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741 Commits

Author SHA1 Message Date
R. RyanTM
d1414f543e
python311Packages.snakemake: 8.11.3 -> 8.11.4 (#311726) 2024-05-14 18:43:12 -04:00
R. Ryantm
f8210014c0 snakemake: 8.11.2 -> 8.11.3 2024-05-11 12:31:55 -04:00
Dmitry Kalinkin
a94aef18bd
Merge pull request #308497 from guitargeek/root_clad 
root: enable `clad` for automatic differentiation and clean CMake flags
 2024-05-08 20:20:16 -04:00
R. Ryantm
fd93e8c04a snakemake: 8.11.0 -> 8.11.2 2024-05-08 16:17:32 -04:00
Jonas Rembser
db942c10c8 root: update homepage 
We try to promote the URL that is just `root.cern` nowadays.
 2024-05-05 23:32:17 +02:00
Jonas Rembser
cdefff65b8 root: fix typos 2024-05-05 23:31:57 +02:00
Jonas Rembser
e53cfeee3e root: enable clad for automatic differentiation in ROOT 
Clad is a clang plugin that can be used in Cling to create gradients of
C++ functions.

It is included in ROOT via `ExternalProject_Add`:

https://github.com/root-project/root/blob/master/interpreter/cling/tools/plugins/clad/CMakeLists.txt

Clad is used for example in RooFit to create analytical gradients of
likelihoods.
 2024-05-05 23:31:46 +02:00
Jonas Rembser
35bbca41da root: remove redundant cmake flags 
This commit suggests to remove CMake flags that are the same as the
default in ROOT.

Many of these flags were useful in the past, but in the last years the
default built configuration of ROOT was improved and many toggles are
now unnecessary.

Removing the redundant flags makes it clearer what the differences of
the package to the default configuration are, and it's also more
future-proof in case flags get deprecated or removed.
 2024-05-05 14:22:47 +02:00
Weijia Wang
b6e5ed99c2
Merge pull request #305759 from r-ryantm/auto-update/rink 
rink: 0.7.0 -> 0.8.0
 2024-05-04 15:09:03 +02:00
Peder Bergebakken Sundt
db15bbc3d5
treewide: remove unreferenced patch files (#308127) 
Found with `fd \\.patch$ pkgs/ -x bash -c 'rg -F "{/}" pkgs/ -q || echo {}'`
 2024-05-02 12:41:45 +00:00
Jonas Rembser
50a020aa56 root: add back explicit disabling of compiler warnings for clang 
This reverts commit 6665f67b4e.

I misunderstood something when preparing that commit: I thought it was
about compailer warnings when compiling ROOT with clang, but actually it
was to avoid warning *when compiling clang*. This is still necessary.
 2024-05-02 12:28:18 +02:00
Jonas Rembser
afde4332c3 root: don't do anything specific for Python 2 
Python 2 support is deprecated in ROOT 6.30 and will be removed from
6.32, due to release in May:
https://github.com/root-project/root/pull/13948
 2024-05-01 14:58:12 +02:00
Jonas Rembser
ebce8ace41 maintainers: add guitargeek 2024-05-01 14:56:40 +02:00
Jonas Rembser
e81a95f980 root: remove the hack that disables the splash screen by default 
Remove the hack that disables the splash screen by default, as this
has already been done in ROOT itself some time ago:
https://github.com/root-project/root/pull/4187
 2024-05-01 14:44:55 +02:00
Jonas Rembser
6665f67b4e root: remove some explicit disabling of compiler warnings on clang 
Remove some explicit disabling of compiler warnings on clang. There is
no need for that: we saw the warnings on our own CI and made sure to
either fix or disable them.
 2024-05-01 14:43:36 +02:00
Jonas Rembser
9792a8be2b root: remove deprecated build flags 
Remove several deprecated or removed build options.
See https://github.com/root-project/root/blob/v6-30-00-patches/cmake/modules/RootBuildOptions.cmake
 2024-05-01 14:40:44 +02:00
Jonas Rembser
5c6453fd97 root: 6.30.04 -> 6.30.06 2024-05-01 14:34:38 +02:00
R. Ryantm
f2c7ecb8a4 snakemake: 8.10.7 -> 8.11.0 2024-04-28 19:43:09 -04:00
R. Ryantm
3ddef8d06e rink: 0.7.0 -> 0.8.0 2024-04-28 05:00:00 +02:00
Matthias Beyer
2da6875b98
Merge pull request #304273 from r-ryantm/auto-update/gplates 
gplates: 2.4 -> 2.5
 2024-04-25 10:48:11 +02:00
R. Ryantm
ed91464081 python311Packages.snakemake: 8.10.6 -> 8.10.7 2024-04-22 16:11:46 -04:00
R. Ryantm
1063186a66 cwltool: 3.1.20240112164112 -> 3.1.20240404144621 2024-04-15 22:31:58 -04:00
R. Ryantm
2ff5b02ffe gplates: 2.4 -> 2.5 2024-04-15 13:09:35 +00:00
Weijia Wang
7d31098bc9
Merge pull request #300785 from r-ryantm/auto-update/boinc 
boinc: 7.24.3 -> 8.0.1
 2024-04-11 05:11:04 +02:00
R. Ryantm
ef1c3ced3f snakemake: 8.10.4 -> 8.10.6 2024-04-10 02:29:57 -04:00
Weijia Wang
dca627c9d4
Merge pull request #300290 from NixOS/colmap-autoadd 
colmap: use pkgs.autoAddDriverRunpath
 2024-04-02 00:59:06 +02:00
R. Ryantm
71caf0987d boinc: 7.24.3 -> 8.0.1 2024-04-01 20:55:53 +00:00
Jonathan Ringer
47bd04c9d8
colmap: use pkgs.autoAddDriverRunpath 2024-04-01 09:53:08 -07:00
Dmitry Kalinkin
924bfa96b6 snakemake: 8.4.12 -> 8.10.4 2024-03-31 00:13:23 -04:00
R. Ryantm
7daf08305b cytoscape: 3.10.1 -> 3.10.2 2024-03-27 01:22:50 +00:00
Someone
e7797267a2
Merge pull request #281576 from yannham/refactor/cuda-setup-hooks-refactor 
cudaPackages: generalize and refactor setup hooks
 2024-03-19 20:06:18 +00:00
stuebinm
ff1a94e523 treewide: add meta.mainProgram to packages with a single binary 
The nixpkgs-unstable channel's programs.sqlite was used to identify
packages producing exactly one binary, and these automatically added
to their package definitions wherever possible.
 2024-03-19 03:14:51 +01:00
Yann Hamdaoui
63746cac08
cudaPackages: generalize and refactor setup hook 
This PR refactor CUDA setup hooks, and in particular
autoAddOpenGLRunpath and autoAddCudaCompatRunpathHook, that were using a
lot of code in common (in fact, I introduced the latter by copy pasting
most of the bash script of the former). This is not satisfying for
maintenance, as a recent patch showed, because we need to duplicate
changes to both hooks.

This commit abstract the common part in a single shell script that
applies a generic patch action to every elf file in the output. For
autoAddOpenGLRunpath the action is just addOpenGLRunpath (now
addDriverRunpath), and is few line function for
autoAddCudaCompatRunpathHook.

Doing so, we also takes the occasion to use the newer addDriverRunpath
instead of the previous addOpenGLRunpath, and rename the CUDA hook to
reflect that as well.

Co-Authored-By: Connor Baker <connor.baker@tweag.io>
 2024-03-15 15:54:21 +01:00
Sergey Vinokurov
3a7feda68d
Update Folding@home client to 8.3.7 (#295745) 
Depend re2, libevent during build sisnce 8.3.7 appears to link with
them. Depend on git because client wan’t to know what revision it
was built from.

Add zlib and expat to FHS environment because some workunits depend on
them and cause lots of rejections if those libraries are not
available. Unfortunately they don’t appear to be bundled as part
of work distribution.
 2024-03-14 12:17:46 +01:00
Yueh-Shun Li
91b3db1309 treewide: fix sourceRoot for fetchgit-based src 
According to Nixpkgs manual[1] and NixOS 23.11 Release Note[2], the
`sourceRoot` attribute passed to `stdenv.mkDerivation` should be
specified as `"${src.name}"` or `"${src.name}/subdir"` when `src` is
produced using `fetchgit`-based fetchers.

`sourceRoot = "source"` or `sourceRoot = "source/subdir"` is based on
the assumption that the `name` attribute of these pre-unpacked fetchers
are always `"source"`, which is not the case. Expecting constant `name`
also makes the source FODs prone to irrelevent hashes during version
bumps.

[1]: https://nixos.org/manual/nixpkgs/unstable/#var-stdenv-sourceRoot
[2]: https://nixos.org/manual/nixos/stable/release-notes#sec-release-23.11
 2024-03-09 07:53:25 +08:00
Mario Rodas
37d0669466
Merge pull request #287403 from trofi/graphia-gcc-13-fix-update 
graphia: 3.2 -> 4.2
 2024-03-01 23:26:37 -05:00
R. Ryantm
6643d56edb snakemake: 8.4.8 -> 8.4.12 2024-02-23 12:38:33 -05:00
Fabian Affolter
4646a0c7db sasview: add changelog to meta 2024-02-19 16:02:14 +01:00
Fabian Affolter
711d382967 sasview: 5.0.4 -> 5.0.6 
Diff: https://github.com/SasView/sasview/compare/refs/tags/v5.0.4...v5.0.6
 2024-02-19 16:01:09 +01:00
OTABI Tomoya
9e52c50c55
Merge pull request #289381 from r-ryantm/auto-update/snakemake 
snakemake: 8.4.4 -> 8.4.8
 2024-02-19 23:16:21 +09:00
Dmitry Kalinkin
cb6f36e8ff
xrootd: fix plugin loading on Linux (#289140) 2024-02-17 15:38:01 -05:00
R. Ryantm
2444fc7fa5 snakemake: 8.4.4 -> 8.4.8 2024-02-16 21:15:11 +00:00
Dmitry Kalinkin
419da635c6
Merge pull request #285505 from GaetanLepage/xroot 
xrootd: 5.5.5 -> 5.6.6, python311Packages.xrootd: init at 5.6.6
 2024-02-14 11:15:22 -05:00
Bouke van der Bijl
91414c639f openmvg: unstable-2022-12-30 -> 2.1 
* Use the nixpkgs libraries instead of the vendored ones
* Add updateScript

Co-authored-by: Nick Cao <nickcao@nichi.co>
 2024-02-14 11:23:46 +01:00
Gaetan Lepage
7b9e11995d xrootd: 5.5.5 -> 5.6.6 
Changelog: https://github.com/xrootd/xrootd/releases/tag/v5.6.6

Structured attrs don't work with cmakeFlags - only first item is passed.

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2024-02-13 16:45:54 -05:00
R. Ryantm
1128be2775 openrefine: 3.7.7 -> 3.7.9 2024-02-11 17:18:59 +00:00
Weijia Wang
b95f9bd48c javaPackages.jogl_2_4_0: rename to jogl 2024-02-10 18:00:38 +01:00
Sergei Trofimovich
e006445420 graphia: 3.2 -> 4.2 
The main change is the build fis against `gcc-13`
https://hydra.nixos.org/build/247540136:

    /build/source/source/thirdparty/breakpad/src/client/linux/handler/minidump_descriptor.h:115:3: error: 'uintptr_t' does not name a type
      115 |   uintptr_t address_within_principal_mapping() const {
          |   ^~~~~~~~~

Changes:
- https://github.com/graphia-app/graphia/releases/tag/4.0
- https://github.com/graphia-app/graphia/releases/tag/4.1
- https://github.com/graphia-app/graphia/releases/tag/4.2
 2024-02-08 23:30:17 +00:00
R. Ryantm
0b9427cf71 snakemake: 8.3.2 -> 8.4.4 2024-02-06 18:59:24 -05:00
Raphael Das Gupta
13f6915775 openrefine: set meta.mainProgram 2024-02-06 13:49:34 +01:00
Weijia Wang
ab45f7963c
Merge pull request #282757 from r-ryantm/auto-update/bada-bib 
bada-bib: 0.8.0 -> 0.8.1
 2024-02-04 23:44:55 +01:00
arthsmn
4ee1815267 gplates: 2.3.0 -> 2.4 2024-02-04 14:19:31 +01:00
Robert Scott
e5e19d75c0
Merge pull request #265959 from risicle/ris-openrefine 
openrefine: init at 3.7.7
 2024-02-03 14:28:55 +00:00
Robert Scott
272f7bb1f4 openrefine: init at 3.7.7 2024-02-03 13:37:59 +00:00
h7x4
51c3e2b494
Merge pull request #285171 from r-ryantm/auto-update/boinc 
boinc: 7.24.2 -> 7.24.3
 2024-02-01 20:17:27 +01:00
Weijia Wang
a07361dd1c
Merge pull request #285382 from wegank/gplates-fix 
gplates: fix runtime error
 2024-02-01 19:42:53 +01:00
Weijia Wang
fa0efec1d5 gplates: fix runtime error 2024-01-31 23:16:41 +01:00
Dmitry Kalinkin
f125235a38
root: 6.30.02 -> 6.30.04 (#285339) 2024-01-31 15:25:14 -05:00
R. Ryantm
6fed14e6ac boinc: 7.24.2 -> 7.24.3 2024-01-31 03:49:58 +00:00
Jonas Chevalier
b1e30d76d4
fahclient: 8.1.18 -> 8.3.1 (#281830) 
* fahclient: 8.1.18 -> 8.3.1

* Update pkgs/applications/science/misc/foldingathome/client.nix

Co-authored-by: Robert Schütz <github@dotlambda.de>

* Update pkgs/applications/science/misc/foldingathome/client.nix

Co-authored-by: Robert Schütz <github@dotlambda.de>

---------

Co-authored-by: Robert Schütz <github@dotlambda.de>
 2024-01-29 18:17:16 +01:00
R. RyanTM
ec66ff787e
snakemake: 8.2.1 -> 8.3.2 (#284218) 2024-01-27 09:26:23 -05:00
R. Ryantm
4765bc88c6 bada-bib: 0.8.0 -> 0.8.1 2024-01-22 02:16:27 +00:00
Fabian Affolter
48433b4d36 cwltool: 3.1.20230213100550 -> 3.1.20240112164112 
Diff: https://github.com/common-workflow-language/cwltool/compare/refs/tags/3.1.20230213100550...3.1.20240112164112

Changelog: https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20240112164112
 2024-01-21 10:32:48 +01:00
Dmitry Kalinkin
346cb05310 snakemake: 8.0.1 -> 8.2.1 2024-01-17 16:28:55 -05:00
Robert Scott
12a82c9c78
Merge pull request #279386 from r-ryantm/auto-update/rink 
rink: 0.6.3 -> 0.7.0
 2024-01-12 22:08:27 +00:00
Dmitry Kalinkin
be5b82b259
Merge pull request #275882 from veprbl/pr/snakemake_8_0_1 
snakemake: 7.32.4 -> 8.0.1
 2024-01-07 11:03:10 -05:00
R. Ryantm
a373789932 rink: 0.6.3 -> 0.7.0 2024-01-07 14:39:33 +00:00
Weijia Wang
553ccf3dfe tulip: fix build on darwin 2024-01-03 22:16:58 +01:00
R. Ryantm
c777f0bfa7 tulip: 5.7.2 -> 5.7.3 2023-12-28 07:46:06 +00:00
Dmitry Kalinkin
7ff81781f2 snakemake: 7.32.4 -> 8.0.1 2023-12-21 14:32:05 -05:00
Dmitry Kalinkin
d245890087
root: 6.28.10 -> 6.30.02 (#274348) 2023-12-17 05:20:40 -05:00
Dmitry Kalinkin
d4af6e420f
root: build with root7 and webgui (#272723) 2023-12-15 08:43:44 -05:00
Dmitry Kalinkin
1a5412e140
toil: 5.7.1 -> 5.12.0 (#273274) 2023-12-12 16:04:33 -05:00
Dmitry Kalinkin
190cb5fc41 root: 6.28.08 -> 6.28.10 2023-12-07 12:36:03 -05:00
Jonas Chevalier
80d540bd31
fahclient: wrap in FHS (#271994) 
Folding@home downloads arbitrary binaries that it runs and that have the
wrong loader.

Fixes https://github.com/NixOS/nixpkgs/pull/246832#issuecomment-1837625014
 2023-12-05 10:04:09 +01:00
sternenseemann
8c59811e4e root5: broken with clang 
Seems like any clang version > 5 doesn't work. Since root >= 6.0 is
available from nixpkgs, I think it is reasonable to mark it as broken
for now. Maybe someone can figure out if it is possible to backport a
fix from root >= 6.0.
 2023-12-04 19:43:08 +01:00
R. Ryantm
fc9bec86de simgrid: 3.34 -> 3.35 2023-11-28 16:59:53 +00:00
Jonas Chevalier
a403a118d1
fahclient: 7.6.21 -> 8.1.18 (#246832) 
Rebuild from source
 2023-11-27 14:20:58 +01:00
Pierre Bourdon
f4db50bafb
Merge pull request #269700 from NixOS/pr/root_warning_fix 
root: fix excessive build log size
 2023-11-25 10:38:13 +01:00
Dmitry Kalinkin
8ae6154b2b root: fix excessive build log size 2023-11-24 14:33:55 -05:00
Renato Garcia
3c87cb32f0
snakemake: 7.29.0 -> 7.32.4 (#266543) 2023-11-10 06:48:45 -05:00
Silvan Mosberger
fb2e311d1e root5: Fix build with Python 3.11 
Was broken since the Python update from https://github.com/NixOS/nixpkgs/pull/251878

This should fix the apfelgrid and applgrid builds, not tested yet
 2023-11-09 19:01:58 +01:00
Weijia Wang
5827957a06 root: drop patches 2023-11-07 02:42:16 +01:00
R. Ryantm
9ca6747e6b boinc: 7.24.1 -> 7.24.2 2023-10-31 08:44:00 +00:00
github-actions[bot]
fb3e2499b7
Merge master into staging-next 2023-10-21 00:02:17 +00:00
R. Ryantm
06c6fb463b root: 6.28.06 -> 6.28.08 2023-10-20 14:40:50 -04:00
github-actions[bot]
c61915bc96
Merge master into staging-next 2023-10-17 06:01:22 +00:00
Weijia Wang
9f628e292e tulip: 5.6.1 -> 5.7.2 2023-10-17 00:10:30 +02:00
Maximilian Bosch
5497c7ac5d
root: fix build w/ glibc-2.38 
Failing Hydra build: https://hydra.nixos.org/build/230518136
 2023-09-24 15:12:03 +02:00
Fabián Heredia Montiel
d32595dad1
Merge pull request #249590 from Luflosi/update/boinc 
boinc: 7.22.2 -> 7.24.1
 2023-09-13 23:26:57 -05:00
R. Ryantm
7310af91d4 cytoscape: 3.10.0 -> 3.10.1 2023-09-05 11:47:11 +00:00
Dmitry Kalinkin
3c15feef77
root: 6.26.10 -> 6.28.06 (#215187) 2023-09-04 12:24:30 -04:00
ajs124
de1d98cabe vite: 1.2pre1543 -> unstable-2022-05-17 2023-09-04 13:54:49 +02:00
Weijia Wang
2a01448de1
Merge pull request #248805 from r-ryantm/auto-update/openmvs 
openmvs: 2.1.0 -> 2.2.0
 2023-09-01 13:52:30 +02:00
Michael Raskin
5ab5c5d6c7 golly: 4.1 -> 4.2 2023-08-31 00:45:02 +02:00
Luflosi
dc24d56846
boinc: 7.22.2 -> 7.24.1 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.24%2F7.24.0
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.24%2F7.24.1
 2023-08-16 18:35:16 +02:00
Pol Dellaiera
3eb7f7a63b
Merge pull request #248683 from oxij/tree/source-root-continues-3 
treewide: cleanup `sourceRoot` and `setSourceRoot` usage
 2023-08-15 05:53:52 +02:00
Artturin
25eef24033 treewide: Don't hardcode nix store in patchelf calls 2023-08-13 05:44:01 +03:00
R. Ryantm
ee363c9ad3 openmvs: 2.1.0 -> 2.2.0 2023-08-13 01:21:41 +00:00
Jan Malakhovski
d098c821d6 treewide: remove unneeded dots and slashes in sourceRoots 2023-08-12 08:29:56 +00:00