Commit Graph

298 Commits

Author SHA1 Message Date
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
Anders Riutta
c792fd107b
cytoscape: bump 3.6.1 -> 3.7.1
Needed to update URL, because `wget "http://chianti.ucsd.edu/cytoscape-3.7.1/cytoscape-3.7.1.tar.gz"` returns `404`.
2019-02-27 16:40:50 -08:00
Sebastien Bourdeauducq
3b03b901fb rink: init at 0.4.4 2019-02-03 13:29:18 +08:00
Vladimír Čunát
bde8efe792
Merge branch 'master' into staging-next
A couple thousand rebuilds have accumulated on master.
2019-01-12 12:19:34 +01:00
Dmitry Kalinkin
73625f2522 root5: mark as broken on Linux 2019-01-11 20:45:37 -05:00
Dmitry Kalinkin
0c9335fb1c root, root5: fix build on darwin 2019-01-11 20:45:37 -05:00
Vladimír Čunát
287144e342
Merge branch 'master' into staging-next 2019-01-10 13:07:21 +01:00
Piotr Bogdan
71f216b7e6 golly-beta: link with lib{dl,GL} explicitly 2019-01-04 21:44:19 +00:00
Frederik Rietdijk
0a2caa41fe Python: drop python.majorVersion
Drop `python.majorVersion`. For Python language version, use `python.pythonVersion`.
For implementation version, use `python.sourceVersion`.

Some expressions were broken. Those that were identified were fixed.

fixup major
2019-01-04 10:45:22 +01:00
c0bw3b
0f868d8116 Treewide: use HTTPS on SourceForge 2018-12-02 15:33:08 +01:00
Vladimír Čunát
a5de78b7d7
Merge branch 'master' into staging-next 2018-11-26 10:28:00 +01:00
c0bw3b
0ea604ac1d Treewide: use https for SourceForge 2018-11-24 19:58:03 +01:00
Frederik Rietdijk
c31cb577ae Merge master into staging-next 2018-11-22 09:57:08 +01:00
worldofpeace
2e70b40f58
Merge pull request #49376 from dpaetzel/package-netlogo
NetLogo: init 6.0.4
2018-11-21 21:37:01 -05:00
David Pätzel
fa623ad828 netlogo: init 6.0.4 2018-11-21 09:38:22 +01:00
Frederik Rietdijk
0d0d7dcd06 Merge staging-next into staging 2018-11-18 10:41:34 +01:00
Kevin Liu
c93b16829c
boinc: 7.8.0 -> 7.14.2 2018-11-16 15:52:22 -05:00
Patrick Hilhorst
9ec40cc3bf
treewide: Fix overrides having wrong versions 2018-11-06 00:06:21 +01:00
Tristan Helmich (omniIT)
4f8cac02c6 simgrid: 3.20 -> 3.21 2018-11-02 14:23:39 +01:00
Adam Washington
6be90bf8d7
sasmodels: unstable -> 4.2.0 2018-10-17 14:36:46 +01:00
Dmitry Kalinkin
3187db6e8d root5: init at 5.34.36 2018-09-24 14:34:49 -04:00
Markus Kowalewski
70e254d6bd
root: add license 2018-09-08 14:51:28 +02:00
Renato Garcia
318c9296fa snakemake: add maintainers (#46117) 2018-09-05 21:46:17 +02:00
Sebastian Meric de Bellefon
93ce77af40 python.pkgs.snakemake: init at 5.2.2 2018-09-01 09:18:19 -04:00
Vladimír Čunát
cbabebcc2e
Merge branch 'master' into staging-next
Hydra: ?compare=1473892
2018-08-17 13:45:21 +02:00
Michael Mercier
b8566965df Update simgrid 3.19.1 -> 3.20 + parallel tests + enable darwin (#42721)
* simgrid: 3.19.1 -> 3.20

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/simgrid/versions.

These checks were done:

- built on NixOS
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpicc passed the binary check.
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpicxx passed the binary check.
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpirun passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/tesh had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid-colorizer passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid_update_xml had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid_convert_TI_traces passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpimain had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/graphicator passed the binary check.
- 6 of 9 passed binary check by having a zero exit code.
- 4 of 9 passed binary check by having the new version present in output.
- found 3.20 with grep in /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20
- directory tree listing: https://gist.github.com/edefc2f1a2e81412484edc2e45986e03
- du listing: https://gist.github.com/a44f7d57537e93152a8e6c569f8ed1ae

* simgrid: 3.19.1 -> 3.20 + add darwin

- Fix dependencies to enable build on darwin
- Add ctest flag to enable parallel testing

* Use simpler parallel testing logic

because it is already done in nixpkgs/pkgs/stdenv/generic/setup.sh
2018-08-15 19:54:41 -05:00
John Ericson
db965063b3 treewide: Make configureFlags lists 2018-08-03 17:06:03 -04:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
volth
87f5930c3f [bot]: remove unreferenced code 2018-07-20 18:48:37 +00:00
R. RyanTM
d25ec8df03 golly: 3.1 -> 3.2
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.
2018-07-13 03:02:59 -07:00
Matthew Bauer
2171fc4d55
Merge pull request #42590 from TimPut/openmvsbuildfix
openmvs: build with CGAL 4.12
2018-06-28 22:33:40 -04:00
tim put
385114da68 openmvs: fix CGAL 4.12 dependency
patch executables with openMVS library path
2018-06-26 21:55:15 -06:00
tim put
a47a16a887 openmvg: 1.1 -> 1.3 2018-06-25 16:12:26 -06:00