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316 Commits

Author SHA1 Message Date
Phillip Seeber
0261a4fc37 cp2k: 2023.1 -> 2023.2 2023-07-31 12:33:37 +02:00
Theodore Ni
b3fce87bc5
ergoscf: disable fortify3 hardening flag 2023-07-12 21:32:09 -07:00
Markus Kowalewski markus.kowalewski@fysik.su.se
3cbc4483f3 octopus: 12.2 -> 13.0 2023-07-06 15:25:28 +02:00
R. Ryantm
fac18fdb2c autodock-vina: 1.2.3 -> 1.2.5 2023-07-04 13:13:22 +00:00
Martin Weinelt
5a193fb4dd
Merge pull request #232469 from natsukium/autodock-vina/init 
autodock-vina: init at 1.2.3
 2023-07-02 23:45:13 +02:00
Markus Kowalewski
a9d8ac0b1e
openmolcas: fix hash 2023-06-19 15:11:32 +02:00
Markus Kowalewski
cb5504b21c
openmolcas: 23.02 -> 23.06 2023-06-17 22:38:08 +02:00
R. Ryantm
bc62c28b22 jmol: 16.1.9 -> 16.1.13 2023-06-09 20:47:32 +00:00
natsukium
d515191577
autodock-vina: init at 1.2.3 2023-05-28 16:17:36 +09:00
Weijia Wang
915219ace4
Merge pull request #192219 from r-ryantm/auto-update/marvin 
marvin: 22.13.0 -> 23.4.0
 2023-05-24 02:11:57 +03:00
OTABI Tomoya
bb820fbaf6
apbs: init at 3.4.1 (#230644) 
* apbs: init at 3.4.1

* Update pkgs/applications/science/chemistry/apbs/default.nix

---------

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2023-05-23 01:10:16 +02:00
Markus Kowalewski
ceca790324
wxmacmolplt: fix typo 2023-05-12 10:41:17 +02:00
Weijia Wang
419d7f9c8d
Merge pull request #230753 from fetsorn/typos 
several typos
 2023-05-09 19:16:12 +03:00
fetsorn
f14fbf0278 siesta: fix typos 
"manualy" -> "manually"
"becuase" -> "because"
 2023-05-09 18:02:16 +04:00
Markus Kowalewski
d6b6fd9544
nwchem: enable new features (dftd3, libxc, plumed) 2023-05-08 14:24:07 +02:00
Markus Kowalewski
621e086136 nwchem: 7.0.2 -> 7.2.0 2023-05-05 12:43:59 +02:00
Markus Kowalewski
94add42651
octopus: 12.1 -> 12.2 2023-04-23 21:53:05 +02:00
natsukium
23e78ca2fc
jmol: 16.1.3 -> 16.1.9 2023-04-17 17:53:08 +09:00
natsukium
5ac95120d5
pymol: remove broken mark for darwin 
The bug has been resolved by changing the backend to Qt
in this commit, ab3f0771a4.
 2023-04-01 20:41:01 +09:00
R. Ryantm
4da1bc0bfa marvin: 22.13.0 -> 23.4.0 2023-03-21 07:22:28 +00:00
Markus Kowalewski
545b5d04f4
openmolcas: 22.10 -> 23.02 2023-03-17 13:33:41 +01:00
Phillip Seeber
09b52c631a cp2k: enable plumed plugin 
cp2k: enable plumed plugin


cp2k: use mpicxx to figure out link lines
 2023-03-16 14:30:27 +01:00
Artturin
f9fdf2d402 treewide: move NIX_CFLAGS_COMPILE to the env attrset 
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper

this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists
in env cause a eval failure
 2023-02-22 21:23:04 +02:00
R. Ryantm
9286a75505 jmol: 14.32.83 -> 16.1.3 2023-02-14 11:27:30 +00:00
Vladimír Čunát
3356399453
Merge branch 'master' into staging-next 2023-02-07 17:36:16 +01:00
Phillip Seeber
0079d43275 nwchem: init at 7.0.2 2023-02-07 10:40:14 +01:00
github-actions[bot]
b30088fc3f
Merge master into staging-next 2023-02-07 00:02:12 +00:00
markuskowa
f6b2d49d65
Merge pull request #214931 from sheepforce/wxmacmolplt 
wxmacmolplt: init at 7.7.2
 2023-02-06 19:23:33 +01:00
Phillip Seeber
2051d47229 mopac: init at 22.0.6 2023-02-06 16:54:14 +01:00
Phillip Seeber
f1b553de8e wxmacmolplt: init at 7.7.2 
wxmacmolplt: restrict evaluation to linux


wxmacmolplt: move into chemistry section in all-packages
 2023-02-06 16:50:51 +01:00
github-actions[bot]
6d7be19afb
Merge master into staging-next 2023-02-02 18:01:08 +00:00
OPNA2608
c9b4c7dccd treewide: Rename libyamlcpp* to yaml-cpp* 2023-01-31 16:22:54 +01:00
Artturin
37dede4296 octopus: use lib.getX 2023-01-30 18:05:36 +02:00
R. Ryantm
d0852f2fdf cp2k: 2022.2 -> 2023.1 2023-01-14 20:34:50 +00:00
R. Ryantm
c6588f1cb5 jmol: 14.32.76 -> 14.32.83 2023-01-10 12:22:33 +00:00
Rick van Schijndel
9833d56c24 treewide: mark packages broken that never built on PLATFORM 
Done with the help of https://github.com/Mindavi/nixpkgs-mark-broken
Tool is still WIP but this is one of the first results.

I manually audited the results and removed some results that were not valid.

Note that some of these packages maybe should have more constrained platforms set
instead of broken set, but I think not being perfectly correct is better than
just keep trying to build all these things and never succeeding.

Some observations:

- Some darwin builds require XCode tools
- aarch64-linux builds sometimes suffer from using gcc9
  - gcc9 is getting older and misses some new libraries/features
- Sometimes tools try to do system detection or expect some explicit settings for
  platforms that are not x86_64-linux
 2022-12-13 21:40:12 +01:00
Sergei Trofimovich
e4d99ffc58
Merge pull request #201383 from yurket/d-seams_zhf_fix 
d-seams: fix failing build
 2022-11-15 22:57:02 +00:00
yurket
4e4a021fd7 d-seams: fix failing builds 
cxxopts failing to build with clang11:

  /build/source/src/include/external/cxxopts.hpp:488:42: error: no member named 'numeric_limits' in namespace 'std'
            if (u > static_cast<U>(-std::numeric_limits<T>::min()))

Use the patch from upstream, which updates cxxopts 2.2.0 -> 3.0.0
 2022-11-15 14:05:05 -08:00
Aaron Jheng
678ccdf716
element: mark as broken on darwin 2022-11-14 02:16:43 +00:00
Markus Kowalewski
b931e2bb82
octopus: add arpack ILP64 check 2022-11-03 12:50:08 +01:00
R. Ryantm
f75ed7fcef element: 1.0.0 -> 1.0.1 2022-11-01 18:43:56 +00:00
markuskowa
f67325ac2c
Merge pull request #197390 from markuskowa/upd-openmolcas 
openmolcas: 22.06 -> 22.10
 2022-10-24 10:55:56 +02:00
Markus Kowalewski
bd5597dce4
openmolcas: 22.06 -> 22.10 2022-10-23 18:06:56 +02:00
Markus Kowalewski
f6771d4d15
octopus: 12.0 -> 12.1 2022-10-23 17:51:24 +02:00
R. Ryantm
68a8e9aa62 jmol: 14.32.75 -> 14.32.76 2022-10-05 04:43:26 +00:00
markuskowa
c17f8f9e76
Merge pull request #194421 from sheepforce/avogadro2 
avogadro2: 1.95.1 -> 1.97.0
 2022-10-04 17:09:20 +02:00
Phillip Seeber
b070c222d1 avogadro2: 1.95.1 -> 1.97.0 2022-10-04 16:34:10 +02:00
Phillip Seeber
c75b4ee2f0 cp2k: 9.1.0 -> 2022.2 2022-10-04 15:42:45 +02:00
Dmitry Kalinkin
846f382e4b
Merge pull request #192660 from samlich/master 
pymol: use Qt instead of Tk; fixes #192555
 2022-10-03 12:45:25 -04:00
Markus Kowalewski
4d6abfa6b4
octopus: 11.4 -> 12.0 2022-10-03 11:12:28 +02:00