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5513 commits

Author SHA1 Message Date
Felix Buehler 2f4a86e7d7 messer-slim: switch to fetchFromGitHub 2021-12-23 19:11:17 +01:00
Felix Buehler e1bd890fb0 niftyseg: switch to fetchFromGitHub 2021-12-23 19:11:17 +01:00
Felix Buehler cb448459d0 potassco: switch to fetchFromGitHub 2021-12-23 19:11:17 +01:00
github-actions[bot] 5e2c1acfa3
Merge master into staging-next 2021-12-22 18:01:00 +00:00
Justin Bedo fa6244b712
picard-tools: 2.26.6 -> 2.26.9 2021-12-22 22:20:36 +11:00
7c6f434c 080d8f0d72
Merge pull request #151635 from collares/sage-fonttools
[staging-next] sage: assume fonttools DeprecationWarnings are expected for now
2021-12-22 07:50:33 +00:00
Mauricio Collares 93f9a9c36d sage: assume fonttools DeprecationWarnings are expected for now 2021-12-21 23:10:07 -03:00
github-actions[bot] 39d035c4cf
Merge master into staging-next 2021-12-22 00:01:35 +00:00
Kierán Meinhardt 4bff3d7346 astrolog: init at 7.30 2021-12-21 22:24:48 +01:00
github-actions[bot] a7f62c75af
Merge master into staging-next 2021-12-21 18:01:15 +00:00
FliegendeWurst c080917139 geogebra: 5-0-662-0 -> 5-0-680-0 2021-12-21 17:09:50 +01:00
7c6f434c d5db292192
Merge pull request #151424 from collares/sage-matplotlib
[staging-next] sage: import matplotlib and sphinx update patches
2021-12-21 12:55:50 +00:00
Felix Buehler f4931dfaee ekrhyper: refactor 2021-12-21 12:44:01 +01:00
Dmitry Kalinkin ac40a963c9
Merge branch 'master' into staging-next
Conflicts:
	pkgs/applications/editors/vim/common.nix
	pkgs/development/python-modules/jellyfin-apiclient-python/default.nix
	pkgs/development/python-modules/pymavlink/default.nix
2021-12-20 12:09:28 -05:00
Mauricio Collares 3eaca311d4 sage: import matplotlib and sphinx update patches 2021-12-20 10:09:35 -03:00
Doron Behar e6647de754
Merge pull request #151281 from r-ryantm/auto-update/qalculate-gtk 2021-12-19 22:40:43 +02:00
Dmitry Kalinkin bbea48728b
Merge pull request #151151 from veprbl/pr/libcxx_no_apple_availability
llvmPackages.libcxx: unset _LIBCPP_USE_AVAILABILITY_APPLE
2021-12-19 11:42:28 -05:00
Gabriel Ebner a3bbbe08bd
Merge pull request #151328 from Kha/elan-lean-cc
elan: set LEAN_CC to stdenv cc
2021-12-19 17:39:28 +01:00
Sebastian Ullrich b20024dd3a elan: set LEAN_CC to stdenv cc
This ensures that `leanc` understands cc-wrapper vars such as `NIX_LDFLAGS`
2021-12-19 17:27:10 +01:00
Bobby Rong 856672f2ce
Merge pull request #151249 from lopsided98/mavproxy-update
mavproxy: 1.8.45 -> 1.8.46
2021-12-19 22:21:30 +08:00
R. Ryantm 57ff8c2e36 qalculate-gtk: 3.21.0 -> 3.22.0 2021-12-19 07:38:29 +00:00
github-actions[bot] 2e447628d8
Merge master into staging-next 2021-12-19 06:01:16 +00:00
qbg 24111d6a7a
mathematica: 12.3.1 -> 13.0.0 (#151213)
https://wolfram.com/mathematica/quick-revision-history.html#v130
2021-12-18 23:24:27 -05:00
R. Ryantm d14a6ef13e mavproxy: 1.8.45 -> 1.8.46 2021-12-18 20:04:55 -05:00
Dmitry Kalinkin da8f155b2a
Merge branch 'master' into staging-next
Conflicts:
	pkgs/development/python-modules/sphinxext-opengraph/default.nix
2021-12-18 10:18:14 -05:00
Dmitry Kalinkin e1aaaa90fe
llvmPackages.libcxx: unset _LIBCPP_USE_AVAILABILITY_APPLE 2021-12-18 10:09:25 -05:00
Bobby Rong bcaa1b4633
Merge pull request #149151 from Luflosi/update/boinc
boinc: 7.14.2 -> 7.18.1
2021-12-18 21:32:22 +08:00
github-actions[bot] 2749f6983a
Merge master into staging-next 2021-12-17 06:01:26 +00:00
Dmitry Kalinkin 50a4c52747
Merge pull request #147648 from veprbl/pr/mxnet_1_8_0
mxnet: 1.6.0 -> 1.8.0, enable on darwin
2021-12-16 22:37:03 -05:00
mucaho 1509f463a0 clingcon: 3.3.0 -> 5.0.0 2021-12-16 20:28:19 +01:00
github-actions[bot] 9c7ec75d6b
Merge master into staging-next 2021-12-16 06:01:09 +00:00
Silvan Mosberger e30a4fa4bd
Merge pull request #149404 from Infinisil/remove-scyther 2021-12-16 01:56:39 +01:00
Dmitry Kalinkin a7a3675563
gromacs: fix build on darwin 2021-12-15 15:22:10 -05:00
sternenseemann d860ba7f09 Merge remote-tracking branch 'origin/master' into staging-next 2021-12-15 11:30:31 +01:00
Justin Bedő f6e14b6ada
Merge pull request #150628 from jbedo/subread
subread: init 2.0.3
2021-12-15 13:46:45 +11:00
github-actions[bot] 0242879f3f
Merge master into staging-next 2021-12-14 12:01:17 +00:00
Bobby Rong e5a6bba62b
Merge pull request #150447 from r-ryantm/auto-update/seaview
seaview: 5.0.4 -> 5.0.5
2021-12-14 18:38:55 +08:00
7c6f434c b862304c67
Merge pull request #150597 from collares/sage-arb
arb: 2.20.0 -> 2.21.1
2021-12-14 08:56:42 +00:00
Justin Bedo 6a1f4a51eb
subread: init 2.0.3 2021-12-14 13:30:23 +11:00
github-actions[bot] 784572e7cf
Merge master into staging-next 2021-12-13 18:01:18 +00:00
Mauricio Collares 9b35049770 sage: import arb 2.21.0 test fixes 2021-12-13 11:16:33 -03:00
Dmitry Kalinkin 8f0a587d4a
z3: fix darwin build 2021-12-13 07:42:47 -05:00
Oleksii Filonenko a400948064
Merge pull request #149167 from r-ryantm/auto-update/rink
rink: 0.6.1 -> 0.6.2
2021-12-13 14:40:57 +02:00
Martin Weinelt 423119b70b
Merge branch 'master' into staging-next 2021-12-13 12:20:07 +01:00
Felix Buehler 4cc23f2b1e why3.withProvers: add dontUnpack 2021-12-12 20:33:14 +01:00
R. Ryantm d4a5bdc264 seaview: 5.0.4 -> 5.0.5 2021-12-12 15:59:16 +00:00
Dmitry Kalinkin 1dcb22acc9
Merge branch 'master' into staging-next
Conflicts:
	pkgs/development/python-modules/gdown/default.nix
2021-12-12 00:00:04 -05:00
Mario Rodas e09a539ccb
Merge pull request #150166 from r-ryantm/auto-update/gmsh
gmsh: 4.8.4 -> 4.9.0
2021-12-11 22:52:19 -05:00
Ryan Mulligan 9e570d0034
Merge pull request #150031 from r-ryantm/auto-update/jmol
jmol: 14.31.49 -> 14.32.2
2021-12-11 16:23:05 -08:00
Dmitry Kalinkin b6b59334bb
Merge branch 'master' into staging-next
Conflicts:
	pkgs/development/python-modules/celery/default.nix
	pkgs/development/python-modules/kombu/default.nix
2021-12-11 13:15:49 -05:00
Jörg Thalheim 453b06c677
Merge pull request #150121 from markuskowa/fix-cp2k
cp2k: make elpa optional
2021-12-11 14:04:41 +00:00
Jörg Thalheim 4e5d03cd21
Merge pull request #150111 from r-ryantm/auto-update/gretl
gretl: 2021b -> 2021d
2021-12-11 13:34:40 +00:00
Jörg Thalheim 953bdd43bf
Merge pull request #150124 from r-ryantm/auto-update/gwyddion
gwyddion: 2.59 -> 2.60
2021-12-11 13:31:59 +00:00
Jörg Thalheim 2a322411ff
Merge pull request #150217 from r-ryantm/auto-update/cryptoverif
cryptoverif: 2.04 -> 2.05
2021-12-11 12:53:42 +00:00
R. Ryantm 50554a43cf cryptoverif: 2.04 -> 2.05 2021-12-11 10:05:51 +00:00
R. Ryantm 2d939d3262 gmsh: 4.8.4 -> 4.9.0 2021-12-11 01:08:58 +00:00
R. Ryantm baf80d066b gama: 2.14 -> 2.16 2021-12-10 22:15:01 +00:00
R. Ryantm 7bbf6a048b gwyddion: 2.59 -> 2.60 2021-12-10 20:19:55 +00:00
Markus Kowalewski 6d1f54dc5d
cp2k: make elpa optional 2021-12-10 20:56:21 +01:00
R. Ryantm 7abc2f38b4 gretl: 2021b -> 2021d 2021-12-10 19:06:52 +00:00
github-actions[bot] cc51bd619c
Merge master into staging-next 2021-12-10 18:01:06 +00:00
Ryan Mulligan 76d64cf517
Merge pull request #149908 from r-ryantm/auto-update/marvin
marvin: 21.9.0 -> 21.18.0
2021-12-10 06:36:30 -08:00
R. Ryantm a1fa86e691 jmol: 14.31.49 -> 14.32.2 2021-12-10 10:13:57 +00:00
github-actions[bot] b2a2a5759e
Merge master into staging-next 2021-12-10 06:01:17 +00:00
Maximilian Bosch c87f93843c
Merge pull request #148905 from r-ryantm/auto-update/calc
calc: 2.13.0.1 -> 2.14.0.8
2021-12-10 01:22:16 +01:00
github-actions[bot] 92aabc6576
Merge master into staging-next 2021-12-10 00:01:53 +00:00
7c6f434c 26b52ea6a6
Merge pull request #149596 from r-ryantm/auto-update/polymake
polymake: 4.4 -> 4.5
2021-12-09 22:48:21 +00:00
R. Ryantm 806d3e25cd marvin: 21.9.0 -> 21.18.0 2021-12-09 19:20:04 +00:00
github-actions[bot] 379c22dbb3
Merge master into staging-next 2021-12-09 18:01:06 +00:00
Vincent Laporte a2dc97cd5c proverif: 2.03 → 2.04 2021-12-09 17:45:15 +01:00
Vincent Laporte a160defe64 coq_8_15: init at 8.15+rc1 2021-12-09 15:46:06 +01:00
Alyssa Ross c9a581b05f
Merge remote-tracking branch 'nixpkgs/master' into staging-next
CONFLICT (rename/add): Rename pkgs/development/python-modules/jsonwatch/default.nix->pkgs/tools/misc/jsonwatch/default.nix in nixpkgs/master.  Added pkgs/tools/misc/jsonwatch/default.nix in HEAD
2021-12-09 01:43:58 +00:00
Jörg Thalheim 2808a3bc74
Merge pull request #149465 from r-ryantm/auto-update/openmvg
openmvg: 1.6 -> 2.0
2021-12-08 15:15:48 +00:00
R. Ryantm 5a5f052be8 polymake: 4.4 -> 4.5 2021-12-08 10:49:07 +00:00
Alyssa Ross 16fb150e03
Merge remote-tracking branch 'nixpkgs/master' into staging-next
Conflicts:
	pkgs/development/libraries/libunwind/default.nix
2021-12-07 23:56:16 +00:00
R. Ryantm 3112fe2ace openmvg: 1.6 -> 2.0 2021-12-07 20:17:43 +00:00
Silvan Mosberger 55af3549a3 scyther: remove since it only supports Python 2
See https://github.com/cascremers/scyther/issues/20
2021-12-07 17:58:03 +01:00
R. Ryantm d337b164d6 minimap2: 2.22 -> 2.23 2021-12-07 15:04:36 +00:00
R. Ryantm 817561795f logisim-evolution: 3.7.1 -> 3.7.2 2021-12-07 12:21:37 +00:00
Jonathan Ringer 9dd8bffe92
Merge remote-tracking branch 'origin/master' into staging-next
Conflicts:
	pkgs/development/python-modules/aiocron/default.nix
2021-12-07 00:11:07 -08:00
Artturi 84bd0d6b7b
Merge pull request #147023 from wackbyte/fix-groove
groove: 5.7.4 -> 5.8.1 and jre -> jre8
2021-12-07 05:12:15 +02:00
R. Ryantm 5517f74759 rink: 0.6.1 -> 0.6.2 2021-12-06 23:57:17 +00:00
Luflosi ca87168c6e
boinc: copy systemd service file to output 2021-12-06 23:56:06 +01:00
Luflosi 4e0d9003fc
boinc: 7.14.2 -> 7.18.1 2021-12-06 23:56:06 +01:00
Luflosi a7be4f3840
boinc: add Luflosi as maintainer 2021-12-06 23:56:05 +01:00
github-actions[bot] ffbac7335b
Merge master into staging-next 2021-12-06 18:01:23 +00:00
7c6f434c 67f094f56b
Merge pull request #149043 from 7c6f434c/golly-update
golly: 3.3 -> 4.1
2021-12-06 16:17:35 +00:00
Michael Raskin 65b2df8b45 golly: 3.3 -> 4.1 2021-12-06 16:27:09 +01:00
R. Ryantm d5368e3bdb clingo: 5.5.0 -> 5.5.1 2021-12-06 09:34:25 +00:00
R. Ryantm 6c000f4835 calc: 2.13.0.1 -> 2.14.0.8 2021-12-06 07:03:08 +00:00
github-actions[bot] 5a1288f93b
Merge master into staging-next 2021-12-05 00:01:53 +00:00
Justin Bedő 711ef56370
Merge pull request #148514 from jbedo/picard
picard-tools: 2.26.4 -> 2.26.6
2021-12-05 06:56:25 +11:00
github-actions[bot] 67691cf506
Merge master into staging-next 2021-12-04 00:01:30 +00:00
markuskowa 660a7744c6
Merge pull request #148303 from markuskowa/add-elpa
elpa: init at 2021.05.002_bugfix
2021-12-03 22:52:58 +01:00
markuskowa 0016232876
Merge pull request #148350 from jbedo/genmap
genmap: init 1.3.0
2021-12-03 21:55:44 +01:00
Justin Bedo 17e3b75414
picard-tools: 2.26.4 -> 2.26.6 2021-12-04 07:51:31 +11:00
Justin Bedo 1a768ef4da
genmap: init 1.3.0 2021-12-04 06:51:16 +11:00
Jonathan Ringer 9fcf9be974
Merge remote-tracking branch 'origin/staging' into staging-next
Conflicts:
	pkgs/development/python-modules/bx-python/default.nix
2021-12-03 00:11:41 -08:00
Austin Seipp 2a295f42c8 symbiyosys: 2021.09.13 -> 2021.11.30
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2021-12-02 21:48:51 -06:00
Austin Seipp a79ca33d94 yosys: 0.10+1 -> 0.11+52, with abc update
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2021-12-02 21:48:51 -06:00
Bobby Rong 296de886d0
Merge pull request #148019 from hjones2199/kstars356
kstars: 3.5.5 -> 3.5.6
2021-12-03 09:24:39 +08:00
Jonathan Ringer 35f45f9dd7
Merge pull request #147426 from NixOS/python-unstable
Python unstable 2021-11-25
2021-12-02 15:56:12 -08:00
wackbyte 6a2815218d groove: 5.7.4 -> 5.8.1 and jre -> jre8
I tested OpenJDK11 but it didn't seem to work.
2021-12-02 22:18:13 +02:00
Markus Kowalewski 53f32adc65 cp2k: build with elpa 2021-12-02 17:22:41 +01:00
qbg b5b4a6ac4f
mathematica: Install desktop items (#147641) 2021-12-02 15:17:23 +02:00
Ryan Burns ac9ad0a998
Merge pull request #148240 from hjones2199/adopt-multi
adopt multiple packages
2021-12-01 23:34:28 -08:00
Hunter Jones b952a9b16e adopt multiple packages 2021-12-01 22:04:14 -06:00
Justin Bedo 82aef7957d
fastp: 0.23.1 -> 0.23.2 2021-12-02 08:03:17 +11:00
Vincent Laporte 48406e3fca coq_8_14: 8.14.0 → 8.14.1
And build Coq ≥ 8.14 with OCaml 4.12
2021-12-01 13:46:15 +01:00
Jörg Thalheim e89d789748
Merge pull request #148096 from arkivm/fix-mrtrix
mrtrix: 3.0.2 -> unstable-2021-11-25
2021-12-01 10:27:11 +00:00
Doron Behar 43ed12450e
Merge pull request #147828 from doronbehar/pkg/maxima 2021-12-01 11:34:38 +02:00
Vikram Narayanan b1d95dca56 mrtrix: 3.0.2 -> unstable-2021-11-25
The latest stable version fails to build with latest eigen (> 3).
https://github.com/MRtrix3/mrtrix3/pull/2368
2021-11-30 21:03:53 -08:00
Fabian Affolter c586350dfb
flatcam: add packaging 2021-11-30 18:52:55 -08:00
Doron Behar 50ba747abe yacas: Fix gui and jupyter build
- Add a patch fixing jsoncpp include.
- Add a build flag for java support.
- Add a `yacas-gui` build that is built with Gui (and jupyter support disabled).
- Enable tests.
- Reformat expression with a 1 input / argument per line.
2021-12-01 01:51:31 +02:00
Sandro 964a962222
Merge pull request #143545 from r-ryantm/auto-update/betaflight-configurator 2021-11-30 18:13:23 +01:00
Hunter Jones b04ef6a552 kstars: 3.5.5 -> 3.5.6 2021-11-30 08:13:12 -06:00
tilcreator 5989d54401 inav-configurator: init at 3.0.2 2021-11-30 15:11:55 +01:00
Sandro ebdd276b68
Merge pull request #147499 from trofi/fix-samtools-for-ncurses-6.3 2021-11-29 20:33:45 +01:00
Doron Behar 57ab62314b maxima, sage: Simplify lisp-compiler arguments namings
Make clearer the difference between `maxima` and `maxima-ecl` top-level
attributes. Use the `lisp-compiler` as a passthru for all of sage's
expressions. Add the `pname` attribute for `ecl` for compatibility with
other lisp implementations.
2021-11-29 15:51:30 +02:00
Doron Behar 8d17f4babf maxima: 5.45.0 -> 5.45.1
- Reformat expression with 1 line per input / argument
- Add @doronbehar as maintainer.
2021-11-29 15:51:29 +02:00
Doron Behar 8d227fe05c wxmaxima: 21.05.2 -> 21.11.0
- Remove the `Version-` prefix from the version.
- Add @doronbehar as maintainer.
2021-11-29 14:41:57 +02:00
Dmitry Kalinkin 51bf009063
mxnet: 1.6.0 -> 1.8.0 2021-11-28 17:27:31 -05:00
Dmitry Kalinkin b39504da72
mxnet: fix for gcc10+, enable on darwin 2021-11-28 17:27:11 -05:00
Markus Kowalewski 5cfe3c4e82
gromacs: fix double precission build on aarch64 2021-11-28 12:43:57 +01:00
Dmitry Kalinkin b1b02f09ad
Merge pull request #147671 from trofi/fix-root5-for-binutils-2.36
root5: binutils 2.37 fix
2021-11-28 04:43:28 -05:00
Bernardo Meurer 51694b0af4 root5: binutils 2.37 fix
Co-authored-by: TredwellGit <tredwell@tutanota.com>
2021-11-28 08:49:32 +00:00
Sandro 5d6a70c260
Merge pull request #147202 from voidIess/u/geogebra_6_0_672_0 2021-11-28 03:51:46 +01:00
Markus Kowalewski 8fb36866b8
octopus: 11.2 -> 11.3 2021-11-28 00:04:47 +01:00
Chad Jablonski 7944324d80 programmer-calculator: 2.1 -> 2.2 2021-11-26 23:19:39 -05:00
Sergei Trofimovich 8147fb683c samtools: pull upstream fix for ncurses-6.3
Without the fix build on ncurses-6.3 fails as:

    bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
       88 |     mvprintw(y,x,str);
          |     ^~~~~~~~
2021-11-26 13:02:05 +00:00
Ellie Hermaszewska 7282988ce9
Merge pull request #147394 from wirew0rm/bumpPicoscope
picoscope: 7.0.83 -> 7.0.86 + LANG=C
2021-11-26 09:33:26 +08:00
Sandro eff5cece35
Merge pull request #146648 from florentc/tlaplus 2021-11-25 12:38:31 +01:00
Justin Bedo c1eb0dddea
delly: 0.8.7 -> 0.9.1 2021-11-25 21:19:48 +11:00
Florent C b5d3526bab tlaplus: 1.7.0 -> 1.7.1
This updates tlaplus to the most recent stable version and directly
fetches the tlatools jar file from the official Github release page
instead of building from the sources. In the previous tlaplus nix
package, there was an issue with the tools when passing some command
line arguments such as `-workers 4` for TLC. A java string method was
not found and the program would not proceed correctly. This solves this
issue.
2021-11-25 10:56:11 +01:00
voidless a34736a38f geogebra6 6-0-644-0 -> 6-0-676-0 2021-11-24 23:15:54 +01:00
Alexander Krimm e248ab379a picoscope: set LANG=C in wrapper
The picoscope application seems to crash for non-english locales. This
overrides the LANG environment variable to C. This does not affect the
language selected in the mono gtk GUI.
2021-11-23 11:26:40 +01:00
Alexander Krimm d56073935d picoscope: 7.0.83 -> 7.0.86
Update performed via update.py, other affected versions:
libps*: 2.1.75 -> 2.1.76
libpicoipp: 1.3.0-4r121 -> 1.3.0-4r130
2021-11-23 11:21:26 +01:00
evils decac5a0d2
kicad-unstable: 2021-07-12 -> 6.0.0-rc1 (#142261)
* kicad-unstable: 2021-07-12 -> 2021-11-10

with changes to library paths

Plugin and Content Manager seems to work
  (not related to the library paths changes)

* kicad-unstable: 2021-11-10 -> 6.0.0-rc1
2021-11-23 00:05:57 -05:00
evils d2c4e0a3ba
kicad: 5.1.11 -> 5.1.12 (#145403)
very minor change
5.1.11 was never officially released
  due to a re-tag
2021-11-23 00:05:27 -05:00
github-actions[bot] 18ad263272
Merge master into staging-next 2021-11-21 18:01:07 +00:00
Artturi 8d6a02b049
Merge pull request #146787 from risicle/ris-hmmer-x86_64 2021-11-21 17:46:47 +02:00
Sandro 07f29d2db2
Merge pull request #146829 from r-burns/isx86 2021-11-21 14:20:12 +01:00
github-actions[bot] c68c4b3db8
Merge master into staging-next 2021-11-21 12:01:20 +00:00
7c6f434c b56d7a70a7
Merge pull request #146792 from SuperSandro2000/R
R: manually fix things after patches got applied
2021-11-21 08:57:26 +00:00
github-actions[bot] 6ad93ecdbb
Merge master into staging-next 2021-11-21 06:01:18 +00:00
Ryan Burns 2175b157ac treewide: refactor isi686 && isx86_64 -> isx86 2021-11-20 17:50:41 -08:00
Mauricio Collares 1ee4cb8d93
sage: patch test so that new pari warning doesn't cause failures (#4) 2021-11-20 20:13:07 -03:00
Sandro 00a52ef677
R: manually fix things after patches got applied
This prevents conflicts in case a patch changes the same line
2021-11-20 21:10:28 +01:00
Robert Scott ec24bab90e hmmer: restrict platforms to x86_64
technically big-endian powerpc with VMX is also supported, but
on x86, SSE is apparently *required* which means we can't build
a pure i686 version
2021-11-20 19:17:57 +00:00
AndersonTorres dc2cad8150 gp2c: cosmetical changes 2021-11-19 20:35:16 -03:00