Commit Graph

4623 Commits

Author SHA1 Message Date
Ryan Mulligan
c72c9f46e2
Merge pull request #122391 from r-ryantm/auto-update/jmol
jmol: 14.31.36 -> 14.31.38
2021-05-10 10:17:33 -07:00
Jan Tojnar
594a885912
Merge branch 'staging-next' into staging 2021-05-10 09:45:47 +02:00
github-actions[bot]
1e3d91bd19
Merge master into staging-next 2021-05-10 00:48:32 +00:00
R. RyanTM
4ff0c782a3 jmol: 14.31.36 -> 14.31.38 2021-05-09 20:32:06 +00:00
Ben Siraphob
418a37d99c coq2html: 20170720 -> 1.2 2021-05-09 22:00:15 +02:00
Vladimír Čunát
5663b2b2d3
Merge branch 'master' into staging-next
(a trivial conflict in transmission)
2021-05-09 09:31:55 +02:00
R. RyanTM
2c143443f7 libpoly: 0.1.8 -> 0.1.9 2021-05-08 18:34:00 -07:00
R. RyanTM
5ab09faafb gretl: 2021a -> 2021b 2021-05-08 17:11:36 -07:00
Jan Tojnar
dd78ce1c53
Merge branch 'staging-next' into staging 2021-05-08 20:59:05 +02:00
Martin Weinelt
9651084620 Merge remote-tracking branch 'origin/master' into staging-next 2021-05-08 14:43:43 +02:00
Jonathan Ringer
1d85caaa26 root: fix build 2021-05-08 01:29:18 -07:00
Jan Tojnar
468cb5980b gnome: rename from gnome3
Since GNOME version is now 40, it no longer makes sense to use the old attribute name.
2021-05-08 09:47:42 +02:00
Daniël de Kok
85f96822a0 treewide: fix cargoSha256/cargoHash
Rust 1.50.0 incorporated a Cargo change (rust-lang/cargo#8937) in
which cargo vendor erroneously changed permissions of vendored
crates. This was fixed in Rust
1.51.0 (rust-lang/cargo#9131). Unfortunately, this means that all
cargoSha256/cargoHashes produced during the Rust 1.50.0 cycle are
potentially broken.

This change updates cargoSha256/cargoHash tree-wide.

Fixes #121994.
2021-05-08 00:36:37 -07:00
github-actions[bot]
b4416b52c5
Merge master into staging-next 2021-05-08 00:46:50 +00:00
Malte Brandy
2a11f1f5cc
Merge branch 'master' into haskell-updates 2021-05-07 15:03:54 +02:00
github-actions[bot]
12193913a1
Merge staging-next into staging 2021-05-07 12:23:21 +00:00
Robert Hensing
aaec26af39
Merge pull request #121896 from raboof/extract-version-test-to-utility
test-utilities: version test
2021-05-07 11:56:01 +02:00
Arnout Engelen
b68130fd2c
test-utilities: version test
Extract 'version test' to a reusable test utility as discussed in
https://github.com/NixOS/nixpkgs/pull/119636#issuecomment-826137021 and
2021-05-07 09:53:35 +02:00
sternenseemann
eaeb69862c petrinizer: restrict platforms by sbv
sbv has the most limited range of platforms of the dependencies.
2021-05-06 16:24:58 +02:00
sternenseemann
73c2dd4aa6 petrinizer: fix build
* take z3 haskell package from haskellPackages
* take sbv 7.13 from haskellPackages, apply patch fixing build
  with GHC >= 8.8.8
2021-05-06 11:43:59 +02:00
github-actions[bot]
dbc1478d23
Merge staging-next into staging 2021-05-05 06:21:29 +00:00
R. RyanTM
59cd52dc40 gmsh: 4.8.3 -> 4.8.4 2021-05-05 01:26:49 -04:00
github-actions[bot]
98d7aac597
Merge staging-next into staging 2021-05-04 00:49:43 +00:00
Dmitry Kalinkin
1cfcfccc6e
Merge pull request #121411 from veprbl/pr/xfitter_darwin_fix
xfitter: fix for darwin
2021-05-03 17:37:34 -04:00
github-actions[bot]
5e177b16b1
Merge staging-next into staging 2021-05-03 18:25:49 +00:00
edef
4e4c45efac
Merge pull request #121375 from deviant/bump-rink
rink: 0.6.0 -> 0.6.1
2021-05-03 13:57:36 +00:00
github-actions[bot]
a4c3a2d732
Merge staging-next into staging 2021-05-03 12:26:48 +00:00
Gabriel Ebner
62458574e3
Merge pull request #121361 from r-ryantm/auto-update/lean
lean: 3.29.0 -> 3.30.0
2021-05-03 11:13:53 +02:00
github-actions[bot]
a7e07bddd5
Merge staging-next into staging 2021-05-02 12:24:53 +00:00
Luke Granger-Brown
884cf29501 dcm2niix: 1.0.20201102 -> 1.0.20210317 2021-05-02 11:10:40 +00:00
R. RyanTM
ad5f251230 dcm2niix: 1.0.20200331 -> 1.0.20201102 2021-05-02 03:14:11 +00:00
github-actions[bot]
e6037ce5fe
Merge staging-next into staging 2021-05-02 00:58:46 +00:00
Luke Granger-Brown
ebf371726d sumorobot-manager: fix compilation 2021-05-02 00:12:19 +00:00
R. RyanTM
99f8bc3e03 sumorobot-manager: 0.9.0 -> 1.0.0 2021-05-02 00:02:46 +00:00
github-actions[bot]
49721bed32
Merge staging-next into staging 2021-05-01 18:26:21 +00:00
Dmitry Kalinkin
c846fa1674
xfitter: fix for darwin
Fixes: 8984fc29 ('xfitter: fix build w/glibc-2.32')
2021-05-01 13:15:06 -04:00
Sandro
4b2c9640e7
Merge pull request #120613 from erikbackman/master 2021-05-01 18:42:40 +02:00
V
5a835e6e92 rink: 0.6.0 -> 0.6.1 2021-05-01 10:46:51 +02:00
R. RyanTM
96e1cc0768 lean: 3.29.0 -> 3.30.0 2021-05-01 05:49:45 +00:00
John Ericson
17305d2df0
Merge pull request #111487 from Ericson2314/llvm-outputs-and-cross-compile-tools
llvmPackages: Clean up outputs
2021-04-30 11:28:08 -04:00
github-actions[bot]
d7882499f8
Merge staging-next into staging 2021-04-30 12:26:14 +00:00
Michael Raskin
ee4684f052
Merge pull request #117716 from idontgetoutmuch/master
Fix https://github.com/NixOS/nixpkgs/issues/117715
2021-04-30 07:28:43 +00:00
Andrew Childs
7869d16545 llvmPackages: Multuple outputs for everythting
Also begin to start work on cross compilation, though that will have to
be finished later.

The patches are based on the first version of
https://reviews.llvm.org/D99484. It's very annoying to do the
back-porting but the review has uncovered nothing super major so I'm
fine sticking with what I've got.

Beyond making the outputs work, I also strove to re-sync the packages,
as they have been drifting pointlessly apart for some time.

----

Other misc notes, highly incomplete

- lvm-config-native and llvm-config are put in `dev` because they are
  tools just for build time.

- Clang no longer has an lld dep. That was introduced in
  db29857eb3, but if clang needs help
  finding lld when it is used we should just pass it flags / put in the
  resource dir. Providing it at build time increases critical path
  length for no good reason.

----

A note on `nativeCC`:

`stdenv` takes tools from the previous stage, so:

1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.stdenv.cc`: `(?0, ?1, x)`

while:

1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.targetPackages`: `(x, x, ?2)`
3. `pkgsBuildBuild.targetPackages.stdenv.cc`: `(?1, x, x)`
2021-04-30 05:41:00 +00:00
github-actions[bot]
3ad64733d9
Merge staging-next into staging 2021-04-29 18:28:08 +00:00
Dominic Steinitz
732ab3d4e2 Incorporate suggeston by collares 2021-04-29 17:34:34 +01:00
R. RyanTM
5b7a76e2a6 jmol: 14.31.35 -> 14.31.36 2021-04-29 12:39:03 +00:00
github-actions[bot]
01105a117a
Merge staging-next into staging 2021-04-29 06:21:55 +00:00
R. RyanTM
5122077801 gmsh: 4.8.1 -> 4.8.3 2021-04-29 00:17:51 -04:00
R. RyanTM
e99e9f2d47 elan: 1.0.0 -> 1.0.2 2021-04-29 00:04:34 -04:00
github-actions[bot]
655989d7b3
Merge staging-next into staging 2021-04-28 00:15:29 +00:00
Gabriel Ebner
a062505e10
Merge pull request #120177 from r-ryantm/auto-update/elan
elan: 0.11.0 -> 1.0.0
2021-04-27 22:52:12 +02:00
R. RyanTM
32cb3382e5 elan: 0.11.0 -> 1.0.0 2021-04-27 22:32:13 +02:00
Gabriel Ebner
abbc2384d7
Merge pull request #120822 from r-ryantm/auto-update/lean
lean: 3.28.0 -> 3.29.0
2021-04-27 22:28:19 +02:00
erikbackman
95b40e4143 (numworks-epsilon): init at 15.3.2 2021-04-27 19:07:25 +02:00
R. RyanTM
4ccb9422c7 lean: 3.28.0 -> 3.29.0 2021-04-27 05:34:13 +00:00
github-actions[bot]
e30742adc3
Merge staging-next into staging 2021-04-26 12:06:35 +00:00
Vincent Laporte
35dfa0e927 alt-ergo: 2.3.3 → 2.4.0 2021-04-26 08:32:18 +02:00
github-actions[bot]
28c3da370d
Merge staging-next into staging 2021-04-26 06:05:56 +00:00
R. RyanTM
224fc21cc3 tetgen: 1.5.1 -> 1.6.0 2021-04-26 01:32:28 -04:00
github-actions[bot]
8634c6f7d1
Merge staging-next into staging 2021-04-26 00:17:03 +00:00
Mauricio Collares
e1ad2f5aa4 sage: remove cypari2 override
This reverts commit c12ef05bda.
2021-04-25 18:21:58 -03:00
Michael Raskin
14f65f0dc5
Merge pull request #116365 from omasanori/sage-9.3
sage: 9.2 -> 9.3
2021-04-25 21:17:32 +00:00
github-actions[bot]
9a945aac72
Merge staging-next into staging 2021-04-25 18:14:18 +00:00
Eduardo Sánchez Muñoz
6b9e396a07 qalculate-gtk: 3.17.0 -> 3.18.0 2021-04-25 16:17:26 +02:00
github-actions[bot]
944e32775d
Merge staging-next into staging 2021-04-24 00:16:20 +00:00
Alyssa Ross
4f4d95bbc2
Merge remote-tracking branch 'nixpkgs/master' into staging-next
Conflicts:
	pkgs/development/python-modules/pyvex/default.nix
	pkgs/top-level/python-packages.nix
2021-04-23 13:49:12 +00:00
Michael Raskin
2a04a9ce44
Merge pull request #120168 from r-ryantm/auto-update/clingo
clingo: 5.4.1 -> 5.5.0
2021-04-23 08:51:33 +00:00
github-actions[bot]
0d97d9f23b
Merge staging-next into staging 2021-04-23 00:15:42 +00:00
github-actions[bot]
481a9bc47c
Merge master into staging-next 2021-04-23 00:15:39 +00:00
R. RyanTM
82bc3d6c28 clingo: 5.4.1 -> 5.5.0 2021-04-22 07:44:27 +00:00
R. RyanTM
e230004975 calc: 2.12.9.1 -> 2.13.0.1 2021-04-22 06:59:52 +00:00
Masanori Ogino
090b71f627 sage: 9.2 -> 9.3.rc4
Co-authored-by: Mauricio Collares <mauricio@collares.org>
2021-04-22 14:06:56 +09:00
Mauricio Collares
00d2e24395 eclib: 20210223 -> 20190909
This reverts commits 003705ef08
and ef615b5a61.
2021-04-22 14:06:56 +09:00
Garaba Flórián
a0f410646c sage: use threejs fork 2021-04-22 14:06:56 +09:00
Mauricio Collares
090165d7c1 singular: disable vspace on aarch64 2021-04-22 14:06:56 +09:00
Mauricio Collares
cd7cf5942b singular: use older autoconf macro to unbreak aarch64 2021-04-22 09:01:30 +09:00
Mauricio Collares
aebef1703f singular: import aarch64 support patch 2021-04-22 09:01:07 +09:00
Timo Kaufmann
ceaf48fdb2 singular: 4.1.1p2 -> 4.2.0p2
Adds proper tests. Also removes the "enableFactory" option because
singular actually enables factory by default and explicitly disabling it
breaks the build. So the option was never really available.
2021-04-22 09:01:07 +09:00
Mauricio Collares
cd215e793a pynac: 0.7.26 -> 0.7.27 2021-04-22 09:01:07 +09:00
Mauricio Collares
79046fb4f8 gap: 4.10.2 -> 4.11.0 2021-04-22 09:01:07 +09:00
github-actions[bot]
a260b67879
Merge staging-next into staging 2021-04-21 12:06:26 +00:00
github-actions[bot]
9b3e698b14
Merge master into staging-next 2021-04-21 12:06:23 +00:00
Sandro
59f840f3d5
Merge pull request #119055 from eduardosm/kicad 2021-04-21 06:28:21 +02:00
Mario Rodas
8b2b6e4e11
Merge pull request #119682 from marsam/update-beluga
beluga: 2020-03-11 -> 1.0
2021-04-20 22:22:02 -05:00
github-actions[bot]
6929a896cf
Merge staging-next into staging 2021-04-20 12:06:48 +00:00
github-actions[bot]
960439e003
Merge master into staging-next 2021-04-20 12:06:46 +00:00
Maximilian Bosch
8389dcb67d
Merge pull request #119911 from jbedo/octopus
octopus: 0.7.1 -> 0.7.3
2021-04-20 10:58:42 +02:00
github-actions[bot]
cf0edc0dea
Merge staging-next into staging 2021-04-20 06:06:28 +00:00
github-actions[bot]
e605a07cc0
Merge master into staging-next 2021-04-20 06:06:25 +00:00
R. RyanTM
44a83a3cb6 gmsh: 4.8.0 -> 4.8.1 2021-04-19 22:37:39 -04:00
Justin Bedo
def7c82f88
octopus: 0.7.1 -> 0.7.3 2021-04-20 10:13:25 +10:00
Jörg Thalheim
b2a1e04eed
Merge remote-tracking branch 'upstream/staging-next' into HEAD 2021-04-17 16:37:04 +02:00
github-actions[bot]
f620e30ca4
Merge master into staging-next 2021-04-17 00:15:03 +00:00
Vincent Laporte
ab16ad8764 coq_8_13: 8.13.1 → 8.13.2 2021-04-16 22:32:31 +02:00
Alyssa Ross
e459db3f81 glsurf: fix license
The README says GPL 2 or any later version, not LGPL.
2021-04-16 14:06:10 +00:00
Alyssa Ross
70e33e3ae3 glsurf: use current giflib
This requires bumping the version of camlimages used by glsurf to a
version that supports current giflib.  The most recent versions of
camlimages (even of 4.x) don't support ocaml 4.01 any more, so I've
upgraded to 4.1.2 here, the last version that supports ocaml 4.01 (and
which happily supports current giflib).
2021-04-16 14:06:10 +00:00
Alyssa Ross
6e3b5fd046 libungif: remove in favour of giflib
libungif was merged into giflib in 2006, and hasn't been updated
since.  All non-broken packages still using it build fine with giflib.

See <http://giflib.sourceforge.net/history.html>.
2021-04-16 14:06:10 +00:00
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