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631 commits

Author SHA1 Message Date
Markus S. Wamser c9d167f174 pkgs.applications: remove unused args 2022-10-12 16:00:16 +02:00
Franz Pletz 2c10e089b9
root: fix build with libxcrypt 2022-10-09 18:10:46 +02:00
Franz Pletz 6264d94616
root5: fix build with libxcrypt 2022-10-09 18:10:46 +02:00
R. Ryantm cdfcbf552e simgrid: 3.31 -> 3.32 2022-10-06 15:54:46 +08:00
Theodore Ni 2d3705b141
root: mark broken on aarch64 2022-09-29 17:06:14 -07:00
R. Ryantm f28b6e5468 snakemake: 7.14.1 -> 7.14.2 2022-09-27 19:16:23 -04:00
R. Ryantm fe2504c61b snakemake: 7.14.0 -> 7.14.1 2022-09-26 23:13:22 -04:00
Anthony Roussel 341029d5cc
sasview: fix build 
Caused by `asscalar` numpy API removal.
See https://github.com/SasView/sasview/pull/2178
 2022-09-18 20:42:33 +02:00
Sandro Jäckel 224da23db2 sasview: remove unused input 2022-09-11 16:25:56 +02:00
Dmitry Kalinkin ea1dcc4f8b
Merge pull request #189926 from veprbl/pr/root_rip_via_setup_hook 
root: populate ROOT_INCLUDE_PATH via the setupHook
 2022-09-08 19:45:45 -04:00
R. Ryantm 914100fd45 snakemake: 7.12.1 -> 7.14.0 2022-09-08 09:57:07 -04:00
R. Ryantm 76da07ebfb bada-bib: 0.7.2 -> 0.8.0 2022-09-08 04:44:53 +00:00
Dmitry Kalinkin 0fe6d6f6b9
root: populate ROOT_INCLUDE_PATH via the setupHook 2022-09-05 18:47:48 -04:00
tpdcl 4f39ada71b
FAHClient: 7.6.13 -> 7.6.21 (#188476) 
This time also in master so it can get in unstable
 2022-08-29 19:51:58 +02:00
Artturi 79c42aa06c
Merge pull request #186564 from Artturin/crossevalfixes 
Fixes for cross-compilation
 2022-08-27 17:49:00 +03:00
Jonas Heinrich fbf9205774
Merge pull request #185912 from r-ryantm/auto-update/fityk 
fityk: 1.3.1 -> 1.3.2
 2022-08-21 21:34:00 +02:00
Artturin c6568adb00 treewide: makeWrapper buildInputs to nativeBuildInputs 
most found with https://github.com/siraben/nix-lint
 2022-08-16 13:14:19 +03:00
Christian Kögler 121d695571
Merge pull request #183328 from r-ryantm/auto-update/graphia 
graphia: 3.0 -> 3.1
 2022-08-15 14:13:00 +02:00
R. Ryantm 7f3ad42166 snakemake: 7.12.0 -> 7.12.1 2022-08-13 16:16:11 -04:00
R. Ryantm 50f7eed980 fityk: 1.3.1 -> 1.3.2 2022-08-10 13:28:43 +00:00
Dmitry Kalinkin 1e64d9a87c
root: 6.26.04 -> 6.26.06 2022-07-31 19:43:07 -04:00
R. Ryantm 4c3caca96d snakemake: 7.9.0 -> 7.12.0 2022-07-31 11:06:29 -04:00
R. Ryantm 8ecdb52267 graphia: 3.0 -> 3.1 2022-07-28 13:49:36 +00:00
Mario Rodas 0f87b2b305
Merge pull request #181123 from avdv/gephi-0.9.6 
gephi: 0.9.2 -> 0.9.6
 2022-07-24 16:08:03 -05:00
Robert Scott 0b7947c963
Merge pull request #182349 from r-ryantm/auto-update/snakemake 
snakemake: 7.8.5 -> 7.9.0
 2022-07-21 21:35:04 +01:00
R. Ryantm 7a5b52ff26 snakemake: 7.8.5 -> 7.9.0 2022-07-21 15:24:14 +00:00
Bobby Rong b536142220
Merge pull request #181946 from Luflosi/update/boinc 
boinc: 7.20.1 -> 7.20.2
 2022-07-21 20:01:43 +08:00
Dmitry Kalinkin 3518b4ac5a
Merge pull request #182037 from veprbl/pr/root_6_26_04 
root: 6.24.06 -> 6.26.04
 2022-07-20 17:50:18 -04:00
Artturin 6b8c65acd9 treewide: fix fallout from 'cmake/setup-hook.sh: Don't skip build-RPATH' 2022-07-19 17:47:13 +03:00
Dmitry Kalinkin b3df13e2d7
root: 6.24.06 -> 6.26.04 2022-07-18 23:14:15 -04:00
Luflosi bf27ab825e
boinc: 7.20.1 -> 7.20.2 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.20%2F7.20.2
 2022-07-18 14:33:23 +02:00
Vladimír Čunát 0879ac5da6
Merge branch 'master' into staging-next 2022-07-16 20:07:05 +02:00
Mario Rodas 279e1daf20
Merge pull request #180821 from r-ryantm/auto-update/nextinspace 
nextinspace: 2.0.3 -> 2.0.5
 2022-07-16 09:46:22 -05:00
Artturin a584822577 treewide: fix fallout from 'cmake/setup-hook.sh: Don't skip build-RPATH' 
f7414e2
 2022-07-15 02:50:09 +03:00
Vladimír Čunát 8169a7fce0
Merge branch 'master' into staging-next 2022-07-13 09:57:41 +02:00
Jonas Heinrich 2349dd5cb2 graphia: 2.2 -> 3.0 2022-07-12 10:01:03 -04:00
github-actions[bot] 5f2ff17a45
Merge master into staging-next 2022-07-11 18:01:16 +00:00
Thomas Tuegel e1e0d5d513
Merge pull request #108496 from knedlsepp/cmake-rpath 
cmake/setup-hook.sh: Don't skip build-RPATH
 2022-07-11 10:18:47 -05:00
Claudio Bley 16a1651a4a gephi: 0.9.2 -> 0.9.6 
Gephi now requies Java 11+.
 2022-07-11 16:45:30 +02:00
Bobby Rong 06e537ad60
bada-bib: add missing libadwaita and gtksourceview5 dependency 2022-07-11 13:46:57 +08:00
R. Ryantm 58d35e01aa nextinspace: 2.0.3 -> 2.0.5 2022-07-09 07:19:07 +00:00
R. Ryantm 4975868d54 bada-bib: 0.6.2 -> 0.7.2 2022-07-06 00:52:29 +00:00
R. RyanTM 200d8c500a
snakemake: 7.8.3 -> 7.8.5 (#179874) 2022-07-04 12:24:26 -04:00
Josef Kemetmüller bcd7045998 treewide: Remove now-unneeded LD_LIBRARY_PATH in cmake derivations 
Since the setting DCMAKE_SKIP_BUILD_RPATH was disabled, we can now run
the checkPhase of cmake derivations without having to tweak the
LD_LIBRARY_PATH anymore.
 2022-07-04 03:49:01 +03:00
Luflosi 6eea86625e
boinc: 7.20.0 -> 7.20.1 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.20%2F7.20.1
 2022-07-02 15:56:06 +02:00
Lassulus c58d141dcc
Merge pull request #177268 from Luflosi/update/boinc 
boinc: 7.18.1 -> 7.20.0
 2022-06-23 21:14:33 +02:00
Robert Scott 070028a960 fahcontrol: remove autoPatchelfHook argument 
this is confusing as it is not used - the package .deb only contains
python (and bash)
 2022-06-23 18:38:23 +01:00
Robert Scott 466c2e342a treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
R. Ryantm 671aeb2769 snakemake: 7.8.2 -> 7.8.3 2022-06-21 19:01:53 +00:00
Luflosi 0045581c23
boinc: 7.18.1 -> 7.20.0 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.20%2F7.20.0
 2022-06-11 11:26:45 +02:00
R. Ryantm acf23020f0 snakemake: 7.8.1 -> 7.8.2 2022-06-09 19:49:56 +00:00
Robert Scott 3b6bc4b69c treewide: set sourceProvenance for packages containing downloaded jars 
these are the easily identifiable cases and will not be comprehensive
 2022-06-04 19:47:57 +01:00
R. Ryantm e9fb739e59 snakemake: 7.8.0 -> 7.8.1 2022-06-02 01:20:40 +00:00
R. RyanTM 7a54d237e0
snakemake: 7.7.0 -> 7.8.0 (#174592) 2022-05-30 10:51:36 -04:00
Rick van Schijndel 433701147a
treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
Rick van Schijndel 90869787c5 boinc: mark broken for aarch64 2022-05-29 10:56:03 +02:00
Fabian Affolter 44b8ec5ccb
Merge pull request #173416 from r-ryantm/auto-update/snakemake 
snakemake: 7.6.2 -> 7.7.0
 2022-05-17 20:39:48 +02:00
R. Ryantm a52b64015a snakemake: 7.6.2 -> 7.7.0 2022-05-17 16:18:18 +00:00
Dmitry Kalinkin fdf0806386
root5: fix build with recent gcc 2022-05-16 11:53:42 -04:00
R. Ryantm 5b55f851ac snakemake: 7.6.1 -> 7.6.2 2022-05-07 16:16:09 +00:00
R. Ryantm 166b1378fe snakemake: 7.5.0 -> 7.6.1 2022-05-04 16:06:44 +00:00
Fabian Affolter 8b176291d7 snakemake: 6.15.5 -> 7.5.0 2022-05-01 13:02:10 +02:00
Serge K 1248ea16e1
colmap: fix for cuda11.6/gcc11 (#169623) 
* colmap: force nvcc std=c++14 after gcc11 bump

* colmap: optional -> optionals

* colmap: sha256 -> hash

* colmapWithCuda: force CUDA_ENABLED=ON safeguard

* colmapWithCuda: add opengl runpath
 2022-04-27 16:09:30 -07:00
Ryan Mulligan f05a748058
Merge pull request #169246 from r-ryantm/auto-update/bada-bib 
bada-bib: 0.6.1 -> 0.6.2
 2022-04-24 13:58:11 -07:00
veprbl 2511bad8aa
Merge pull request #168973 from veprbl/pr/root5_glibc_fix 
root5: fix for glibc
 2022-04-19 14:56:09 -04:00
R. Ryantm 9919952421 bada-bib: 0.6.1 -> 0.6.2 2022-04-19 00:53:01 +00:00
Dmitry Kalinkin 81f9e28844
root5: fix for glibc 2022-04-16 17:20:16 -04:00
Fabián Heredia Montiel 5275050ab0 fityk: add -std=c++11 flag for gcc11 and later 2022-04-16 11:11:46 -05:00
github-actions[bot] bf63dd7434
Merge staging-next into staging 2022-04-10 18:01:38 +00:00
Lassulus 973fa1917c
Merge pull request #162300 from r-ryantm/auto-update/cwltool 
cwltool: 3.1.20220221074232 -> 3.1.20220224085855
 2022-04-10 13:37:54 +01:00
Martin Weinelt bf1914e12a Merge remote-tracking branch 'origin/staging-next' into staging 2022-04-05 04:05:02 +02:00
Ryan Mulligan b56cf0ed6a
Merge pull request #167069 from r-ryantm/auto-update/bada-bib 
bada-bib: 0.6.0 -> 0.6.1
 2022-04-04 13:51:15 -07:00
Martin Weinelt f95a3d1140 Merge remote-tracking branch 'origin/staging-next' into staging 2022-04-04 00:46:25 +02:00
R. Ryantm 2a5b81d50f bada-bib: 0.6.0 -> 0.6.1 2022-04-03 19:11:54 +00:00
ajs124 f9ad6fb744 openmvs: remove after being marked broken for over two years 
It was marked in commit 796050fedd by Michael Raskin on 2019-04-14 (commited on 2019-04-14)
 2022-04-03 16:14:19 +01:00
github-actions[bot] 9aa014c46a
Merge staging-next into staging 2022-03-31 12:02:10 +00:00
R. Ryantm 53dff2f7c8 rink: 0.6.2 -> 0.6.3 2022-03-28 18:13:37 +00:00
github-actions[bot] 8357b101a5
Merge staging-next into staging 2022-03-25 12:02:05 +00:00
davidak 6ea8d5ee71
Merge pull request #165297 from Stunkymonkey/treewide-pname-version-17 
treewide: rename name to pname&version
 2022-03-24 16:38:33 +01:00
Doron Behar 4a02c56a7d
Merge pull request #164746 from ncfavier/makeWrapper-chdir 2022-03-24 13:51:27 +02:00
Felix Buehler 3bc5196252 treewide: rename name to pname&version 2022-03-23 22:55:50 +01:00
Millian Poquet 9ff032c291 simgrid: 3.30 -> 3.31 
- addition of the optional eigen dependency, used by a new simulation
  model (bmf) that looks very promising to take interference phenomena
  into account while remaining coarse-grained.
- enabled the new dependency by default as I think this is interesting
  for most users.
 2022-03-22 14:52:22 +01:00
Armeen Mahdian 858e03cf1f golly-beta: remove 
Golly is more up to date
 2022-03-21 07:08:53 -05:00
Naïm Favier 9160044f5f
treewide/makeWrapper: replace --run cd with --chdir 
Lay the groundwork for switching to binary wrappers by reducing uses
of `--run` (which is not supported by `makeBinaryWrapper`).
 2022-03-19 09:46:31 +01:00
Rasmus Thomsen 69895c6248
bada-bib: 0.5.1 -> 0.6.0 2022-03-15 12:50:26 +01:00
Dmitry Kalinkin 149d68268d
root: fix ROOTConfig.cmake.in patching 2022-03-04 21:04:19 -05:00
R. Ryantm de0ff65232 cwltool: 3.1.20220221074232 -> 3.1.20220224085855 2022-03-01 03:46:50 +00:00
K900 cb2cfba6f7 treewide: switch all desktop file generators to new API 
Notably:
- remove explicit arguments that match the defaults
- convert everything to the right Nix types
 2022-02-25 13:40:38 -08:00
R. Ryantm d6a24fc108 cwltool: 3.1.20220217222804 -> 3.1.20220221074232 2022-02-24 15:52:49 -05:00
Bobby Rong 93883402a4
Merge pull request #160594 from Cogitri/bada-bib 
bada-bib: 0.4.1 -> 0.5.1
 2022-02-22 12:10:40 +08:00
Rasmus Thomsen 87c1d9f92c
bada-bib: 0.4.1 -> 0.5.1 2022-02-21 16:33:50 +01:00
R. Ryantm c35aa0a0f3 cwltool: 3.1.20220217190813 -> 3.1.20220217222804 2022-02-21 01:31:33 -05:00
Millian Poquet bc2604732e simgrid: mark as broken on darwin 2022-02-19 10:05:17 +01:00
Millian Poquet 3f804f68bc simgrid: 3.28 -> 3.30 + python + clean 
- use latest SimGrid release
- enable the python binding (in new output "python")
- reviews from PR 141040 have been applied
 2022-02-19 10:05:12 +01:00
R. Ryantm b715fcd9d9 cwltool: 3.1.20220210171524 -> 3.1.20220217190813 2022-02-18 00:36:37 -05:00
R. RyanTM ac1c96ecec
colmap: 3.6 -> 3.7 
* colmap: 3.6 -> 3.7 (#159198)

* colmap: license is BSD-3-Clause

Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>
 2022-02-18 00:29:14 +01:00
Daniel Wheeler 4befe7a89f
snakemake: 6.10.0 -> 6.15.5 (#159026) 
Fetch from GitHub rather than PyPI so tests are included.
 2022-02-17 18:06:23 -05:00
Zhong Jianxin e8f3914985 treewide: Replace transfig with fig2dev 
Reasons:

- transfig never get upstream update since it was added to nixpkgs 2006,
  according to [fig2dev Debian changelog][1], upstream maintainership
  was taken over at 2016, and renamed to fig2dev.

- [Debian][2], [ArchLinux][3], [HomeBrew][4] all use fig2dev to replace
  transfig.

- transfig builds [failed][5] on aarch64-darwin, fig2dev builds fine.

- One less package to maintain.

[1]: https://salsa.debian.org/debian/fig2dev/-/blob/debian/1%253.2.6_beta-1/debian/changelog
[2]: https://packages.debian.org/bullseye/transfig
[3]: https://archlinux.org/packages/community/x86_64/fig2dev/
[4]: https://formulae.brew.sh/formula/fig2dev
[5]: https://hydra.nixos.org/build/163404782/nixlog/2
 2022-02-15 10:13:56 +08:00
R. Ryantm 2220d35562 bada-bib: 0.3.0 -> 0.4.1 2022-02-12 22:22:46 -08:00
R. Ryantm 24b505484b cytoscape: 3.9.0 -> 3.9.1 2022-02-12 21:13:11 -08:00
R. Ryantm 1631ffae8d cwltool: 3.1.20220204090313 -> 3.1.20220210171524 2022-02-11 12:44:06 -05:00
R. RyanTM 1bfc1730e1
cwltool: 3.1.20220202173120 -> 3.1.20220204090313 (#158272) 2022-02-05 15:14:21 -05:00
Sandro 63a6539b76
Merge pull request #157198 from afontaine/afontaine/correct-fah-shortcuts 2022-02-04 18:26:20 +01:00
R. Ryantm af3af2df32 cwltool: 3.1.20220124184855 -> 3.1.20220202173120 2022-02-03 20:06:12 -05:00
markuskowa 65bc2de0ef
Merge pull request #152447 from Cogitri/bada-bib 
bada-bib: init at 0.3.0
 2022-02-01 22:26:26 +01:00
Robert Schütz a13fe11c59 sasview: 4.2.0 -> 5.0.4 2022-01-30 20:47:10 +00:00
Andrew Fontaine 3c0680b783
fahviewer: fix variable substitution for shortcut 
Because single quotes are used in the sed command, the application
shortcut had the literal $out instead of the package path.
 2022-01-28 16:47:24 -05:00
Andrew Fontaine ba785adb28
fahcontrol: fix variable substitution for shortcut 
Because single quotes are used in the sed command, the application
shortcut had the literal $out instead of the package path.
 2022-01-28 16:46:52 -05:00
Yipeng Sun 54cbee8d97
root: tweak wrapping flags for auxiliary programs, avoid forcing CMAKE_CXX_STANDARD (#157069) 2022-01-27 19:37:36 -05:00
Sandro 27cccd4e49
Merge pull request #151363 from Stunkymonkey/doc-updateWalker 2022-01-27 14:06:36 +01:00
ajs124 3638ca8be6
Merge pull request #156001 from helsinki-systems/upd/tulip 
tulip: 5.2.1 -> 5.6.1
 2022-01-26 23:33:44 +01:00
Felix Buehler ed7bf9452c treewide: remove *.upstream files from updateWalker 2022-01-26 21:46:07 +01:00
R. Ryantm 6b3bf39220 cwltool: 3.1.20220119140128 -> 3.1.20220124184855 2022-01-25 21:56:09 -05:00
R. Ryantm f888e66ad4 cwltool: 3.1.20211107152837 -> 3.1.20220119140128 2022-01-21 09:09:34 -05:00
ajs124 479ca09609 tulip: 5.2.1 -> 5.6.1 2022-01-21 03:45:21 +01:00
Robert Schütz d5cceedbd1 python,pythonPackages: make aliases 
Since aliases are disallowed in nixpkgs, this makes usage of Python 2
which is EOL more explicit.
 2022-01-16 18:39:59 +00:00
Bobby Rong cb3da55ede
Merge pull request #154988 from veprbl/pr/broken_gplates 
gplates: mark as broken on darwin
 2022-01-15 13:24:14 +08:00
Bobby Rong a6ed245599
Merge pull request #154989 from veprbl/pr/broken_graphia 
graphia: mark as broken on darwin
 2022-01-15 13:23:31 +08:00
Fabian Affolter 49574fc9d5
Merge pull request #154934 from fabaff/fix-toil 
toil: 5.4.0 -> 5.6.0
 2022-01-14 21:16:45 +01:00
Dmitry Kalinkin 2b9f8eb0a2
graphia: mark as broken on darwin 2022-01-14 03:38:54 -05:00
Dmitry Kalinkin 69d78f174a
gplates: mark as broken on darwin 2022-01-14 03:33:15 -05:00
Shamrock Lee cc5ffb3de4 root: Explicit specify -Dtmva=ON 2022-01-14 14:19:33 +08:00
Shamrock Lee 336cc50b1f root: add openblas and lapack into buildInputs for TMVA 2022-01-14 14:15:22 +08:00
Fabian Affolter 32003c3051 toil: 5.4.0 -> 5.6.0 2022-01-13 21:37:08 +01:00
Fabian Affolter 1a549598b4 cwltool: 3.1.20211104071347 -> 3.1.20211107152837 2022-01-12 18:00:43 +01:00
Fabian Affolter b9c6bff4f0 nextinspace: 1.0.6 -> 2.0.3 2022-01-09 01:17:23 +01:00
Ben Siraphob 39a0a70d29
treewide: fix homepages with permanent redirect to https 2021-12-29 22:06:47 +07:00
Rasmus Thomsen 83e5da9238
bada-bib: init at 0.3.0 2021-12-28 12:40:39 +01:00
Dmitry Kalinkin d5bdb7d39d
root: fix installation of bin/rootcint and bin/genreflex 2021-12-26 00:07:49 -05:00
Bobby Rong bcaa1b4633
Merge pull request #149151 from Luflosi/update/boinc 
boinc: 7.14.2 -> 7.18.1
 2021-12-18 21:32:22 +08:00
Oleksii Filonenko a400948064
Merge pull request #149167 from r-ryantm/auto-update/rink 
rink: 0.6.1 -> 0.6.2
 2021-12-13 14:40:57 +02:00
R. Ryantm 3112fe2ace openmvg: 1.6 -> 2.0 2021-12-07 20:17:43 +00:00
R. Ryantm 5517f74759 rink: 0.6.1 -> 0.6.2 2021-12-06 23:57:17 +00:00
Luflosi ca87168c6e
boinc: copy systemd service file to output 2021-12-06 23:56:06 +01:00
Luflosi 4e0d9003fc
boinc: 7.14.2 -> 7.18.1 2021-12-06 23:56:06 +01:00
Luflosi a7be4f3840
boinc: add Luflosi as maintainer 2021-12-06 23:56:05 +01:00
Michael Raskin 65b2df8b45 golly: 3.3 -> 4.1 2021-12-06 16:27:09 +01:00
Bernardo Meurer 51694b0af4 root5: binutils 2.37 fix 
Co-authored-by: TredwellGit <tredwell@tutanota.com>
 2021-11-28 08:49:32 +00:00
Dmitry Kalinkin a1b8eb4a30
Merge pull request #144870 from fabaff/fix-cwltool 
cwltool: 3.1.20210628163208 -> 3.1.20211104071347
 2021-11-11 23:41:46 -05:00
Felix Buehler b52ab3b712 pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
Fabian Affolter 18b531b514 cwltool: 3.1.20210628163208 -> 3.1.20211104071347 2021-11-06 13:01:16 +01:00
R. Ryantm 5ba5ff1a84 cytoscape: 3.8.2 -> 3.9.0 2021-10-29 09:08:26 +00:00
Dmitry Kalinkin 49d19b7945
snakemake: 6.7.0 -> 6.10.0 2021-10-24 17:49:14 -04:00
Vladimir Korolev 72d4a1f13d openmodelica: v1.17.0 -> v1.18.0, add balodja to openmodelica maintainers 2021-10-02 12:39:57 +03:00
Robert Schütz 98c8fc6fd0 gplates: 2.2.0 -> 2.3.0 2021-09-26 23:11:29 -07:00
Dmitry Kalinkin 84f408f206
Merge pull request #136016 from veprbl/pr/root_6_24_04 
root: 6.24.02 -> 6.24.06
 2021-09-15 11:35:07 -04:00
Dmitry Kalinkin 0ec2acf51f
root: build with -Dimt=ON 2021-09-03 12:41:16 -04:00
Dmitry Kalinkin 95b2d74bc5
root: re-enable unvendored LLVM 2021-09-03 12:41:16 -04:00
Dmitry Kalinkin aedfb59c87
root: 6.24.02 -> 6.24.06 2021-09-03 12:41:04 -04:00
Dmitry Kalinkin 0a312a356c
root5: fix for gcc10 2021-09-01 07:14:56 -04:00
Dmitry Kalinkin b8c5c06aab
snakemake: 6.6.1 -> 6.7.0 2021-08-28 02:18:38 -04:00
Dmitry Kalinkin e51edc1e64
Merge pull request #130903 from veprbl/pr/cwltool 
cwltool: init at 3.1.20210628163208
 2021-08-08 11:15:33 -04:00
Ben Siraphob 0f34985134
Merge pull request #122828 from balodja/openmodelica 2021-07-25 09:24:25 +07:00
Vladimir Korolev 5c8561f11a openmodelica: 1.9.3 -> 1.17.0 with lots of changes 
Co-authored-by: Jaakko Luttinen <jaakko.luttinen@iki.fi>

Most of changes are:
* separate packages for different openmodelica components,
* qt4 -> qt5,
* patches to instruct the OMEdit wrapper with stdenv executables
  location,
* adoption of #89731 and #109595,
* openblas -> blas, lapack according to #83888,
* parallel building,
* getting rid of spurious build phases,
* correct the license,
* cross-compilation,
* forcing compiler to clang++ according to OM build recommendations,
* drop of pangox_compat according to #75909 and #76412,
* better dependencies, and more.
 2021-07-24 20:29:26 +03:00
Dmitry Kalinkin 3f24366cda
cwltool: init at 3.1.20210628163208 2021-07-21 22:11:17 -04:00
Sandro d06f7e07a6
Merge pull request #130925 from SuperSandro2000/python-aliases 2021-07-22 03:21:11 +02:00
Sandro Jäckel b4099137b1
pythonPackages: deprecate ConfigArgParse alias 2021-07-21 13:32:54 +02:00
Sandro aee461ddb4
toil: update homepage 2021-07-21 13:28:37 +02:00
Dmitry Kalinkin 866fe59150
toil: init at 5.4.0 2021-07-20 22:18:08 -04:00
Dmitry Kalinkin 3a79b1fece
snakemake: 6.5.3 -> 6.6.1 2021-07-19 16:22:36 -04:00
Dmitry Kalinkin a93f2af20b
snakemake: add missing optional dependenices 
These are needed to generate reports
 2021-07-19 16:19:27 -04:00
Millian Poquet c6f34aeaef simgrid: compile tests in parallel 2021-07-19 14:05:17 +02:00
Millian Poquet c4ec6ffb78 simgrid: fix paths in smpicc/smpicxx 2021-07-19 14:04:57 +02:00
Millian Poquet 33f915f241 simgrid: propagate boost 
Since SimGrid include files directly include boost files,
most SimGrid users need boost as well.
 2021-07-19 14:03:50 +02:00
Millian Poquet 2d05c2d535 simgrid: 3.27 -> 3.28 2021-07-19 14:01:30 +02:00
Felix Buehler 82cb33a0ae treewide: remove meta.version 2021-07-18 00:07:38 +02:00
Dmitry Kalinkin 1cbb9c64d1
root,root5: apply nixpkgs-fmt 2021-07-14 16:23:09 -04:00
Dmitry Kalinkin 62ab958fb0
root: 6.24.00 -> 6.24.02 2021-07-14 14:58:15 -04:00
Dmitry Kalinkin 45bed6d99f
snakemake: 6.5.0 -> 6.5.3 2021-07-11 10:40:09 -04:00
Andrew Childs 55dcd99859 root: use pure CoreSymbolication on Darwin 
The current build works by linking against CoreSymbolication in
/System/Library/PrivateFrameworks. This is impure and doesn't work in
newer versions of macOS.

See https://github.com/NixOS/nixpkgs/issues/128576
 2021-06-29 11:00:05 +09:00
Dmitry Kalinkin e3678ae8a6
snakemake: 6.0.5 -> 6.5.0 2021-06-24 11:36:26 -04:00
Sandro 47480918a5
Merge pull request #125802 from yipengsun/root-6-24-00 2021-06-09 15:42:05 +02:00
Yipeng Sun ffced8d681 root: 6.22.08 -> 6.24.00 
We switched to the bundled llvm-clang combo because to use the llvm
provided in nixpkgs, clang also needs to be patched and built
externally, which is too much trouble.
 2021-06-09 14:06:13 +02:00
Sandro c037394f5f
Merge pull request #117606 from bgamari/graphia 2021-06-05 16:31:10 +02:00
Ben Gamari dcfaa98677 graphia: init at 2.2 
Graphia is a relatively new tool for graph visualisation and analysis,
in the same vain as gephi.
 2021-06-02 09:07:32 -04:00
Sandro Jäckel d6ff646b3f pythonPackages.smart_open: rename to smart-open 2021-05-22 15:02:50 -07:00
Stéphan Kochen 7e9451ffb3
rink: fix darwin build (#123501) 2021-05-18 10:34:25 -04:00
Jonathan Ringer 1d85caaa26 root: fix build 2021-05-08 01:29:18 -07:00
V 5a835e6e92 rink: 0.6.0 -> 0.6.1 2021-05-01 10:46:51 +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
Dmitry Kalinkin 1d93243467
root: 6.22.06 -> 6.22.08 2021-04-06 02:41:06 -04:00
Sandro Jäckel 3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Millian Poquet 99a5de6ebc simgrid: 3.26 -> 3.27 2021-03-29 21:20:27 +02:00
Dmitry Kalinkin 8887f4655e
snakemake: 5.28.0 -> 6.0.5 2021-03-26 18:32:26 -04:00
Ben Siraphob e03c068af5 treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
Sandro Jäckel 6ad10c3bcd
treewide: Remove doBuild cause it does not exist 2021-02-02 14:46:06 +01:00
Pavol Rusnak a6ce00c50c
treewide: remove stdenv where not needed 2021-01-25 18:31:47 +01:00
Jonathan Ringer 9bb3fccb5b treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 
continuation of #109595

pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.

python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
 2021-01-19 01:16:25 -08:00
Ben Siraphob badf51221d treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
Profpatsch 4a7f99d55d treewide: with stdenv.lib; in meta -> with lib; 
Part of: https://github.com/NixOS/nixpkgs/issues/108938

meta = with stdenv.lib;

is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.

This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.

The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
 2021-01-11 10:38:22 +01:00
Frederik Rietdijk b20838eb4a Merge staging-next into staging 2021-01-04 20:51:32 +01:00
Sandro 6ac4c2d1f6
Merge pull request #107962 from flyfloh/colmap-36 2021-01-04 14:25:21 +01:00
Ben Siraphob 3ae5e6ce03 treewide: remove enableParallelBuilding = true if using cmake 2021-01-03 18:37:40 +07:00
github-actions[bot] 0eb369d907
Merge staging-next into staging 2021-01-01 18:39:12 +00:00
Dmitry Kalinkin 8bee208bf8
Merge pull request #107335 from veprbl/pr/root_6_20_08 
root: 6.18.04 -> 6.22.06, don't build vendored LLVM
 2021-01-01 12:28:37 -05:00
Ben Siraphob b04fc593e7 treewide: cmake buildInputs to nativeBuildInputs, minor cleanups 2021-01-01 11:52:33 +07:00
Florian Pester b740afa546 colmap: 3.5 -> 3.6 2020-12-31 09:56:07 +01:00
Florian Pester 75eef96f08 colmapWithCuda: fix build 2020-12-31 09:56:07 +01:00
Dmitry Kalinkin a30bff21e8
root: use llvm_5 from nixpkgs 2020-12-21 18:24:25 -05:00