JakeHillion/nixpkgs
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9445 Commits

Author SHA1 Message Date
Franz Pletz
70d4cc383a
Merge pull request #311154 from TomaSajt/pynac 2024-05-13 00:31:48 +02:00
TomaSajt
b797c8531e
pynac: fix build 2024-05-12 21:37:39 +02:00
Mauricio Collares
fdc1aec9e2
Merge pull request #308430 from r-ryantm/auto-update/jmol 
jmol: 16.1.63 -> 16.2.15
 2024-05-12 12:20:51 -03:00
OTABI Tomoya
e1fce3f66f
Merge pull request #308490 from natsukium/migrate/update 
migrate: 3.7.2 -> 5.0.6
 2024-05-12 10:59:02 +09:00
R. Ryantm
f8210014c0 snakemake: 8.11.2 -> 8.11.3 2024-05-11 12:31:55 -04:00
Martin Weinelt
28187dfed1
sage: relax networkx constraint 2024-05-10 21:51:12 +02:00
Markus Kowalewski
430b6438b6
Merge pull request #310583 from r-ryantm/auto-update/octopus 
octopus: 14.0 -> 14.1
 2024-05-10 14:48:51 +00:00
R. Ryantm
6a40ae7789 octopus: 14.0 -> 14.1 2024-05-10 13:16:47 +00:00
R. Ryantm
c03b718053 jmol: 16.1.63 -> 16.2.15 2024-05-10 09:09:40 +00:00
Doron Behar
a2c5b31e72
Merge pull request #310464 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 24.02.2 -> 24.05.0
 2024-05-10 11:25:08 +03:00
R. Ryantm
d3667ff278 nvc: 1.12.0 -> 1.12.1 2024-05-10 00:52:16 +00:00
R. Ryantm
066f706e1c wxmaxima: 24.02.2 -> 24.05.0 2024-05-10 00:37:46 +00:00
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
Gaetan Lepage
eba8c579be mujoco: 3.1.4 -> 3.1.5 
Diff: https://github.com/google-deepmind/mujoco/compare/refs/tags/3.1.4...3.1.5

Changelog: https://github.com/google-deepmind/mujoco/releases/tag/3.1.5
 2024-05-07 23:31:59 +02:00
Doron Behar
b771106b51
Merge pull request #309607 from alyaeanyx/qalculate-5.1.0 
{libqalculate, qalculate-gtk, qalculate-qt}: 5.0.0 -> 5.1.0
 2024-05-07 08:43:58 +03:00
7c6f434c
791853141d
Merge pull request #309548 from Tom-Hubrecht/sagemath-deps 
sage: Add as passthru.tests to critical dependencies
 2024-05-07 05:17:31 +00:00
Tom Hubrecht
de1618552c sage: Add as passthru.tests to critical dependencies 2024-05-06 19:51:19 +02:00
alyaeanyx
3489da471e {libqalculate, qalculate-gtk, qalculate-qt}: 5.0.0 -> 5.1.0 2024-05-06 19:28:29 +02:00
Nick Cao
d2e6f60e02
Merge pull request #309432 from r-ryantm/auto-update/messer-slim 
messer-slim: 4.2.1 -> 4.2.2
 2024-05-06 10:34:40 -04:00
OTABI Tomoya
5656abaea3
Merge pull request #308676 from natsukium/dssp/update 
dssp: 4.4.5 -> 4.4.7, libcifpp: 7.0.3 -> 7.0.4
 2024-05-06 23:20:52 +09:00
R. Ryantm
d5edb2e2f5 messer-slim: 4.2.1 -> 4.2.2 2024-05-06 01:54:25 +00:00
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
Nick Cao
f68bc714df
Merge pull request #309136 from TomaSajt/getdp 
getdp: fix hash
 2024-05-05 10:05:42 -04:00
Nick Cao
f3b0480d94
Merge pull request #309230 from r-ryantm/auto-update/eigenmath 
eigenmath: 0-unstable-2024-04-26 -> 0-unstable-2024-05-03
 2024-05-05 10:01:07 -04:00
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
R. Ryantm
ae9edd3d07 eigenmath: 0-unstable-2024-04-26 -> 0-unstable-2024-05-03 2024-05-05 09:28:51 +00:00
TomaSajt
4b0b8cca0c
getdp: fix hash 2024-05-05 00:31:28 +02:00
Weijia Wang
875e3375d8
Merge pull request #307629 from r-ryantm/auto-update/gretl 
gretl: 2023c -> 2024a
 2024-05-04 22:45:17 +02:00
Weijia Wang
b8cb60c6fe
Merge pull request #306674 from r-ryantm/auto-update/jbrowse 
jbrowse: 2.5.0 -> 2.11.0
 2024-05-04 15:49:20 +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
Vladimír Čunát
e96601ecf0
Merge #306080: staging-next 2024-04-22 2024-05-03 17:36:08 +02:00
7c6f434c
87d41cc77a
Merge pull request #308403 from r-ryantm/auto-update/eprover 
eprover: 3.0.03 -> 3.1
 2024-05-03 15:02:03 +00:00
Thomas Gerbet
6a3601a1c6 R: apply patch for CVE-2024-27322 
https://hiddenlayer.com/research/r-bitrary-code-execution/

Patch has been identified by checking the SCM logs.
I was not able to find another part of the patch.
Fedora 39 went the same way in b1a4e124f2
See also https://github.com/spack/spack/issues/43932
 2024-05-03 13:40:24 +02:00
natsukium
7d27d397a5
dssp: 4.4.5 -> 4.4.7 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.5...v4.4.7

Changelog:
https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.7
 2024-05-03 10:51:52 +09:00
github-actions[bot]
31135daf48
Merge master into staging-next 2024-05-02 18:01:05 +00:00
Pixis
b87a96cf1d
digital: fix desktop item and copy icons (#305171) 
* digital: refactor desktopItem

fix desktopName
change name, exec and icon to pname

* digital: refactor installPhase

copy icons
run pre and post install hooks (we need postInstall to actually run copyDesktopItems)
 2024-05-02 21:42:04 +08:00
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
natsukium
21c42b3d39
migrate: refactor 2024-05-02 19:36:15 +09:00
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
natsukium
f5d23a16ed
migrate: add meta.mainProgram 2024-05-02 19:08:25 +09:00
natsukium
e789c579c1
migrate: 3.7.2 -> 5.0.6 2024-05-02 19:07:53 +09:00
natsukium
77dc1504a2
migrate: format with nixfmt 2024-05-02 18:44:09 +09:00
Vladimír Čunát
725f48a252
Merge branch 'master' into staging-next 2024-05-02 09:05:49 +02:00
Weijia Wang
0599892e8e
Merge pull request #308244 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.118 -> 3.3.119
 2024-05-02 08:50:18 +02:00
R. Ryantm
9664aea5d1 eprover: 3.0.03 -> 3.1 2024-05-02 00:48:29 +00:00
Sandro
3eabaa6c36
Merge pull request #305305 from pmiddend/update-crystfel-to-0.11.0 
crystfel: 0.10.2 -> 0.11.0
 2024-05-01 23:30:02 +02:00
R. RyanTM
a16ec6bad3
last: 1542 -> 1543 (#307730) 2024-05-01 22:49:48 +02:00