 18:15:51 +01:00
Mauricio Collares
bab25a7a3a lean: 3.40.0 -> 3.41.0 2022-03-11 11:40:27 -03:00
R. Ryantm
f764458ed2 siril: 0.99.10.1 -> 1.0.0 2022-03-10 22:40:03 +00:00
Justin Bedo
3739a7819d
R: 4.1.2 -> 4.1.3 2022-03-10 22:31:13 +11:00
github-actions[bot]
f6b4a4048a
Merge staging-next into staging 2022-03-09 12:01:59 +00:00
github-actions[bot]
201cc2f89b
Merge master into staging-next 2022-03-09 00:02:05 +00:00
Luflosi
0e4d199cbd
abc-verifier: 2021.11.12 -> 2022.03.04 2022-03-08 18:28:13 +01:00
R. Ryantm
e0c3da7946 jmol: 14.32.28 -> 14.32.30 2022-03-08 16:34:40 +00:00
github-actions[bot]
69e1d85d54
Merge staging-next into staging 2022-03-06 18:01:46 +00:00
github-actions[bot]
68a45fb1f2
Merge master into staging-next 2022-03-06 18:01:10 +00:00
R. Ryantm
f3288c60f0 marvin: 22.3.0 -> 22.7.0 2022-03-06 07:45:27 +00:00
github-actions[bot]
6933fb31ab
Merge staging-next into staging 2022-03-06 06:01:40 +00:00
github-actions[bot]
3f8e60728f
Merge master into staging-next 2022-03-06 06:01:06 +00:00
Bobby Rong
cf7e4cac05
Merge pull request #161194 from wucke13/mission-planner 
mission-planner: 1.3.74 -> 1.3.76
 2022-03-06 13:28:50 +08:00
github-actions[bot]
90f82a2f9a
Merge staging-next into staging 2022-03-06 00:02:44 +00:00
github-actions[bot]
9dd2a8b600
Merge master into staging-next 2022-03-06 00:02:10 +00:00
Dmitry Kalinkin
149d68268d
root: fix ROOTConfig.cmake.in patching 2022-03-04 21:04:19 -05:00
github-actions[bot]
a072933f52
Merge staging-next into staging 2022-03-05 00:02:27 +00:00
github-actions[bot]
d4bfb57f40
Merge master into staging-next 2022-03-05 00:01:54 +00:00
7c6f434c
d5058ae9e5
Merge pull request #162688 from r-ryantm/auto-update/jmol 
jmol: 14.32.24 -> 14.32.28
 2022-03-04 20:43:10 +00:00
github-actions[bot]
d3cf053b7f
Merge staging-next into staging 2022-03-04 18:01:54 +00:00
github-actions[bot]
437813752b
Merge master into staging-next 2022-03-04 18:01:19 +00:00
Bruno Bzeznik
7d62054650 angsd: init at 0.937 2022-03-04 09:17:35 -06:00
Alyssa Ross
c010a19a56
Merge remote-tracking branch 'nixpkgs/staging-next' into staging 
Conflicts:
	pkgs/development/python-modules/hypothesmith/default.nix
 2022-03-04 14:53:05 +00:00
github-actions[bot]
fc22d0d5e2
Merge master into staging-next 2022-03-04 12:01:33 +00:00
Matthew Wakefield
e85b65f986
minimap2: enable aarch64 builds (#161169) 
Co-authored-by: Bobby Rong <rjl931189261@126.com>
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-03-04 12:27:29 +01:00
R. Ryantm
f5258a7d12 jmol: 14.32.24 -> 14.32.28 2022-03-03 23:44:55 +00:00
github-actions[bot]
18a9a18e2b
Merge staging-next into staging 2022-03-02 12:10:55 +00:00
github-actions[bot]
12423e2e92
Merge master into staging-next 2022-03-02 12:05:47 +00:00
R. Ryantm
04ee1b8975 phd2: 2.6.10 -> 2.6.11 2022-03-02 03:13:28 +00:00
Justin Bedo
89eff15f31
last: 1260 -> 1268 2022-03-02 13:35:56 +11:00
Jan van Brügge
c1ef185bdb
isabelle: Use naproche from nixpkgs 2022-03-01 13:43:38 +01:00
Jan van Brügge
2b71e68503
naproche: init at 0.1.0.0 2022-03-01 13:43:37 +01:00
github-actions[bot]
fbd1c5b484
Merge staging-next into staging 2022-03-01 12:11:43 +00:00
github-actions[bot]
4ae3f9a06c
Merge master into staging-next 2022-03-01 12:05:54 +00:00
Gabriel Ebner
8934eb7c91
Merge pull request #157843 from jvanbruegge/isabelle_setup 
isabelle: Rebuild isabelle_setup.jar
 2022-03-01 12:11:25 +01:00
zowoq
64a89aac86 Merge staging-next into staging 
Conflicts:
	pkgs/development/libraries/sqlite/default.nix
 2022-03-01 16:20:52 +10:00
R. Ryantm
de0ff65232 cwltool: 3.1.20220221074232 -> 3.1.20220224085855 2022-03-01 03:46:50 +00:00
grnnja
b6c7526d3a
jflap: init at 7.1 2022-02-28 17:12:08 -08:00
github-actions[bot]
bfb0bc0461
Merge master into staging-next 2022-02-28 18:05:41 +00:00
Sandro
b7ec0afb59
Merge pull request #162205 from Stunkymonkey/treewide-vVersion 2022-02-28 14:26:16 +01:00
Felix Buehler
1573dbdcd0 treewide: fix versions starting with 'v' 2022-02-28 13:05:18 +01:00
github-actions[bot]
f831b62376
Merge staging-next into staging 2022-02-28 12:01:47 +00:00
github-actions[bot]
e71c1249e8
Merge master into staging-next 2022-02-28 12:01:10 +00:00
Felix Buehler
fe7678ca81 raxml-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
Felix Buehler
13dca33cdc neuron-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
Bobby Rong
f35d1b8568
Merge pull request #160332 from florentc/tlaps 
tlaps: 1.4.3 -> 1.4.5
 2022-02-28 16:33:42 +08:00
Jonathan Ringer
3af9faf36d
Merge pull request #133431 from Ma27/glibc-2.34 
glibc: 2.33-108 -> 2.34-115
 2022-02-27 18:07:11 -08:00
github-actions[bot]
6787116890
Merge master into staging-next 2022-02-28 00:02:07 +00:00
Guillaume Girol
b9ecdae495
Merge pull request #161344 from ulrikstrid/ulrikstrid/tree-wide-native-inputs 
ocamlPackages tree-wide: Move buildInputs that should be nativeBuildInputs
 2022-02-27 19:49:07 +00:00
7c6f434c
da576d8a4a
Merge pull request #161876 from FRidh/sage-python 
Sage: make it possible to extend the Python runtime environment with additional packages
 2022-02-27 19:02:59 +00:00
Maximilian Bosch
52bba1de8a
clingcon: fix build w/glibc-2.34 
Failing Hydra build: https://hydra.nixos.org/build/163641612
 2022-02-27 10:26:56 +01:00
AndersonTorres
ed2b1b4b90 Merge branch 'master' into staging-next 2022-02-26 21:04:25 -03:00
Vincent Laporte
68e4b639a3
Merge pull request #161111 from ulrikstrid/ulrikstrid/coq-move-dune-to-native 
coq: Move dune, ocaml and findlib to nativeBuildInputs
 2022-02-26 08:54:53 +01:00
R. Ryantm
21a1125f37 gmsh: 4.9.4 -> 4.9.5 2022-02-25 14:21:11 -08:00
K900
cb2cfba6f7 treewide: switch all desktop file generators to new API 
Notably:
- remove explicit arguments that match the defaults
- convert everything to the right Nix types
 2022-02-25 13:40:38 -08:00
Frederik Rietdijk
330d9344d2 sage: make it possible not to rebuild sage-tests 
Requiring sage-tests as build input just so it gets build is a bit
unfortunatey but understandable. This commit introduces an option to not
add sage-tests as a dependency. This is preferred in case e.g. Python
packages are added to the environment.
 2022-02-25 21:27:14 +01:00
Frederik Rietdijk
7442533bf1 sage: support adding extra Python packages to environment 
mysage = sage.override { extraPythonPackages = ps: with ps; [ dask ]; };

Note that the sage-tests are executed again as well, which is not very nice.
 2022-02-25 21:18:23 +01:00
R. Ryantm
1e7c64aae1 bcftools: 1.14 -> 1.15 2022-02-25 11:12:05 -08:00
markuskowa
49186d631f
Merge pull request #161635 from r-ryantm/auto-update/jmol 
jmol: 14.32.21 -> 14.32.24
 2022-02-25 13:42:31 +01:00
Ulrik Strid
7e20e9039e coqPackages: tree-wide move packages to nativeBuildInputs and add strictDeps = true 
Co-authored-by: Vincent Laporte <vbgl@users.noreply.github.com>
 2022-02-25 07:54:17 +01:00
Vincent Laporte
056c34167d why3: 1.4.0 → 1.4.1 2022-02-25 06:00:09 +01:00
Justin Bedő
6b477d556d
Merge pull request #161695 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.26.10 -> 2.26.11
 2022-02-25 08:27:23 +11:00
R. Ryantm
d6a24fc108 cwltool: 3.1.20220217222804 -> 3.1.20220221074232 2022-02-24 15:52:49 -05:00
R. Ryantm
ce9d28cc49 picard-tools: 2.26.10 -> 2.26.11 2022-02-24 17:34:18 +00:00
Ulrik Strid
48df7cdbba coq: Move dune to nativeBuildInputs and add ocaml, findlib and menhir 2022-02-24 14:39:45 +01:00
Ulrik Strid
a13cdfe520 ocamlPackages tree-wide: Move buildInputs that should be nativeBuildInputs 
To keep this for the future we also strictDeps where possible, including for janePackages, topkg, oasis and ocamlbuild.
This makes some closures significantly smaller and makes cross compilation easier
 2022-02-24 14:39:27 +01:00
R. Ryantm
1b8518cadd jmol: 14.32.21 -> 14.32.24 2022-02-24 08:42:12 +00:00
github-actions[bot]
cd6011bf17
Merge master into staging-next 2022-02-24 00:02:03 +00:00
Renaud
65ecaa9903
Merge pull request #150078 from r-ryantm/auto-update/gurobi 
gurobi: 9.1.2 -> 9.5.0
 2022-02-23 22:08:43 +01:00
github-actions[bot]
37f89e2837
Merge master into staging-next 2022-02-23 18:01:10 +00:00
Markus Kowalewski
469ae42107
gromacs: 2021.5 -> 2022 2022-02-23 14:47:26 +01:00
Renaud
a723c88d4e
Merge pull request #159967 from r-ryantm/auto-update/workcraft 
workcraft: 3.3.5 -> 3.3.6
 2022-02-23 13:30:39 +01:00
github-actions[bot]
10c4b97b44
Merge master into staging-next 2022-02-23 12:01:11 +00:00
Renaud
359d63179e
Merge pull request #160360 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 3.22.0 -> 4.0.0
 2022-02-23 08:30:49 +01:00
Mauricio Collares
4ba9b2d198 lean: 3.39.2 -> 3.40.0 2022-02-22 21:02:08 -03:00
github-actions[bot]
ac0e0313b5
Merge staging-next into staging 2022-02-22 06:01:53 +00:00
Bobby Rong
93883402a4
Merge pull request #160594 from Cogitri/bada-bib 
bada-bib: 0.4.1 -> 0.5.1
 2022-02-22 12:10:40 +08:00
github-actions[bot]
f8210665fc
Merge staging-next into staging 2022-02-22 00:02:51 +00:00
Mauricio Collares
586b897693 sage: update test expectations for stack_data 0.2.0 2022-02-21 14:49:16 -08:00
Wanja Zaeske
2d67cc2bf6 removing maintainer wucke13 from some packages 2022-02-21 22:58:18 +01:00
ajs124
55bf481a21
Merge pull request #159212 from helsinki-systems/init/febio-studio 
febio-studio: init at 1.6.1
 2022-02-21 17:24:33 +01:00
Scriptkiddi
4e60a4823b febio-studio: init at 1.6.1 2022-02-21 16:43:36 +01:00
Rasmus Thomsen
87c1d9f92c
bada-bib: 0.4.1 -> 0.5.1 2022-02-21 16:33:50 +01:00
Wanja Zaeske
58d5eb70e2 mission-planner: 1.3.74 -> 1.3.76 2022-02-21 09:51:16 +01:00
R. Ryantm
c35aa0a0f3 cwltool: 3.1.20220217190813 -> 3.1.20220217222804 2022-02-21 01:31:33 -05:00
markuskowa
48ab0d0233
Merge pull request #160924 from qbg/submit/mathematica-13.0.1 
mathematica: 13.0.0 -> 13.0.1
 2022-02-20 10:23:22 +01:00
R. RyanTM
286ecff9e0
getdp: 3.3.0 -> 3.4.0 
(#150127)
 2022-02-19 22:41:33 +01:00
Mario Rodas
94723d21f9
Merge pull request #159540 from r-ryantm/auto-update/marvin 
marvin: 21.20.0 -> 22.3.0
 2022-02-19 15:59:08 -05:00
qbg
f4f52d9d70 mathematica: 13.0.0 -> 13.0.1 
https://wolfram.com/mathematica/quick-revision-history.html#v130
 2022-02-19 11:26:53 -06:00
Millian Poquet
bc2604732e simgrid: mark as broken on darwin 2022-02-19 10:05:17 +01:00
Millian Poquet
3f804f68bc simgrid: 3.28 -> 3.30 + python + clean 
- use latest SimGrid release
- enable the python binding (in new output "python")
- reviews from PR 141040 have been applied
 2022-02-19 10:05:12 +01:00
Ulrik Strid
4150bf02b5 coq: allow static linking by moving wrapGAppsHook to nativeBuildInputs 
Co-authored-by: Vincent Laporte <vbgl@users.noreply.github.com>
 2022-02-18 15:17:04 +01:00
Mario Rodas
947c98310c
Merge pull request #160545 from collares/lean-3.39.2 
lean: 3.39.1 -> 3.39.2
 2022-02-18 06:26:51 -05:00
R. Ryantm
b715fcd9d9 cwltool: 3.1.20220210171524 -> 3.1.20220217190813 2022-02-18 00:36:37 -05:00
Mauricio Collares
0c36a9cc35 lean: 3.39.1 -> 3.39.2 2022-02-17 23:42:05 -03:00
R. RyanTM
94f61e4c82
SPAdes: 3.15.3 -> 3.15.4 
(#158938)
 2022-02-18 00:55:34 +01:00
R. RyanTM
ac1c96ecec
colmap: 3.6 -> 3.7 
* colmap: 3.6 -> 3.7 (#159198)

* colmap: license is BSD-3-Clause

Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>
 2022-02-18 00:29:14 +01:00
Ben Wolsieffer
1382f006a9
qgroundcontrol: 4.1.4 -> 4.2.0 
* qgroundcontrol: 4.1.4 -> 4.2.0 (#159291)

QGroundControl now tries to download a prebuilt x86_64 .deb package for
the Airmap SDK, so we have to disable this feature. Previously, it was
disabled by default. I guess they were trying to make things easier for
users, but it seems pretty half-baked.

* qgroundcontrol: update homepage

The domain seems to have changed from .org to .com.
 2022-02-18 00:09:39 +01:00
Daniel Wheeler
4befe7a89f
snakemake: 6.10.0 -> 6.15.5 (#159026) 
Fetch from GitHub rather than PyPI so tests are included.
 2022-02-17 18:06:23 -05:00
ajs124
80160499bc
Merge pull request #160340 from helsinki-systems/tetgen 
tetgen: also install library and headers
 2022-02-17 01:57:18 +01:00
Scriptkiddi
c8fb08b1e4 tetgen: also install library and headers 2022-02-17 01:37:28 +01:00
R. Ryantm
581628a7f4 qalculate-gtk: 3.22.0 -> 4.0.0 2022-02-16 19:33:07 +00:00
Florent C
762faa21a2 tlaps: 1.4.3 -> 1.4.5 
This updates tlaps to the most recent stable version and fixes the
template for the url from which the sources are fetched. Previously, the
tarball was fetched from the "current" remote directory from which old
versions are eventually removed. The package was therefore broken.
It also adds myself (florentc) as a maintainer.
 2022-02-16 15:19:51 +01:00
Artturi
83dc7a2714
Merge pull request #159808 from r-ryantm/auto-update/tlaplus 2022-02-16 15:53:15 +02:00
Mauricio Collares
b38b641ff3 sageWithDoc: fix Sphinx warnings which break docgen 2022-02-15 22:37:34 -03:00
Ben Siraphob
521cfab34b
Merge pull request #157626 from siraben/formula-init 2022-02-15 18:38:41 -06:00
Sandro
5c5a8df724
Merge pull request #156420 from azuwis/transfig 2022-02-16 00:49:28 +01:00
7c6f434c
16fe911917
Merge pull request #160088 from r-ryantm/auto-update/jmol 
jmol: 14.32.6 -> 14.32.21
 2022-02-15 21:39:00 +00:00
Kevin Cox
4e883afc5a
Merge pull request #159226 from lorenzleutgeb/gradle 
gradle: 7.3.3 -> 7.4
 2022-02-15 15:26:18 -05:00
Ben Siraphob
7f94906083
formula: init at 2.0 2022-02-15 14:09:16 -06:00
Lorenz Leutgeb
f7e01145af gradle: Update hashes of dependents for 7.4 2022-02-15 09:17:56 +01:00
Zhong Jianxin
507b23f0d1 chemtool: Set platforms to linux 2022-02-15 10:49:51 +08:00
R. Ryantm
099fefbceb jmol: 14.32.6 -> 14.32.21 2022-02-15 02:42:04 +00:00
Zhong Jianxin
e8f3914985 treewide: Replace transfig with fig2dev 
Reasons:

- transfig never get upstream update since it was added to nixpkgs 2006,
  according to [fig2dev Debian changelog][1], upstream maintainership
  was taken over at 2016, and renamed to fig2dev.

- [Debian][2], [ArchLinux][3], [HomeBrew][4] all use fig2dev to replace
  transfig.

- transfig builds [failed][5] on aarch64-darwin, fig2dev builds fine.

- One less package to maintain.

[1]: https://salsa.debian.org/debian/fig2dev/-/blob/debian/1%253.2.6_beta-1/debian/changelog
[2]: https://packages.debian.org/bullseye/transfig
[3]: https://archlinux.org/packages/community/x86_64/fig2dev/
[4]: https://formulae.brew.sh/formula/fig2dev
[5]: https://hydra.nixos.org/build/163404782/nixlog/2
 2022-02-15 10:13:56 +08:00
7c6f434c
a6a1e14e52
Merge pull request #159741 from r-ryantm/auto-update/polymake 
polymake: 4.5 -> 4.6
 2022-02-14 20:52:03 +00:00
7c6f434c
117fdae4b6
Merge pull request #159351 from collares/sage-ipython-8 
sage: don't test for Cython source code in tracebacks (temporarily)
 2022-02-14 17:18:21 +00:00
Jan van Brügge
75f5b1f5b2
isabelle: Rebuild isabelle_setup.jar 
This jar contained a call to /usr/bin/env bash which was causing an
error during the build of the HOL session (which could be ignored) and
caused other errors during the development of https://github.com/NixOS/nixpkgs/pull/157515
 (which could not be ignored). This commit patches the java sources to
 call `bash` directly and rebuild the jar.
 2022-02-14 15:17:58 +01:00
Bobby Rong
8617a5a336
Merge pull request #159645 from r-ryantm/auto-update/openhantek6022 
openhantek6022: 3.2.4 -> 3.2.5
 2022-02-14 19:58:50 +08:00
R. Ryantm
e1f6e33d01 workcraft: 3.3.5 -> 3.3.6 2022-02-14 09:43:01 +00:00
R. Ryantm
240262f564 messer-slim: 3.7 -> 3.7.1 2022-02-14 00:46:29 +00:00
markuskowa
e7a2652f31
Merge pull request #159311 from r-ryantm/auto-update/gmsh 
gmsh: 4.9.2 -> 4.9.4
 2022-02-13 11:48:17 +01:00
R. Ryantm
42d5cbb78e tlaplus: 1.7.1 -> 1.7.2 2022-02-13 10:33:51 +00:00
R. Ryantm
2220d35562 bada-bib: 0.3.0 -> 0.4.1 2022-02-12 22:22:46 -08:00
R. Ryantm
24b505484b cytoscape: 3.9.0 -> 3.9.1 2022-02-12 21:13:11 -08:00
R. Ryantm
ac4ec1ef75 gretl: 2021d -> 2022a 2022-02-12 21:08:09 -08:00
R. Ryantm
154d72f526 ginac: 1.8.1 -> 1.8.2 2022-02-12 20:56:29 -08:00
R. Ryantm
36800803c5 gama: 2.16 -> 2.17 2022-02-12 20:54:56 -08:00
R. Ryantm
0948b62a1f polymake: 4.5 -> 4.6 2022-02-13 04:50:20 +00:00
R. Ryantm
aa982c28cf kstars: 3.5.6 -> 3.5.7 2022-02-12 20:32:52 -08:00
Justin Bedő
2759d6f8d8
Merge pull request #159675 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.26.9 -> 2.26.10
 2022-02-13 09:53:20 +11:00
Justin Bedő
7ff9c00c4b
Merge pull request #159562 from r-ryantm/auto-update/mosdepth 
mosdepth: 0.3.2 -> 0.3.3
 2022-02-13 09:27:54 +11:00
Justin Bedő
28f5937aeb
Merge pull request #159411 from r-ryantm/auto-update/last 
last: 1256 -> 1260
 2022-02-13 09:25:49 +11:00
R. Ryantm
8a4946df2d picard-tools: 2.26.9 -> 2.26.10 2022-02-12 22:20:29 +00:00
R. Ryantm
80175b54cc openhantek6022: 3.2.4 -> 3.2.5 2022-02-12 20:37:00 +00:00
Robert Scott
83ea8999d4 gmsh: enable tests 2022-02-12 16:15:57 +00:00
Robert Scott
61dc066799 gmsh: enable for darwin 2022-02-12 16:13:53 +00:00
R. Ryantm
8bb7bc766f mosdepth: 0.3.2 -> 0.3.3 2022-02-12 14:31:47 +00:00
Mario Rodas
0ff383436d
Merge pull request #159009 from r-ryantm/auto-update/bcal 
bcal: 2.3 -> 2.4
 2022-02-12 08:39:47 -05:00
R. Ryantm
983beb2b8b marvin: 21.20.0 -> 22.3.0 2022-02-12 12:52:40 +00:00
7c6f434c
bff729efd3
Merge pull request #158992 from collares/R-stackprotector 
R: disable stack protector on aarch64-darwin
 2022-02-12 11:32:56 +00:00
Kim Lindberger
c7df3bf58c
Merge pull request #155108 from fedeinthemix/add-xyce-2 
Add Xyce 7.4 (second attempt)
 2022-02-12 11:34:10 +01:00
Federico Beffa
10b7f30936 xyce,xyce-parallel: init at 7.4 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com> and
                Kim Lindberger <kim.lindberger@gmail.com>
 2022-02-12 10:26:05 +01:00
R. Ryantm
6ca5bb6e20 last: 1256 -> 1260 2022-02-12 02:52:18 +00:00
Mauricio Collares
c763432549 sage: don't test for Cython source code in tracebacks (temporarily) 2022-02-11 19:13:34 -03:00
R. Ryantm
772c6b674c gmsh: 4.9.2 -> 4.9.4 2022-02-11 18:31:28 +00:00
R. Ryantm
1631ffae8d cwltool: 3.1.20220204090313 -> 3.1.20220210171524 2022-02-11 12:44:06 -05:00
evils
bb8a321187
kicad: 6.0.1 -> 6.0.2 (#159132) 2022-02-11 01:15:42 -05:00
Angus Trau
18592865d7 maintainers: update emilytrau 2022-02-11 04:45:03 +00:00
7c6f434c
06ff90f540
Merge pull request #159020 from collares/arb-2.22.1 
arb: 2.21.1 -> 2.22.1
 2022-02-10 23:56:18 +00:00
R. RyanTM
b6869047c5
lepton-eda: 1.9.16-20210731 -> 1.9.17-20211219 
(#152772)
 2022-02-10 21:43:31 +01:00
R. Ryantm
288ba3f85b scilab-bin: 6.0.2 -> 6.1.1 2022-02-10 11:56:08 -08:00
Mauricio Collares
b8c69782a2 sage: adapt tests to arb 2.22 2022-02-10 16:40:41 -03:00
R. Ryantm
fa133a26f3 rofi-calc: 2.0.0 -> 2.1.0 2022-02-10 11:32:09 -08:00
R. Ryantm
172ba8b474 bcal: 2.3 -> 2.4 2022-02-10 19:05:57 +00:00
Mauricio Collares
4536186f18 R: disable stack protector on aarch64-darwin 2022-02-10 14:01:08 -03:00
Mauricio Collares
58f58c8de6 lean: 3.39.0 -> 3.39.1 2022-02-08 12:24:19 -03:00
Ben Siraphob
3594565a7e
Merge pull request #156629 from siraben/coq-mainprogram 
coq: add meta.mainProgram
 2022-02-06 21:43:01 +00:00
Ben Siraphob
6ad0e10dd3
coq: add meta.mainProgram 2022-02-06 15:42:47 -06:00
Ben Siraphob
33489310eb
Merge pull request #158358 from c0bw3b/fix/homepages 
A batch of homepage (and source) updates
 2022-02-06 20:02:50 +00:00
Renaud
2ddcc2b369 hisat2: update homepage 
and use SPDX 3.0 license identifier
 2022-02-06 15:10:53 +01:00
Renaud
d968838c90 gravit: update homepage and source URLs 
and use SPDX 3.0 license identifier
 2022-02-06 15:10:47 +01:00
Renaud
3e5d286cc4 eagle7: update homepage 
www.cadsoftusa.com and www.cadsoft.de are gone
 2022-02-06 15:10:29 +01:00
R. RyanTM
1bfc1730e1
cwltool: 3.1.20220202173120 -> 3.1.20220204090313 (#158272) 2022-02-05 15:14:21 -05:00
Sandro
63a6539b76
Merge pull request #157198 from afontaine/afontaine/correct-fah-shortcuts 2022-02-04 18:26:20 +01:00
R. Ryantm
af3af2df32 cwltool: 3.1.20220124184855 -> 3.1.20220202173120 2022-02-03 20:06:12 -05:00
Timo Kaufmann
0371c7ba56
Merge pull request #157981 from collares/sage-fonttools-revert 
sage: no longer assume fonttools emits deprecation warnings
 2022-02-03 18:03:39 +01:00
Artturi
0f491bd7a3
Merge pull request #157264 from FliegendeWurst/disable-broken-parallel 2022-02-03 16:04:57 +02:00
Mauricio Collares
0ebdfab88b lean: 3.38.0 -> 3.39.0 2022-02-03 09:21:20 -03:00
Mauricio Collares
778b1f8b4f sage: no longer assume fonttools emits deprecation warnings 2022-02-03 08:28:22 -03:00
Bobby Rong
46a4949078
Merge pull request #157927 from r-ryantm/auto-update/vowpal-wabbit 
vowpal-wabbit: 8.11.0 -> 9.0.1
 2022-02-03 17:28:02 +08:00
R. Ryantm
6d957f73ab vowpal-wabbit: 8.11.0 -> 9.0.1 2022-02-03 02:08:33 +00:00
Сухарик
3f90b3a1e1 anders: init at 1.1.1 2022-02-02 12:31:53 +03:00
markuskowa
65bc2de0ef
Merge pull request #152447 from Cogitri/bada-bib 
bada-bib: init at 0.3.0
 2022-02-01 22:26:26 +01:00
Martin Weinelt
778d148959
Merge pull request #155061 from piegamesde/gnome 2022-02-01 20:53:10 +01:00
Bruno Bzeznik
77682cf879
shtns: init at 3.5.1 (#151061) 2022-01-31 21:28:05 +01:00
R. Ryantm
d44e044d84 kallisto: 0.46.2 -> 0.48.0 2022-01-31 09:53:54 -08:00
Bruno Bzeznik
b6fa4975cf
repseek: init at 9Sep2014 (#148017) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-01-31 14:59:32 +01:00
7c6f434c
9b76122d71
Merge pull request #140889 from collares/sage-9.5 
sage: 9.4 -> 9.5
 2022-01-31 13:24:26 +00:00
Robert Schütz
a13fe11c59 sasview: 4.2.0 -> 5.0.4 2022-01-30 20:47:10 +00:00
Mauricio Collares
8ec9a32829 sageWithDoc: do not autodetect optional features when testing dochtml 2022-01-30 13:15:22 -03:00
Mauricio Collares
cecbb55fb0 sage: 9.4 -> 9.5 2022-01-30 13:15:20 -03:00
Sandro
a724f8dc29
Merge pull request #155897 from FliegendeWurst/key-2.10 2022-01-30 01:21:43 +01:00
piegames
9a2a3d0395 gfm: drop 
It does not appear to have an attribute that references it anymore?
(Not sure though, that name's hard to grep for)
 2022-01-29 18:09:16 +01:00
piegames
5ffbf9ed81 tilp2: drop 
While tilp2's libglade dependency is optional, it still has a hard dependency
on it via gfm
 2022-01-29 18:08:52 +01:00
markuskowa
01f1b41a7d
Merge pull request #156381 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.4.4 -> 2.4.5
 2022-01-29 14:56:23 +01:00
FliegendeWurst
a43431f376 alliance: disable parallel build 2022-01-29 11:40:09 +01:00
FliegendeWurst
48a133a066 key: add a desktop item 2022-01-29 10:14:54 +01:00
Vegard Strand Lende
41f927b433
verilator: 4.210 -> 4.218 (#157122) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-01-29 02:30:41 +01:00
Andrew Fontaine
3c0680b783
fahviewer: fix variable substitution for shortcut 
Because single quotes are used in the sed command, the application
shortcut had the literal $out instead of the package path.
 2022-01-28 16:47:24 -05:00
Andrew Fontaine
ba785adb28
fahcontrol: fix variable substitution for shortcut 
Because single quotes are used in the sed command, the application
shortcut had the literal $out instead of the package path.
 2022-01-28 16:46:52 -05:00
Yipeng Sun
54cbee8d97
root: tweak wrapping flags for auxiliary programs, avoid forcing CMAKE_CXX_STANDARD (#157069) 2022-01-27 19:37:36 -05:00
Sandro
27cccd4e49
Merge pull request #151363 from Stunkymonkey/doc-updateWalker 2022-01-27 14:06:36 +01:00
ajs124
3638ca8be6
Merge pull request #156001 from helsinki-systems/upd/tulip 
tulip: 5.2.1 -> 5.6.1
 2022-01-26 23:33:44 +01:00
Felix Buehler
09e3b7a570 treewide: remove all updateWalker/downloadURLRegexp 2022-01-26 21:46:08 +01:00
Felix Buehler
ed7bf9452c treewide: remove *.upstream files from updateWalker 2022-01-26 21:46:07 +01:00
Gabriel Ebner
b27b115b41
Merge pull request #154272 from jvanbruegge/isabelle-build-hol 
isabelle: Prebuild HOL session
 2022-01-26 16:37:18 +01:00
Dmitry Kalinkin
f66b63a7cb
Merge pull request #156217 from smancill/shogun-fixes 
Shogun: use Python 3 and fix CMake targets
 2022-01-26 04:25:27 -05:00
R. Ryantm
6b3bf39220 cwltool: 3.1.20220119140128 -> 3.1.20220124184855 2022-01-25 21:56:09 -05:00
Vincent Laporte
8187f6500d tamarin-prover: install emacs-mode 2022-01-25 15:54:15 +01:00
Vincent Laporte
20e7213d16 coq_8_15: 8.15+rc1 → 8.15.0 2022-01-25 10:53:57 +01:00
Mauricio Collares
0aef6270cd sage: generate setup.cfg and requirements.txt for sagelib 2022-01-24 20:54:53 -03:00
Mauricio Collares
0a6b5115f6 singular: 4.2.0p2 -> 4.3.0 2022-01-24 20:54:53 -03:00
R. RyanTM
8bd7d6d6e0
star: 2.7.9a -> 2.7.10a 
(#155868)
 2022-01-24 19:51:44 +01:00
R. Ryantm
ebb9e86bf9 bowtie2: 2.4.4 -> 2.4.5 2022-01-23 22:45:59 +00:00
Mario Rodas
111d7dc831
Merge pull request #156014 from r-ryantm/auto-update/deeptools 
deeptools: 3.5.0 -> 3.5.1
 2022-01-22 23:45:09 -05:00
Justin Bedő
c24af4642c
sambamba: 0.8.1 -> 0.8.2 (#155972) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-01-23 04:51:46 +01:00
Alexandra
7267839e76
gprojector: init at 3.0.2 (#154932) 2022-01-23 04:04:10 +01:00
Sebastián Mancilla
c03c5c1500 shogun: fix CMake targets 
CMake uses the directory of the configuration files to calculate
the path to the installed library and headers. But now that shogun uses
multiple outputs, this results in the $dev output being used for the
location of the shared library instead of $out.

Path the targets file to use the right location for the shared library.
 2022-01-22 18:41:49 -03:00
Sebastián Mancilla
aaea9844c6 shogun: use Python 3 as build dependency 
Also default pythonSupport to false because it's broken for Python 3.

In any case the Python interface has been disabled for almost 2 years
now because the wrong CMake flag was being passed, so the build stays
the same.

But do use the proper flag now.
 2022-01-22 18:36:06 -03:00
FliegendeWurst
28b43ffd54 key: 2.6.3 -> 2.10.0 2022-01-22 15:55:25 +01:00
R. Ryantm
f888e66ad4 cwltool: 3.1.20211107152837 -> 3.1.20220119140128 2022-01-21 09:09:34 -05:00
R. Ryantm
227011af59 deeptools: 3.5.0 -> 3.5.1 2022-01-21 05:36:24 +00:00
ajs124
479ca09609 tulip: 5.2.1 -> 5.6.1 2022-01-21 03:45:21 +01:00
markuskowa
1c0f3cd8df
Merge pull request #155893 from markuskowa/fix-molden-url 
molden: fix download URL
 2022-01-20 16:55:51 +01:00
Markus Kowalewski
bb6bc8b315
molden: fix download URL 2022-01-20 15:47:46 +01:00
R. Ryantm
84930221fc sherpa: 2.2.11 -> 2.2.12 2022-01-20 08:36:02 -05:00
Armeen Mahdian
2d207146ee
mathematica: Refactor install process with autoPatchelfHook (#154295) 
- Call appropriate hooks at beginning/end of each phase

  - No longer assume current working dir in installPhase

  - Add support for udev rules installation (required for VernierLink)

  - Use -verbose with MathInstaller for detailed progress

  - Use patchShebangs or MathInstaller

  - Remove broken hostname call, root user check, and Avahi daemon
    check in MathInstaller

  - Add proper error checking after MathInstaller call

  - Skip configure phase

  - Create wrappers for relevant executables

  - Set $HOME to $TMPDIR/home temporarily so MathInstaller
    succeeds

  - Replace dd with tail for simplicity and performance
 2022-01-19 12:35:38 -05:00
Jan van Brügge
d653b33f20
maintainers: add jvanbruegge 2022-01-19 18:25:27 +01:00
Jan van Brügge
6fff929c5e
isabelle: Prebuild HOL session 
Upstream isabelle ships with this session, but the changes done for
nixpkgs invalidate it, requiring every user to build it again.
 2022-01-19 18:25:26 +01:00
evils
ba7c4fa91d
kicad: enable i18n by default (#155065) 
without i18n
/nix/store/xgs0n52djlqqmw6qlvg6j2jxpzdpsi92-kicad-6.0.1   7269408096
/nix/store/k7ra3zkx6mp0b3ivsf0ba14mbinwws0w-kicad-unstable-33a4c9b08e   7277796352
with i18n
/nix/store/2xh82r2znqipky0sny49h9cs5fbhmh4v-kicad-6.0.1   7286672288
/nix/store/532r1f3j8xjki8g87400n0gnd594pcbm-kicad-unstable-33a4c9b08e   7294795424
 2022-01-18 13:06:30 -05:00
Markus Kowalewski
17d0b66cf6
gromacs: 2021.4 -> 2021.5 2022-01-17 15:50:31 +01:00
Bobby Rong
9b59effb02
Merge pull request #154798 from collares/lean-3.38 
lean: 3.37.0 -> 3.38.0
 2022-01-17 21:40:56 +08:00
Frederik Rietdijk
afef6d0e81
Merge pull request #154687 from dotlambda/python-alias 
python,pythonPackages: make aliases
 2022-01-17 09:37:49 +01:00
R. RyanTM
4fa7c297f2
minimap2: 2.23 -> 2.24 
* minimap2: 2.23 -> 2.24 (#153189)

* minimap2: no support for aarch64

Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>
 2022-01-17 08:49:35 +01:00
Robert Schütz
d5cceedbd1 python,pythonPackages: make aliases 
Since aliases are disallowed in nixpkgs, this makes usage of Python 2
which is EOL more explicit.
 2022-01-16 18:39:59 +00:00
Robert Schütz
65e959eb9a tebreak: also use python3 for tests 2022-01-16 18:00:59 +00:00
Martin Weinelt
492e5e07c9
lumpy: drop 
Removed because it requires python2 and the upstream repository looks
undermaintained.
 2022-01-16 02:36:23 +01:00
R. RyanTM
1e4664e1a0
betaflight-configurator: 10.7.1 -> 10.7.2 
(#154383)
 2022-01-15 23:12:31 +01:00
R. RyanTM
0c7342b6e7
horizon-eda: 2.1.0 -> 2.2.0 
(#154557)
 2022-01-15 22:09:09 +01:00
pennae
59505f5c08
Merge pull request #154395 from r-ryantm/auto-update/calc 
calc: 2.14.0.13 -> 2.14.0.14
 2022-01-15 10:32:41 +00:00
Bobby Rong
cb3da55ede
Merge pull request #154988 from veprbl/pr/broken_gplates 
gplates: mark as broken on darwin
 2022-01-15 13:24:14 +08:00
Bobby Rong
a6ed245599
Merge pull request #154989 from veprbl/pr/broken_graphia 
graphia: mark as broken on darwin
 2022-01-15 13:23:31 +08:00
Fabian Affolter
49574fc9d5
Merge pull request #154934 from fabaff/fix-toil 
toil: 5.4.0 -> 5.6.0
 2022-01-14 21:16:45 +01:00
Dmitry Kalinkin
2b9f8eb0a2
graphia: mark as broken on darwin 2022-01-14 03:38:54 -05:00