Commit Graph

9076 Commits

Author SHA1 Message Date
annalee
8e038835fe
Merge remote-tracking branch 'upstream/master' into staging-next 2024-03-13 00:38:07 +00:00
Pol Dellaiera
03540ae131
Merge pull request #295193 from emilytrau/fritzing-darwin
fritzing: support darwin
2024-03-12 22:07:30 +01:00
Pol Dellaiera
81074976b7
Merge pull request #295306 from r-ryantm/auto-update/magic-vlsi
magic-vlsi: 8.3.463 -> 8.3.464
2024-03-12 21:56:19 +01:00
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
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]
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
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
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
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
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
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
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
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
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
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
Alois Wohlschlager
aecaeee645
geogebra: fix 3D view again 2024-03-03 20:05:36 +01:00
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