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9180 Commits

Author SHA1 Message Date
Pol Dellaiera
37b4a69489
Merge pull request #295208 from r-ryantm/auto-update/igv 
igv: 2.17.2 -> 2.17.3
 2024-03-12 21:36:29 +01:00
Thiago Kenji Okada
1040e5688c
Merge pull request #294869 from atorres1985-contrib/primecount 
primecount, primesieve: refactor
 2024-03-12 19:20:56 +00:00
Nick Cao
6ad9c21bb7
Merge pull request #295171 from r-ryantm/auto-update/seqkit 
seqkit: 2.7.0 -> 2.8.0
 2024-03-12 14:40:56 -04:00
Doron Behar
4a414671ac qalculate-qt: 4.9.0 -> 5.0.0 
Diff: https://github.com/qalculate/qalculate-qt/compare/v4.9.0...v5.0.0
 2024-03-12 16:59:25 +02:00
Doron Behar
b668267edd qalculate-gtk: 4.9.0 -> 5.0.0 
Diff: https://github.com/qalculate/qalculate-gtk/compare/v4.9.0...v5.0.0
 2024-03-12 16:59:24 +02:00
R. Ryantm
7d8d32ba15 magic-vlsi: 8.3.463 -> 8.3.464 2024-03-12 12:47:29 +00:00
R. Ryantm
c66736f8e0 eigenmath: unstable-2024-03-06 -> unstable-2024-03-11 2024-03-12 07:13:32 +00:00
github-actions[bot]
0917422ffe
Merge staging-next into staging 2024-03-12 06:01:24 +00:00
Vincent Laporte
0521702b1d coq_8_19: 8.19.0 → 8.19.1 2024-03-12 05:49:59 +01:00
R. Ryantm
c91acf3624 igv: 2.17.2 -> 2.17.3 2024-03-12 02:48:25 +00:00
Emily Trau
5005010f1d fritzing: support darwin 2024-03-12 12:30:01 +11:00
R. Ryantm
8cc0f796eb seqkit: 2.7.0 -> 2.8.0 2024-03-12 00:29:44 +00:00
github-actions[bot]
87dfdf055e
Merge master into haskell-updates 2024-03-12 00:12:17 +00:00
github-actions[bot]
06e5eb63d3
Merge staging-next into staging 2024-03-11 18:01:53 +00:00
Pol Dellaiera
54c52cb276
Merge pull request #294334 from ShamrockLee/sourceroot-fix 
treewide: fix hard-coded `sourceRoot` prefix for `fetchgit`-based `src`
 2024-03-11 16:50:57 +01:00
R. Ryantm
daf9f70d56 palp: 2.20 -> 2.21 2024-03-11 15:19:05 +00:00
Anderson Torres
0c68a08dd7 primecount: migrate to by-name 2024-03-11 11:04:30 -03:00
Anderson Torres
0aedcfc0b0 primesieve: migrate to by-name 2024-03-11 11:04:30 -03:00
R. Ryantm
6c08d7994a calcmysky: 0.3.1 -> 0.3.2 2024-03-11 12:27:56 +00:00
Mauricio Collares
2e1ebdb6e0 singular: 4.3.2p2 -> 4.3.2p16 2024-03-11 12:15:41 +01:00
Mauricio Collares
294aaa8575 nauty: 2.7r4 -> 2.8.8 2024-03-11 12:15:41 +01:00
Mauricio Collares
4acba6cff5 conway_polynomials: remove 2024-03-11 12:15:40 +01:00
a-n-n-a-l-e-e
ce789e7e35
llvmPackages_{12,13,14,15,16,17,git}.{libcxx,libcxxabi}: merge libcxxabi into libcxx (#292043) 
- merge libcxxabi into libcxx for LLVM 12, 13, 14, 15, 16, 17, and git.
- remove the link time workaround `-lc++ -lc++abi` from 58 packages as it is no longer required.
- fixes https://github.com/NixOS/nixpkgs/issues/166205
- provides alternative fixes for. https://github.com/NixOS/nixpkgs/issues/269548 https://github.com/NixOS/nix/issues/9640
- pkgsCross.x86_64-freebsd builds work again

This change can be represented in 3 stages
1. merge libcxxabi into libcxx -- files: pkgs/development/compilers/llvm/[12, git]/{libcxx, libcxxabi}
2. update stdenv to account for merge -- files: stdenv.{adapters, cc.wrapper, darwin}
3. remove all references to libcxxabi outside of llvm (about 58 packages modified)

### merging libcxxabi into libcxx
- take the union of the libcxxabi and libcxx cmake flags
- eliminate the libcxx-headers-only package - it was only needed to break libcxx <-> libcxxabi circular dependency
- libcxx.cxxabi is removed. external cxxabi (freebsd) will symlink headers / libs into libcxx.
- darwin will re-export the libcxxabi symbols into libcxx so linking `-lc++` is sufficient.
- linux/freebsd `libc++.so` is a linker script `LINK(libc++.so.1, -lc++abi)` making `-lc++` sufficient.
- libcxx/default.nix [12, 17] are identical except for patches and `LIBCXX_ADDITIONAL_LIBRARIES` (only used in 16+)
- git/libcxx/defaul.nix  does not link with -nostdlib when useLLVM is true so flag is removed. this is not much different than before as libcxxabi used -nostdlib where libcxx did not, so libc was linked in anyway.

### stdenv changes
- darwin bootstrap, remove references to libcxxabi and cxxabi
- cc-wrapper: remove c++ link workaround when libcxx.cxxabi doesn't exist (still exists for LLVM pre 12)
- adapter: update overrideLibcxx to account for a pkgs.stdenv that only has libcxx

### 58 package updates
- remove `NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}` as no longer needed
- swift, nodejs_v8 remove libcxxabi references in the clang override

https://github.com/NixOS/nixpkgs/pull/292043
 2024-03-11 03:53:37 -07:00
github-actions[bot]
97e35dcd05
Merge master into haskell-updates 2024-03-11 00:12:54 +00:00
R. Ryantm
1e6c427404 primesieve: 12.0 -> 12.1 2024-03-10 13:30:57 +00:00
Joachim Breitner
af10a63043 Revert "elan: revert temporary directory creation" 
This reverts commit 66e4e61595.
 2024-03-09 16:50:49 +01:00
Joachim Breitner
5681570171 fix: elan: use relative paths in wrapper script 
since 3.1.1, `elan` extracts to a temporary location and then moves to a
final location, this threw the wrapper script off. Updating the patch to
use paths relative to the wrapper script, so that it works independent
of absolute location.
 2024-03-09 16:01:03 +01:00
R. Ryantm
a312b41117 deeptools: 3.5.4 -> 3.5.5 2024-03-09 10:06:54 +00:00
github-actions[bot]
54e3ad5442
Merge master into haskell-updates 2024-03-09 00:11:53 +00:00
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
Mauricio Collares
119b065fec
Merge pull request #293065 from r-ryantm/auto-update/jmol 
jmol: 16.1.53 -> 16.1.63
 2024-03-08 12:25:12 +01:00
R. Ryantm
8d3ed85daa jmol: 16.1.53 -> 16.1.63 2024-03-08 09:48:22 +00:00
Weijia Wang
40f9f30edf
Merge pull request #292724 from r-ryantm/auto-update/cvc5 
cvc5: 1.1.1 -> 1.1.2
 2024-03-08 08:48:25 +01:00
github-actions[bot]
a32bb438c0
Merge master into haskell-updates 2024-03-08 00:12:53 +00:00
Pol Dellaiera
983f7e7cfb
Merge pull request #293432 from alois31/geogebra-3d 
geogebra: fix 3D view again
 2024-03-07 19:53:05 +01:00
Nick Cao
48a8aef2f3
Merge pull request #294100 from r-ryantm/auto-update/eigenmath 
eigenmath: unstable-2024-02-25 -> unstable-2024-03-06
 2024-03-07 12:57:05 -05:00
R. Ryantm
f4a362ed25 eigenmath: unstable-2024-02-25 -> unstable-2024-03-06 2024-03-07 17:49:19 +00:00
Robert Hensing
7d2a83e6c2 Merge branch 'master' into HEAD 2024-03-07 18:39:12 +01:00
Samuel Ainsworth
a417c4b9ec
Merge pull request #293773 from GaetanLepage/mujoco 
mujoco: 3.1.2 -> 3.1.3
 2024-03-07 11:03:32 -05:00
Weijia Wang
13a97affb1
Merge pull request #291880 from r-ryantm/auto-update/pari 
pari: 2.15.4 -> 2.15.5
 2024-03-07 16:56:45 +01:00
Gaetan Lepage
d62f208672 mujoco: 3.1.2 -> 3.1.3 
Diff: https://github.com/google-deepmind/mujoco/compare/refs/tags/3.1.2...3.1.3

Changelog: https://github.com/google-deepmind/mujoco/releases/tag/3.1.3
 2024-03-07 15:41:37 +01:00
Weijia Wang
dba4cc979f
Merge pull request #287372 from r-ryantm/auto-update/cryptominisat 
cryptominisat: 5.11.15 -> 5.11.21
 2024-03-07 15:23:07 +01:00
7c6f434c
40ddcd77cf
Merge pull request #293918 from r-ryantm/auto-update/opensmt 
opensmt: 2.5.2 -> 2.6.0
 2024-03-07 11:22:39 +00:00
Weijia Wang
b2a57ed0b9
Merge pull request #285423 from r-ryantm/auto-update/diamond 
diamond: 2.1.8 -> 2.1.9
 2024-03-07 11:24:20 +01:00
Weijia Wang
c02fcb5130
Merge pull request #287668 from r-ryantm/auto-update/igv 
igv: 2.17.1 -> 2.17.2
 2024-03-07 09:31:05 +01:00
Weijia Wang
05bdea1c17
Merge pull request #291482 from r-ryantm/auto-update/verilator 
verilator: 5.020 -> 5.022
 2024-03-07 08:08:34 +01:00
Weijia Wang
cbf8d3d567
Merge pull request #292044 from r-ryantm/auto-update/mavproxy 
mavproxy: 1.8.66 -> 1.8.70
 2024-03-07 07:58:16 +01:00
Mario Rodas
66e4e61595 elan: revert temporary directory creation 2024-03-07 04:20:00 +00:00
R. Ryantm
08a8c74c4b opensmt: 2.5.2 -> 2.6.0 2024-03-07 01:36:53 +00:00
github-actions[bot]
8534fb2f53
Merge master into haskell-updates 2024-03-07 00:10:05 +00:00
Weijia Wang
d83c961db0
Merge pull request #289177 from r-ryantm/auto-update/clingcon 
clingcon: 5.2.0 -> 5.2.1
 2024-03-06 23:48:05 +01:00
Weijia Wang
aac102629b
Merge pull request #290917 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.460 -> 8.3.463
 2024-03-06 22:24:44 +01:00
R. Ryantm
9bb1834bfa cadical: 1.9.4 -> 1.9.5 2024-03-06 15:23:48 +00:00
R. Ryantm
6473b3f6b7 getdp: 3.5.0 -> 3.6.0 2024-03-06 02:37:46 +00:00
R. Ryantm
66d4364107 magic-vlsi: 8.3.460 -> 8.3.463 2024-03-05 20:26:29 +00:00
Markus Kowalewski
d73e602b44 gromacs: 2024 -> 2024.1 2024-03-05 14:38:54 +01:00
github-actions[bot]
1ad8409e69
Merge master into haskell-updates 2024-03-05 00:12:06 +00:00
Mario Rodas
4ca2b298cc lean4: 4.6.0 -> 4.6.1 
Diff: https://github.com/leanprover/lean4/compare/v4.6.0...v4.6.1

Changelog: https://github.com/leanprover/lean4/blob/v4.6.1/RELEASES.md
 2024-03-04 04:20:00 +00:00
github-actions[bot]
153ed76492
Merge master into haskell-updates 2024-03-04 00:13:07 +00:00
Alois Wohlschlager
aecaeee645
geogebra: fix 3D view again 2024-03-03 20:05:36 +01:00
github-actions[bot]
b74f04cf79
Merge master into haskell-updates 2024-03-03 00:13:21 +00:00
R. Ryantm
16d5b925a8 lammps-mpi: 2Aug2023_update2 -> 2Aug2023_update3 2024-03-02 20:33:42 +00:00
Doron Behar
bef4ada0eb
Merge pull request #292584 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 24.02.1 -> 24.02.2
 2024-03-02 18:21:28 +02:00
R. Ryantm
b4acd43269 cvc5: 1.1.1 -> 1.1.2 2024-03-02 04:58:08 +00:00
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
github-actions[bot]
38eff76eca
Merge master into haskell-updates 2024-03-02 00:11:53 +00:00
R. Ryantm
3f388279f7 nnpdf: 4.0.8 -> 4.0.9 2024-03-01 12:36:01 -05:00
R. Ryantm
39b24670d7 wxmaxima: 24.02.1 -> 24.02.2 2024-03-01 13:40:14 +00:00
Mario Rodas
7767a0f22d
Merge pull request #292202 from marsam/update-lean4 
lean4: 4.5.0 -> 4.6.0
 2024-02-29 20:49:17 -05:00
github-actions[bot]
a1ed79952d
Merge master into haskell-updates 2024-03-01 00:14:10 +00:00
Justin Bedő
5deb2a3b18
Merge pull request #289911 from r-ryantm/auto-update/last 
last: 1541 -> 1542
 2024-03-01 08:59:19 +11:00
github-actions[bot]
47e7b83fd1
Merge master into haskell-updates 2024-02-29 00:12:06 +00:00
R. Ryantm
93030f9ff7 mavproxy: 1.8.66 -> 1.8.70 2024-02-28 09:50:10 +00:00
R. Ryantm
c2338e336f eigenmath: unstable-2024-02-04 -> unstable-2024-02-25 2024-02-28 07:51:09 +00:00
Mario Rodas
468b7bae7f lean4: 4.5.0 -> 4.6.0 
Diff: https://github.com/leanprover/lean4/compare/v4.5.0...v4.6.0

Changelog: https://github.com/leanprover/lean4/blob/v4.6.0/RELEASES.md
 2024-02-28 04:20:00 +00:00
R. Ryantm
9b570f04bc pari: 2.15.4 -> 2.15.5 2024-02-27 15:53:35 +00:00
R. Ryantm
a8a2cc301b verilator: 5.020 -> 5.022 2024-02-26 05:26:02 +00:00
github-actions[bot]
70706e07ef
Merge master into haskell-updates 2024-02-26 00:12:47 +00:00
Nick Cao
c063b9b052
Merge pull request #291307 from trofi/sortmerna-gcc-13-fix 
sortmerna: fix `gcc-13` build
 2024-02-25 11:12:12 -05:00
Sergei Trofimovich
0c544b0f0f sortmerna: fix gcc-13 build 
Without the change the build on `master` fails as
https://hydra.nixos.org/build/249070958:

    In file included from /build/source/src/sortmerna/kseq_load.cpp:38:
    /build/source/include/kseq_load.hpp:61:12: error: 'uint64_t' has not been declared
       61 |            uint64_t number_total_read,
          |            ^~~~~~~~
 2024-02-25 07:49:10 +00:00
github-actions[bot]
257171f024
Merge master into haskell-updates 2024-02-25 00:13:49 +00:00
Sergei Trofimovich
b4e6152dc5 starspace: mark broken 
THe build fails against `zlib-1.3` in `master` as
https://hydra.nixos.org/build/249158742:

    3rdparty/zlib.h:1468:32: error: expected initializer before 'Z_ARG'
     1468 | ZEXTERN int ZEXPORTVA gzprintf Z_ARG((gzFile file, const char *format, ...));
          |                                ^~~~~

The upstream repository did not see updates for past 5 years and is
archived. Let's schedule it for removal.
 2024-02-24 22:44:20 +00:00
github-actions[bot]
57bbe4245f
Merge master into haskell-updates 2024-02-24 00:11:45 +00:00
Fabián Heredia Montiel
db1ee6dfe6 Merge remote-tracking branch 'origin/master' into staging-next 
fastcdr was moved to by-name

Related to:

- https://github.com/NixOS/nixpkgs/pull/290836
 2024-02-23 16:47:01 -06:00
Pol Dellaiera
6c2979370b
Merge pull request #290850 from raboof/gnucap-by-name 
gnucap: move to by-name
 2024-02-23 22:58:44 +01:00
github-actions[bot]
b67dbe0ff1
Merge master into staging-next 2024-02-23 18:01:06 +00:00
R. Ryantm
6643d56edb snakemake: 8.4.8 -> 8.4.12 2024-02-23 12:38:33 -05:00
github-actions[bot]
d08f9b5833
Merge master into staging-next 2024-02-23 12:01:18 +00:00
Luke Granger-Brown
ed88887f50
Merge pull request #290693 from simonhollingshead/boolector-3.2.3-plus-cpp14 
boolector: 3.2.2 -> 3.2.3 + upstream patch for C++14 compatibility.
 2024-02-23 11:19:22 +00:00
Mario Rodas
03c08e4262
Merge pull request #290735 from marsam/update-elan 
elan: 3.1.0 -> 3.1.1
 2024-02-23 06:11:10 -05:00
Arnout Engelen
68d9ecff4c
gnucap: move to by-name 
tested gnucap-full still works as well
 2024-02-23 12:01:37 +01:00
github-actions[bot]
c1d60ca8ac
Merge master into haskell-updates 2024-02-23 00:12:05 +00:00
Justin Bedő
26037c1a65
Merge pull request #290162 from trofi/octopus-caller-gcc-13-fix 
octopus-caller: fix `gcc-13` build failure (drop `-Werror`)
 2024-02-23 09:38:42 +11:00
markuskowa
b665514a11
Merge pull request #290665 from markuskowa/fix-gromacs 
gromacs: fix CUDA build
 2024-02-22 22:01:26 +01:00
Simon Hollingshead
f0b157a764 boolector: 3.2.2 -> 3.2.3 + upstream patch for C++14 compatibility. 
https://github.com/Boolector/boolector/compare/3.2.2...3.2.3
cc13f371c0
 2024-02-22 19:48:14 +00:00
Markus Kowalewski
f6616d2e3a gromacs: require single precssion when building with CUDA 2024-02-22 17:47:11 +01:00
Markus Kowalewski
eb93eb95ac gromacs: fix CUDA build 2024-02-22 17:39:02 +01:00
Mauricio Collares
464832df1d
Merge pull request #290040 from r-ryantm/auto-update/primesieve 
primesieve: 11.2 -> 12.0
 2024-02-22 10:21:06 +01:00
Fabian Affolter
85611f8249
Merge pull request #290454 from fabaff/strictdoc-fix 
strictdoc: refactor
 2024-02-22 08:33:27 +01:00
Mario Rodas
e4de5ceffd elan: 3.1.0 -> 3.1.1 
Diff: https://github.com/leanprover/elan/compare/v3.1.0...v3.1.1

Changelog: https://github.com/leanprover/elan/blob/v3.1.1/CHANGELOG.md
 2024-02-22 04:20:00 +00:00