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330 Commits

Author SHA1 Message Date
Dmitry Kalinkin
7d6e0d5324
root: 6.18.04 -> 6.20.08 2020-12-20 23:49:54 -05:00
Millian Poquet
15ab96d5a7 simgrid: 3.25 -> 3.26 2020-12-19 14:03:33 +01:00
Sandro
b2219a326b
Merge pull request #101922 from penguwin/nextinspace 
nextinspace: init at 1.0.6
 2020-11-23 20:09:09 +01:00
Dmitry Kalinkin
68e06c19d6
snakemake: 5.19.3 -> 5.28.0 2020-11-17 17:37:35 -05:00
Nicolas Martin
9af958340a
nextinspace: init at 1.0.6 2020-11-17 15:41:53 +01:00
Oleksii Filonenko
512c3c0a05 maintainers: rename filalex77 -> Br1ght0ne 2020-11-17 13:09:31 +02:00
R. RyanTM
e3cf6e12bc
fahcontrol: 7.6.13 -> 7.6.21 (#103677) 2020-11-14 16:39:37 +00:00
R. RyanTM
68f44d990d
fahviewer: 7.6.13 -> 7.6.21 (#103688) 2020-11-14 16:39:20 +00:00
Orivej Desh
0c75dfb732
convertall: init at 0.8.0 (#103108) 2020-11-09 01:45:09 +00:00
R. RyanTM
41e1c236bf cytoscape: 3.8.1 -> 3.8.2 2020-11-02 08:20:13 -08:00
Ben Siraphob
db74029e3e treewide: remove package names from prefix of descriptions 2020-10-27 09:15:07 -07:00
evils
b8a03a66b3
fahclient: 7.6.9 -> 7.6.13 (#99595) 2020-10-05 14:40:10 +02:00
R. RyanTM
e66a7e2fb7 cytoscape: 3.8.0 -> 3.8.1 2020-09-25 04:38:49 +00:00
R. RyanTM
f47530237d rink: 0.5.0 -> 0.5.1 2020-09-05 16:48:17 +00:00
Daniël de Kok
3ab2bf69ce
Merge pull request #85330 from chkno/openmvg 
openmvg: 1.3 -> 1.5 (unbreak)
 2020-08-16 09:39:38 +02:00
Scott Worley
05a16be9c5 openmvg: 1.3 -> 1.6 (unbreak) 2020-08-16 08:35:54 +02:00
Jonathan Ringer
23d6cd325f root: don't propagated python interpreter 2020-08-09 10:44:15 -07:00
John Ericson
ef81828143
Merge pull request #94047 from kmicklas/fix-gplates 
gplates: 2.0.0 -> 2.2.0, unbreak
 2020-07-31 19:57:01 -04:00
Ken Micklas
7ae6e51bd4 gplates: 2.0.0 -> 2.2.0, unbreak 2020-07-27 20:54:18 -04:00
Vladyslav M
2076487221
rink: 0.4.5 -> 0.5.0 2020-07-18 13:30:05 +03:00
Dmitry Kalinkin
eb121e0901
snakemake: 5.17.0 -> 5.19.3 2020-07-02 23:36:20 -04:00
Markus Kowalewski
187b4a2e04
root: add license 2020-06-27 00:43:21 +02:00
Dmitry Kalinkin
df3a188b46
root5: 5.34.36 -> 5.34.38 
Fixes: https://nvd.nist.gov/vuln/detail/CVE-2017-1000203
 2020-06-18 16:42:02 -04:00
1000101
277bbb8efe formatting: fix missing leading whitespace 2020-06-08 09:37:17 +02:00
R. RyanTM
c1b7c7e87c
snakemake: 5.16.0 -> 5.17.0 (#88766) 2020-05-24 13:32:14 -04:00
zimbatm
28357868f8
Merge pull request #88482 from r-ryantm/auto-update/fahcontrol 
fahcontrol: 7.6.9 -> 7.6.13
 2020-05-21 12:12:37 +02:00
zimbatm
1f6fcc7025
Merge pull request #88493 from r-ryantm/auto-update/fahviewer 
fahviewer: 7.6.9 -> 7.6.13
 2020-05-21 12:12:01 +02:00
R. RyanTM
f52889cd38 fahviewer: 7.6.9 -> 7.6.13 2020-05-21 08:53:14 +00:00
R. RyanTM
0cc843b538 fahcontrol: 7.6.9 -> 7.6.13 2020-05-21 06:24:27 +00:00
Lancelot SIX
b7c5508bfc
Merge pull request #86910 from lsix/cytoscape-3.8.0 
cytoscape: 3.7.2 -> 3.8.0
 2020-05-19 08:32:48 +01:00
Matt Huszagh
e8215cd634 colmap: update boost to 1.72 to fix build 2020-05-15 09:42:36 -07:00
R. RyanTM
92d970c766
snakemake: 5.15.0 -> 5.16.0 (#87496) 2020-05-10 10:09:53 -04:00
Lancelot SIX
b9d13090a8
cytoscape: 3.7.2 -> 3.8.0 
See https://cytoscape.org/release_notes_3_8_0.html for release
information
 2020-05-05 09:52:27 +01:00
evils
e257a92472
foldingathome: 7.5.1 -> 7.6.9 (#86171) 2020-04-28 17:20:43 +00:00
Renato Garcia
22133c6bf3
snakemake: 5.13.0 -> 5.15.0 (#85913) 2020-04-25 09:19:54 -04:00
Konrad Borowski
f527f9db3a snakemake: update homepage link to use HTTPS 2020-04-24 19:44:59 -07:00
Konrad Borowski
40dd2c27c6 rink: update homepage link to use HTTPS 2020-04-24 19:44:59 -07:00
Matthew Bauer
1c8aba8334 treewide: use blas and lapack 
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.

treewide: cleanup from blas/lapack changes

A few issues in the original treewide:

- can’t assume blas64 is a bool
- unused commented code
 2020-04-17 16:24:09 -05:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
R. RyanTM
cff5adc2fb
snakemake: 5.10.0 -> 5.13.0 (#83839) 2020-03-31 00:39:00 -04:00
Jörg Thalheim
e841dce44a
rink: fix strict deps build 2020-03-29 12:37:25 +01:00
Claudio Bley
39767f8ae5
foldingathome: Make FAHControl be able to start the FAHViewer (#82925) 
The command to run when clicking the button is configurable, but by default it
tries to run `FAHViewer`.
 2020-03-19 13:05:54 +00:00
Dmitry Kalinkin
68db99ad97 snakemake: 5.9.1 -> 5.10.0 2020-03-14 15:58:24 -07:00
zimbatm
001be890f7 folding@home: 6.02 -> 7.5.1 
The v7 series is very different.

This commit introduces the 3 packages: fahclient, fahcontrol and
fahviewer. It also rebuilds the NixOS module to map better with the new
client.
 2020-03-14 13:01:26 -07:00
Benjamin Hipple
ad30a30488 rustPlatform.fetchCargo: handle custom Cargo.lock patchfiles with validation 
Previously, we would asssert that the lockfiles are consistent during the
unpackPhase, but if the pkg has a patch for the lockfile itself then we must
wait until the patchPhase is complete to check.

This also removes an implicity dependency on the src attribute coming from
`fetchzip` / `fetchFromGitHub`, which happens to name the source directory
"source". Now we glob for it, so different fetchers will work consistently.
 2020-02-28 18:54:23 -08:00
Benjamin Hipple
eb11feaa0b treewide: change fetchCargoTarball default to opt-out 
Changes the default fetcher in the Rust Platform to be the newer
`fetchCargoTarball`, and changes every application using the current default to
instead opt out.

This commit does not change any hashes or cause any rebuilds. Once integrated,
we will start deleting the opt-outs and recomputing hashes.

See #79975 for details.
 2020-02-13 22:41:37 -08:00
Millian Poquet
150f4a967c simgrid: 3.24 -> 3.25 2020-02-03 10:37:03 -08:00
R. RyanTM
a94c66bc88 snakemake: 5.8.1 -> 5.9.1 2020-01-30 09:44:26 +00:00
Oleksii Filonenko
bc8dc2bd0a
rink: add filalex77 to maintainers 2020-01-06 12:41:19 +02:00
Oleksii Filonenko
8d8ce109cb
rink: 0.4.4 -> 0.4.5 2020-01-06 12:39:32 +02:00
Frederik Rietdijk
6d059becd3 Merge gcc-9 into staging (#68029) 2019-12-30 16:38:38 +01:00
Merijn Broeren
133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Robin Gloster
1065d80dd3
simgrid: *Flags are lists 2019-12-30 12:15:25 +01:00
Dmitry Kalinkin
0b28198f23
root: wrap python executables 
In normal use of ROOT the PYTHONPATH is intended to be set when user
sources the thisroot.{,s}sh. We do that in the setupHook. This covers
the case when thisroot.sh was not sourced.
 2019-12-26 11:49:12 -05:00
Franz Pletz
77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9 2019-12-26 14:17:36 +01:00
Jan Tojnar
aee453e5c9
openmodelica: remove pangox dependency 
It was probably just a dependency of `gtkglext` since I cannot find any reference to `pangox` in the repo.

But cannot verify build since it is broken.
 2019-12-24 16:13:13 +01:00
Dmitry Kalinkin
b6d8873825 root: 6.12.06 -> 6.18.04 
Also switch to python3.
 2019-12-14 01:28:27 -08:00
R. RyanTM
13c757e69c snakemake: 5.7.4 -> 5.8.1 (#74637) 2019-12-09 20:47:24 +01:00
Calvin Pritchard
1850d616ac NetLogo: 6.0.4 -> 6.1.1 2019-12-07 22:24:26 +01:00
Mateusz Kowalczyk
1451a52a38 Remove myself (fuuzetsu) from maintainer lists 
I haven't been doing any maintenance for a long time now and not only
do I get notified, it also creates a fake impression that all these
packages had at least one maintainer when in practice they had none.
 2019-12-05 16:29:48 +09:00
Jonathan Ringer
0c1c18ca44
Merge branch 'master' into staging-next 2019-11-27 22:57:50 -08:00
Dmitry Kalinkin
bd0c4dd6ab
root: fix setupHook to work with "set -u" 2019-11-24 17:51:46 -05:00
Michael Raskin
c5e3aec122 golly: fix build 2019-11-22 17:41:46 +01:00
adisbladis
c9d8624ccd
treewide: Get rid of libGLU_combined 2019-11-18 20:10:43 +00:00
Dmitry Kalinkin
93ee8095b0 snakemake: 5.4.4 -> 5.7.4 (#72929) 
(#72929)
 2019-11-13 00:46:56 +01:00
Franz Pletz
dffcb87383
colmap: fix build with gcc9 2019-11-03 14:43:33 +01:00
R. RyanTM
b73b9399ba golly: 3.2 -> 3.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/golly/versions
 2019-10-21 11:24:52 -07:00
Millian Poquet
5b9cbeb75c simgrid: 3.23 -> 3.24 2019-10-14 16:08:43 +02:00
Aaron Andersen
063c82fd2f
Merge pull request #68773 from mimame/update/cytoscape-3.7.2 
cytoscape: 3.7.1 -> 3.7.2
 2019-09-15 09:43:11 -04:00
Miguel Madrid Mencía
148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
Miguel Madrid Mencía
40b760e07c
cytoscape: 3.7.1 -> 3.7.2 2019-09-14 10:52:46 +02:00
volth
7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Frederik Rietdijk
98ef78326d Merge staging-next into staging 2019-08-31 18:07:33 +02:00
Frederik Rietdijk
96e5474329 Merge master into staging-next 2019-08-31 18:04:31 +02:00
Alexander
35ac3344e7 colmap: init at 3.5 (#67759) 
* colmap: init at 3.5
 2019-08-31 08:06:46 -04:00
volth
7bb6b373ab treewide: name -> pname (#67513) 2019-08-31 07:41:22 -04:00
volth
08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Vladimír Čunát
2e6bf42a22
Merge branch 'master' into staging-next 
There ver very many conflicts, basically all due to
name -> pname+version.  Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job.  There might be some fallback to these
conflicts, but I believe it should be minimal.

Hydra nixpkgs: ?compare=1538299
 2019-08-24 08:55:37 +02:00
R. RyanTM
187ec1a8c6 tulip: 5.1.0 -> 5.2.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/tulip/versions
 2019-08-20 19:45:43 -07:00
volth
c814d72b51 treewide: name -> pname 2019-08-17 10:54:38 +00:00
volth
46420bbaa3 treewide: name -> pname (easy cases) (#66585) 
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
 2019-08-15 13:41:18 +01:00
Lancelot SIX
2e955ca4c5
motu_client: drop 
This fork of cls-motu is unmaintained. Remove it from nixpkgs.
 2019-08-05 14:32:25 +02:00
Orivej Desh
b5d1d50aa9 google-gflags: move to aliases.nix 
google-gflags were renamed to gflags in 2012:
https://github.com/gflags/gflags/#25-january-2012

gflags.name will be updated in staging.
 2019-07-25 09:18:32 +00:00
Frederik Rietdijk
79a03641d5 Merge staging-next into staging 2019-07-09 15:46:26 +02:00
Millian Poquet
0513ae77ff simgrid: 3.22.2 -> 3.23 2019-07-08 14:00:14 +02:00
Daiderd Jordan
da7bcec42f
root: remove cf-private 2019-07-03 22:20:22 +02:00
Alyssa Ross
062210bdff treewide: update cargoSha256 hashes for cargo-vendor upgrade 
A recent upgrade of cargo-vendor changed its output slightly, which
broke all cargoSha256 hashes in nixpkgs.
See https://github.com/NixOS/nixpkgs/issues/60668 for more information.

Since then, a few hashes have been fixed in master by hand, but there
were a lot still to do, so I did all of the ones left over with some
scripts I wrote.

The one hash I wasn’t able to update was habitat's, because it’s
currently broken and the build doesn’t get far enough to produce a
hash anyway.
 2019-06-01 15:17:52 +00:00
Millian Poquet
13aa449bab simgrid: remove unneeded 'name' definition 2019-05-15 12:35:12 +02:00
Millian Poquet
00fc5bd08f simgrid: override checkPhase -> preCheck 
This commit changes how failing tests are ignored.
- Previously, the whole checkPhase was overridden.
- Now, preCheck generates a ctest ignore file.

ctest doc: https://gitlab.kitware.com/cmake/community/wikis/doc/ctest/Testing-With-CTest#customizing-ctest
 2019-05-14 18:27:51 +02:00
Millian Poquet
aa29b79e8a simgrid: fetchgit -> fetchFromGitLab 2019-05-13 21:26:09 +02:00
Millian Poquet
c7ab2b9499 simgrid: 3.21 -> 3.22.2 
- GitHub -> Framagit (SimGrid main repo has moved)
- Test binaries must now be explicitly compiled (`make tests`)
- Fix broken documentation link
 2019-05-13 18:58:27 +02:00
Daniel Schaefer
bac4d95aa2 treewide: Change URLs to HTTPS 
Lots of URLs were HTTP redirect to HTTPS. Changed those and checked them
if there's actual content. Inspired by
https://github.com/NixOS/nixpkgs/issues/60004
 2019-04-22 10:19:54 +02:00
Matthew Bauer
f475aeaf29
Merge pull request #59535 from matthewbauer/homepage-fixes 
treewide: update homepages to https where available
 2019-04-15 20:47:30 -04:00
Matthew Bauer
290a5d916e treewide: update homepages to https where available 
Based on "problems" from repology:

https://repology.org/repository/nix_unstable/problems

Mostly simple changes to reflect redirects.
 2019-04-15 10:10:05 -04:00
Michael Raskin
796050fedd openmvs: mark as broken 2019-04-14 17:45:21 +02:00
Dmitry Kalinkin
c321b64b3f
snakemake: 5.2.2 -> 5.4.4 2019-04-10 14:18:26 -04:00
Dmitry Kalinkin
c36f841ec7
root5: fix build 2019-03-20 00:26:13 -04:00
Peter Hoeg
136126ceae
Merge pull request #56498 from ariutta/patch-1 
cytoscape: bump 3.6.1 -> 3.7.1
 2019-03-11 11:20:50 +08:00
Jan Tojnar
d3ff902e94
webkit: move to aliases 2019-03-06 00:20:55 +01:00
Dmitry Kalinkin
aa4f5cc4a3
simgrid: Fix the upstream project URL 
Closes: #56849
 2019-03-04 16:42:46 -05:00