Commit graph

303 commits

Author SHA1 Message Date
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
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