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4476 Commits

Author SHA1 Message Date
Martin Weinelt
7cf67850c0
Merge branch 'master' into staging-next 2021-04-15 01:01:26 +02:00
Sandro
28fb287d4b
Merge pull request #118610 from GregorySchwartz/init/macs2 2021-04-14 21:15:38 +02:00
Gregory W. Schwartz
b7763a8287 macs2: init at 2.2.7.1 
Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Renamed package, updated version, set pypi, and added import test.

Update pkgs/applications/science/biology/MACS2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Add comment about error for checking.

Two spaces indent.
 2021-04-14 10:17:53 -04:00
Vladimír Čunát
d2eb7a7887
Merge branch 'staging' into staging-next 
A few conflicts but relatively clear ones (I think).
 2021-04-14 10:08:25 +02:00
Dmitry Kalinkin
a469a7be55
sherpa: compile with --enable-pythia flag 2021-04-13 09:34:42 -04:00
Luke Granger-Brown
08b22e605b Merge remote-tracking branch 'upstream/staging-next' into down-integrate-staging 2021-04-12 18:49:01 +00:00
hjones2199
79c3609603
celestia: 1.6.1 -> 1.6.2.2 (#117999) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2021-04-12 20:17:17 +02:00
Fabian Affolter
e4149e6e0b
rink: specify license 2021-04-11 23:18:32 +02:00
R. RyanTM
12518ff683 rink: 0.5.1 -> 0.6.0 2021-04-11 14:49:45 +00:00
Eduardo Sánchez Muñoz
b5c90bb4da kicad: fix license 
https://kicad.org/about/licenses/
 2021-04-10 20:39:02 +02:00
Eduardo Sánchez Muñoz
427edc8b5a kicad: include desktop, icon and mime files 
Fixes https://github.com/NixOS/nixpkgs/issues/106295.
 2021-04-10 18:55:04 +02:00
Jan Tojnar
625ce6c7f6 Merge branch 'staging-next' into staging 
In python-packages.nix, resolve conflict between 50d604314e and 187d0371ab.
 2021-04-08 17:14:31 +02:00
Sandro
32b567d9e6
Merge pull request #118775 from lopsided98/qgroundcontrol-update 
qgroundcontrol: 4.1.1 -> 4.1.2
 2021-04-08 09:57:15 +02:00
Ben Wolsieffer
1e52d002bb qgroundcontrol: 4.1.1 -> 4.1.2 2021-04-08 00:04:07 -04:00
github-actions[bot]
1bd1969867
Merge staging-next into staging 2021-04-06 18:15:33 +00:00
Jan Tojnar
70babe5bcf Merge branch 'staging-next' into staging 2021-04-06 16:25:41 +02:00
voidless
b6c315b4fb geogebra6: 6_0_620_0 -> 6_0_631_0 2021-04-06 10:52:30 +02:00
Dmitry Kalinkin
1d93243467
root: 6.22.06 -> 6.22.08 2021-04-06 02:41:06 -04:00
Gregory Schwartz
9bf867612d
meme-suite: init at 5.1.1 (#118603) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2021-04-05 22:43:27 +02:00
Sandro Jäckel
3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Frederik Rietdijk
1e7ed8b2f3
Merge branch 'staging' into python-unstable 2021-04-04 12:59:12 +02:00
Sandro Jäckel
33a395f195
yacc: deprecate alias 
and add a new line after the alphabetically sorting to please my inner monk
 2021-04-04 03:18:58 +02:00
Frederik Rietdijk
c12ef05bda sage: keep cypari2 at 2.1.1 2021-04-03 17:49:44 +02:00
Frederik Rietdijk
d20a05e963 libpoly: use python3 2021-04-03 17:06:22 +02:00
Frederik Rietdijk
7865ac1046 lean2: stay with python2 
broken, so who knows...
 2021-04-03 17:06:21 +02:00
Frederik Rietdijk
7368564f99 gurobi: stay with python2 2021-04-03 17:06:08 +02:00
Frederik Rietdijk
ee258981bf ginac: use python3 2021-04-03 17:06:07 +02:00
Jack Gerrits
dfab218b9b vowpal-wabbit: 8.9.2 -> 8.10.0 2021-04-01 13:46:09 -04:00
Mario Rodas
d2275796d1 beluga: 2020-03-11 -> 1.0 2021-04-01 04:20:00 +00:00
Sandro
498cb76bdf
Merge pull request #117799 from LeSuisse/aliza-1.98.57 
aliza: 1.98.43 -> 1.98.57
 2021-03-30 17:18:15 +02:00
Sandro
9e24497453
Merge pull request #117970 from mpoquet/simgrid-3.26-to-3.27 
simgrid: 3.26 -> 3.27
 2021-03-30 14:28:37 +02:00
Ryan Mulligan
f3262c2a3e
Merge pull request #117648 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.25.0 -> 2.25.1
 2021-03-29 16:10:25 -07:00
Millian Poquet
99a5de6ebc simgrid: 3.26 -> 3.27 2021-03-29 21:20:27 +02:00
Justin Bedo
76bd953162 bedops: init 2.4.39 2021-03-28 22:27:51 -04:00
Maximilian Bosch
b8779b59d5
Merge pull request #117760 from r-ryantm/auto-update/calc 
calc: 2.12.9.0 -> 2.12.9.1
 2021-03-28 23:35:49 +02:00
Maximilian Bosch
4fc2ef2c5e
stellarium: 0.20.4 -> 0.21.0 
ChangeLog: https://github.com/Stellarium/stellarium/releases/tag/v0.21.0
 2021-03-28 22:46:57 +02:00
Ryan Mulligan
9a35bc87e8
Merge pull request #117607 from r-ryantm/auto-update/marvin 
marvin: 21.2.0 -> 21.3.0
 2021-03-27 20:35:56 -07:00
Thomas Gerbet
f801e2e92c aliza: 1.98.43 -> 1.98.57 2021-03-27 23:49:33 +01:00
R. RyanTM
190a6f04b6 calc: 2.12.9.0 -> 2.12.9.1 2021-03-27 07:21:16 +00:00
Sandro
53734a4355
Merge pull request #117730 from veprbl/pr/snakemake_6_0_5 
snakemake: 5.28.0 -> 6.0.5
 2021-03-27 02:44:44 +01:00
Dmitry Kalinkin
8887f4655e
snakemake: 5.28.0 -> 6.0.5 2021-03-26 18:32:26 -04:00
Gabriel Ebner
109d6b3bdb
Merge pull request #117712 from gebner/elan0110 
elan: 0.10.3 -> 0.11.0
 2021-03-26 19:58:29 +01:00
Dominic Steinitz
9eb60bee0e Fix https://github.com/NixOS/nixpkgs/issues/117715 2021-03-26 18:18:42 +00:00
Gabriel Ebner
0661cf4882 elan: 0.10.3 -> 0.11.0 
Also adapt the patchelf patch from rustup, since Lean 4 now dynamically
links to gmp.
 2021-03-26 19:16:33 +01:00
R. RyanTM
49e4c1e323 picard-tools: 2.25.0 -> 2.25.1 2021-03-26 03:16:44 +00:00
Mario Rodas
01f3ceeaa9
Merge pull request #116630 from r-ryantm/auto-update/lean 
lean: 3.27.0 -> 3.28.0
 2021-03-25 19:15:00 -05:00
Florian Klink
7d19272ef2
Merge pull request #115820 from flokli/xmedcon 
xmedcon: init at 0.21.0
 2021-03-25 23:01:58 +01:00
Dmitry Kalinkin
bf5c995ad2
Merge pull request #116487 from veprbl/pr/professor_init 
professor: init at 2.3.3
 2021-03-25 16:07:55 -04:00
R. RyanTM
3b3f141837 marvin: 21.2.0 -> 21.3.0 2021-03-25 17:58:45 +00:00
Frederik Rietdijk
5a5cb718a5 bedtools: use python3 2021-03-25 10:42:32 +01:00
Frederik Rietdijk
2c00aed6b1 bcftools: use python3 2021-03-25 10:39:47 +01:00
Timo Kaufmann
82e1bfa53d
Merge pull request #117123 from collares/cypari-update 
cypari2, cysignals: updates
 2021-03-24 21:38:04 +00:00
Sandro
489ca6979e
Merge pull request #117335 from bzizou/spades 
SPAdes: 3.15.1 -> 3.15.2 + fix license and platform
 2021-03-24 19:54:23 +01:00
Mauricio Collares
812ffed96b gap: backport aarch64 patch 2021-03-23 22:09:29 -03:00
Mauricio Collares
594eda3b7d sage: patch intermittently failing test 2021-03-23 22:09:29 -03:00
Mauricio Collares
15fd117e71 cypari2: 2.1.1 -> 2.1.2 
* cypari2: 2.1.1 -> 2.1.2, patch to fix segfault

* sage: update test expectations
 2021-03-23 22:09:29 -03:00
Ryan Mulligan
db21819e91
Merge pull request #117345 from r-ryantm/auto-update/jmol 
jmol: 14.31.34 -> 14.31.35
 2021-03-23 09:14:57 -07:00
R. RyanTM
8ab6893632 jmol: 14.31.34 -> 14.31.35 2021-03-23 11:29:06 +00:00
Bruno Bzeznik
f0eef16f9c SPAdes: 3.15.1 -> 3.15.2 + fix license and platform 2021-03-23 10:51:01 +01:00
Paul Liétar
6f8eb1e65a coq: enable coqide on darwin 
This was disabled a while ago, when itstool was broken on darwin.
Now that itstool works again, it can be re-enabled.
 2021-03-23 08:17:13 +01:00
mtreca
ff64acacba sumo: init at 1.8.0 2021-03-22 12:17:15 +01:00
Sandro
1c3d923aaa
Merge pull request #115685 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 20.06.6 -> 21.02.0
 2021-03-22 01:08:42 +01:00
Sandro
593cc0d5ee
Merge pull request #111224 from r-ryantm/auto-update/gwyddion 
gwyddion: 2.56 -> 2.57
 2021-03-21 05:22:26 +01:00
Florian Klink
275cc4e9c7 xmedcon: init at 0.21.0 
This allows reading DICOM images, including 3d stacks.
 2021-03-20 21:36:38 +01:00
Sandro
edac82660c
Merge pull request #117039 from raboof/gnucap-init-at-20210107 
gnucap: init at 20210107
 2021-03-20 19:49:27 +01:00
Arnout Engelen
52b7bd1e77
gnucap: init at 20210107 
Submitting on behalf of kvtb,
https://discourse.nixos.org/t/casual-nixpkgs-contributions/9607/13
 2021-03-20 16:36:48 +01:00
Mauricio Collares
c0b869f19f sage: re-add pkgconfig input, it's not duplicated 2021-03-20 06:43:23 -03:00
github-actions[bot]
c804f22a81
Merge master into staging-next 2021-03-19 12:26:52 +00:00
Doron Behar
23ef497c17
Merge pull request #111237 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.107 -> 3.3.108
 2021-03-19 10:24:36 +00:00
github-actions[bot]
6ffd2fe000
Merge master into staging-next 2021-03-19 06:17:55 +00:00
Jack Gerrits
a364fb6557 vowpal-wabbit: init at 8.9.2 2021-03-18 18:41:07 -07:00
Jan Tojnar
2445e9a681
Merge branch 'master' into staging-next 2021-03-18 19:24:39 +01:00
Thomas Mader
09acdfde94
sambamba: 0.7.1 -> 0.8.0 
Getting rid of dmd dependency and compile with ldc
 2021-03-18 17:41:30 +02:00
Jan Tojnar
0136206b12
Merge branch 'master' into staging-next 2021-03-18 13:35:59 +01:00
R. RyanTM
fadcc52955 lean: 3.27.0 -> 3.28.0 2021-03-17 14:16:02 +00:00
Sandro
fe4a249718
Merge pull request #116594 from NixOS/SuperSandro2000-patch-1 
sage: remove duplicated pkgconfig
 2021-03-17 11:10:10 +01:00
Sandro
2d01f4a96a
sage: remove duplicated pkgconfig 2021-03-17 09:24:07 +01:00
Samuel Gräfenstein
d90e7ac2e1
kicad: gnome3.dconf -> dconf 
Fix building with `config.allowAliases = false;`.
 2021-03-17 00:00:17 +01:00
Samuel Gräfenstein
b72ee5775c
treewide: gnome2.gtk -> gtk2 
Fix building with `config.allowAliases = false;`.
 2021-03-17 00:00:16 +01:00
Samuel Gräfenstein
672cd0c8e7
treewide: gnome3.gtkmm -> gtkmm3 
Fix building with `config.allowAliases = false;`.
 2021-03-17 00:00:15 +01:00
Samuel Gräfenstein
9517398973
treewide: gnome3.defaultIconTheme -> gnome3.adwaita-icon-theme 
Fix building with `config.allowAliases = false;`.
 2021-03-17 00:00:15 +01:00
Dmitry Kalinkin
7adf3f8127
professor: init at 2.3.3 2021-03-16 11:14:00 -04:00
github-actions[bot]
c7b23f6440
Merge master into staging-next 2021-03-14 18:17:08 +00:00
R. RyanTM
7c14c1a8d0 pcb: 4.2.2 -> 4.3.0 2021-03-14 13:34:35 -04:00
Martin Weinelt
0241873f7f
Merge branch 'master' into staging-next 2021-03-14 17:35:32 +01:00
mucaho
ddf1821112 tla-toolbox: 1.7.0 -> 1.7.1 
* updates package version
* fixes #114741
* fixes TLC model check call
 2021-03-14 12:27:35 -04:00
Ryan Mulligan
0e63a1bb33
Merge pull request #115579 from r-ryantm/auto-update/stacks 
stacks: 2.53 -> 2.55
 2021-03-14 07:47:22 -07:00
Ryan Mulligan
03754f91eb
Merge pull request #115574 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.14.1 -> 3.15.1
 2021-03-14 07:46:58 -07:00
github-actions[bot]
3b97019142
Merge master into staging-next 2021-03-14 06:17:28 +00:00
R. RyanTM
29bf7e2b89 jmol: 14.31.32 -> 14.31.34 2021-03-14 01:06:53 -05:00
R. RyanTM
621f19d89c calc: 2.12.8.2 -> 2.12.9.0 2021-03-13 23:43:28 -05:00
github-actions[bot]
d6257d451b
Merge master into staging-next 2021-03-11 18:23:54 +00:00
Guillaume Girol
a72148f3bc
Merge pull request #114881 from collares/sage-dependencies 
sage dependency updates
 2021-03-11 17:52:16 +00:00
github-actions[bot]
6a3a358b0d
Merge master into staging-next 2021-03-10 18:23:15 +00:00
Austin Seipp
b54b679c90
Merge pull request #115717 from r-ryantm/auto-update/verilator 
verilator: 4.108 -> 4.110
 2021-03-10 08:49:38 -06:00
github-actions[bot]
aea4725648
Merge master into staging-next 2021-03-10 12:21:24 +00:00
Sandro
bb0bb13f32
Merge pull request #115621 from jbedo/octopus 
octopus: 0.7.0 -> 0.7.1
 2021-03-10 10:03:42 +01:00
R. RyanTM
5a9a1b3545 verilator: 4.108 -> 4.110 2021-03-10 07:47:54 +00:00
R. RyanTM
6dc1177c24 wxmaxima: 20.06.6 -> 21.02.0 2021-03-10 03:37:07 +00:00
github-actions[bot]
149a81c88d
Merge master into staging-next 2021-03-10 00:39:07 +00:00