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7733 Commits

Author SHA1 Message Date
Weijia Wang
9845f9dade
Merge pull request #229602 from r-ryantm/auto-update/clp 
clp: 1.17.7 -> 1.17.8
 2023-05-23 01:16:56 +03:00
Mauricio Collares
f5373a830b
Merge pull request #233453 from collares/sage-platforms 
sage: add meta.platforms
 2023-05-22 20:58:34 +02:00
pennae
229321224a
Merge pull request #233441 from evils/kicad 
kicad: make KICAD7_TEMPLATE_DIR a single path
 2023-05-22 19:25:12 +02:00
Mauricio Collares
c88e999122 sage: add meta.platforms 2023-05-22 18:30:39 +02:00
kilianar
41f1482be7 lean: 3.50.3 -> 3.51.0 
https://github.com/leanprover-community/lean/releases/tag/v3.51.0
 2023-05-22 18:10:56 +02:00
Evils
e1a80940a5 kicad: make KICAD7_TEMPLATE_DIR a single path 
workaround for the upstream issue of not searching a : separated path
 2023-05-22 17:43:27 +02:00
Ryan Lahfa
b6beee67f0
Merge pull request #233336 from smancill/shogun-fix-build 
shogun: fix build
 2023-05-22 13:47:52 +02:00
Sandro
1e71d2aa88
Merge pull request #218014 from collares/singular431p3 2023-05-22 13:27:15 +02:00
Weijia Wang
6d71b5d6de iqtree: set platforms 2023-05-22 11:14:57 +03:00
R. Ryantm
b36979ec74 iqtree: 2.2.0.4 -> 2.2.2.4 2023-05-22 04:48:16 +00:00
Sebastián Mancilla
70b3662a67 shogun: disable broken test 
Shogun has been broken for a while [0].

Looks like the latest update to openblas, by f07a0615ea (openblas:
0.3.20 -> 0.3.21, 2022-08-10), broke the `libshogun-mathematics_lapack`
example. It calculates the eigenvectors for a matrix, but the assertions
now fail:

    compute_eigenvectors
    A=[
    [       -0.500000000000000111,  0.707106781186547351,   0.5],
    [       0.707106781186547351,   1.04083408558608426e-16,        0.707106781186547129],
    [       -0.499999999999999722,  -0.707106781186547462,  0.5]
    ]
    eigenvalues=[-1.41421356237309492,1.04083408558608426e-17,1.41421356237309492]
    terminate called after throwing an instance of 'shogun::ShogunException'

The darwin build output shows a bit more detail:

    assertion is_equal(A(0,0), 0.5, eps) failed in void test_ev()
    file /tmp/nix-build-shogun-6.1.4.drv-0/source/examples/undocumented/libshogun/mathematics_lapack.cpp
    line 49

Disable the test to fix the build, although the results seem "correct".
It appears that openblas now calculates values with slightly less
precision, thus the assertion fails due to the expected epsilon.

[0]: https://hydra.nixos.org/build/194671473
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
61fc2d2c89 shogun: disable tests that take too long 
The checkPhase may take from 30 minutes up to 2 hours and 30 minutes on
Hydra due to these tests:

    [...]
    311/375 Test #311: libshogun-evaluation_cross_validation_classification ............   Passed  247.33 sec
    312/375 Test #313: libshogun-evaluation_cross_validation_mkl_weight_storage ........   Passed  428.31 sec
    315/375 Test #312: libshogun-evaluation_cross_validation_locked_comparison .........   Passed  880.44 sec
    341/375 Test #316: libshogun-evaluation_cross_validation_regression ................   Passed  380.48 sec
    342/375 Test #343: libshogun-modelselection_grid_search_kernel .....................   Passed 4866.85 sec
    343/375 Test #344: libshogun-modelselection_grid_search_linear .....................   Passed  574.78 sec
    345/375 Test #342: libshogun-modelselection_combined_kernel_sub_parameters .........   Passed 5929.90 sec
    375/375 Test #346: libshogun-modelselection_grid_search_multiclass_svm .............   Passed 1826.27 sec
    [...]
    Total Test time (real) = 9046.65 sec
    checkPhase completed in 2 hours 30 minutes 47 seconds
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
5873454b52 shogun: fix compiler warnings 
Fix warnings related to virtual destruction. Kinda important to fix.
 2023-05-21 22:34:01 -04:00
Sebastián Mancilla
c812170c74 shogun: refactor derivation 2023-05-21 22:34:00 -04:00
Mauricio Collares
c13e4258f6 sageWithDoc: run src/doc/bootstrap script before docbuild 2023-05-21 22:37:53 +02:00
Mauricio Collares
0edaaae3ff sage: 9.8 -> 10.0 2023-05-21 16:28:24 +02:00
Mauricio Collares
19bf4ba0e0 giac, giac-with-xcas: 1.9.0-29 -> 1.9.0-43 2023-05-21 16:25:47 +02:00
Mauricio Collares
51541df982 singular: 4.3.1p2 -> 4.3.2p1 2023-05-20 16:02:19 +02:00
Mauricio Collares
57c940b93d pari: 2.15.2 -> 2.15.3 2023-05-20 16:02:18 +02:00
Mauricio Collares
d2814c733a maxima-ecl-5_45: remove 2023-05-20 16:02:17 +02:00
figsoda
98b9e41f61 pkgs: fix typos 2023-05-19 22:31:04 -04:00
Weijia Wang
3ff23faf74
Merge pull request #232767 from r-ryantm/auto-update/dataexplorer 
dataexplorer: 3.7.6 -> 3.7.7
 2023-05-20 00:35:21 +03:00
R. Ryantm
1be8707a2c dataexplorer: 3.7.6 -> 3.7.7 2023-05-19 06:08:59 +00:00
Nick Cao
3947c72691
Merge pull request #232547 from r-ryantm/auto-update/cytoscape 
cytoscape: 3.9.1 -> 3.10.0
 2023-05-18 21:28:10 -06:00
Sandro
d6c1f83e99
Merge pull request #232477 from fabaff/strictdoc-fix 
strictdoc: 0.0.26 -> 0.0.40
 2023-05-19 02:32:24 +02:00
R. Ryantm
1c6e2cfbea cytoscape: 3.9.1 -> 3.10.0 2023-05-18 03:01:55 +00:00
Weijia Wang
7c6ca2791b
Merge pull request #231635 from natsukium/bwa/build-on-aarch64 
bwa: 0.7.17 -> unstable-2022-09-23
 2023-05-18 01:10:14 +03:00
Weijia Wang
55e5de416f isabelle-components.isabelle-linter: add platforms 2023-05-17 23:01:48 +03:00
Fabian Affolter
5e342e2a4b strictdoc: 0.0.26 -> 0.0.40 2023-05-17 20:34:49 +02:00
Andreas Vollert
44110aeb11 isabelle-linter: unstable-2022-09-05 -> 1.2.1 2023-05-17 17:42:07 +02:00
Guillaume Maudoux
33399c9de8
Merge pull request #229008 from whonore/dafny-4 
dafny: 2.3.0 -> 4.0.0
 2023-05-17 09:53:06 +02:00
Weijia Wang
184ab791ab
Merge pull request #232217 from r-ryantm/auto-update/primesieve 
primesieve: 11.0 -> 11.1
 2023-05-16 23:49:19 +03:00
R. Ryantm
e72d3d4709 primesieve: 11.0 -> 11.1 2023-05-16 10:45:23 +00:00
Nick Cao
1385ce47b7
Merge pull request #232076 from nagy/betaflight 
betaflight-configurator: reduce size
 2023-05-16 03:23:18 -06:00
Martin Weinelt
177eb5dd49
Merge pull request #231826 from mweinelt/scikitimage-alias 
python310Packages.scikit-image: rename from scikitimage
 2023-05-16 01:53:43 +02:00
Daniel Nagy
66f045a65f
betaflight-configurator: reduce size 
This reduces the size of the output from 512.5M to 233.9M.
 2023-05-15 21:00:00 +02:00
Rabjerg
1784646fc1
fritzing: added meta.mainProgram (#232059) 2023-05-15 21:16:15 +03:00
Nick Cao
906c7dd78c
Merge pull request #231975 from jbedo/fastp 
fastp: 0.23.2 -> 0.23.3
 2023-05-15 05:11:28 -06:00
natsukium
04dd7f41e7
bwa: add runHook 2023-05-15 16:13:49 +09:00
natsukium
c85dced23e
bwa: update license 2023-05-15 16:13:49 +09:00
natsukium
01ddcaa879
bwa: 0.7.17 -> unstable-2022-09-23 
Diff: https://github.com/lh3/bwa/compare/v0.7.17...139f68fc4c3747813783a488aef2adc86626b01b
 2023-05-15 16:13:45 +09:00
Ryan Lahfa
308ee09f2f
Merge pull request #231598 from natsukium/truvari/disable-tests-darwin 
truvari: disable some tests on darwin
 2023-05-15 09:09:09 +02:00
Justin Bedo
60c69da248
fastp: 0.23.2 -> 0.23.3 2023-05-15 15:03:24 +10:00
natsukium
7edb72db10
truvari: add patches to fix truvari anno 2023-05-15 10:01:38 +09:00
Sandro
a94d6c485b
Merge pull request #231516 from benwbooth/jbrowse 
jbrowse: init at 2.5.0
 2023-05-14 23:09:10 +02:00
Martin Weinelt
cddb66d655
python310Packages.scikit-image: rename from scikitimage 
to match the pname and create an alias for the former name.
 2023-05-14 13:04:10 +02:00
R. Ryantm
95832c2802 antiprism: 0.29 -> 0.30 2023-05-13 13:57:15 -03:00
Federico Beffa
9dd76ff79c wolfram-engine: add 13.2.0 2023-05-13 14:46:07 +02:00
Nick Cao
8dd605f358
eigenmath: unstable-2023-04-07 -> unstable-2023-05-12 2023-05-13 10:39:50 +08:00
Nick Cao
bd73712425
Merge pull request #231413 from pmiddend/crystfel-dependencies-update 
crystfel: update dependencies
 2023-05-13 10:02:59 +08:00
Ben Booth
fed8eeba5c jbrowse: init at 2.5.0 2023-05-12 11:24:26 -07:00
Markus Kowalewski
ceca790324
wxmacmolplt: fix typo 2023-05-12 10:41:17 +02:00
Philipp Middendorf
05f9ddb8b5 crystfel: update dependencies 2023-05-12 07:41:39 +02:00
Jonas Heinrich
7c863a8a9f
Merge pull request #231063 from Luflosi/update/boinc 
boinc: 7.22.0 -> 7.22.1
 2023-05-11 01:27:04 +02:00
Jonas Heinrich
af6e6808ac
Merge pull request #231066 from jbedo/subread 
subread: 2.0.5 -> 2.0.6
 2023-05-11 01:22:34 +02:00
sternenseemann
bd8335552e Merge remote-tracking branch 'origin/master' into haskell-updates 2023-05-10 16:32:00 +02:00
sternenseemann
dd6a74bdbe tamarin-prover: allow maude 3.1.1 
See https://github.com/tamarin-prover/tamarin-prover/pull/544.

Added tamarin-prover to passthru.tests of maude to prevent future
regressions of this kind.
 2023-05-10 16:30:39 +02:00
Sandro
4c07adb240
Merge pull request #230773 from SuperSandro2000/labplot-nix-run 2023-05-10 14:33:02 +02:00
Justin Bedo
c7a6773f8e
subread: 2.0.5 -> 2.0.6 2023-05-10 22:30:35 +10:00
Luflosi
2654a46c01
boinc: 7.22.0 -> 7.22.1 
https://github.com/BOINC/boinc/releases/tag/client_release/7.22/7.22.1
 2023-05-10 12:56:39 +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
Weijia Wang
32c81c727a
Merge pull request #230831 from wegank/root-python 
python311Packages.hepmc3: fix build
 2023-05-09 12:12:10 +03:00
Weijia Wang
d63d6cb660 python311Packages.hepmc3: fix build 2023-05-09 11:28:25 +03:00
Sandro Jäckel
e4d83f7129
labplot: fix nix run .#labplot 2023-05-08 23:40:59 +02:00
Sandro
05b1a97381
Merge pull request #179752 from hqurve/cantor 
init labplot, cantor and supporting libraries
 2023-05-08 21:28:08 +02:00
markuskowa
2b54d8d84b
Merge pull request #230671 from markuskowa/upd-nwchem 
nwchem: 7.0.2 -> 7.2.0
 2023-05-08 17:03:50 +02:00
hqurve
842704c7cf
labplot: init at 2.10.0 2023-05-08 14:40:27 +02:00
hqurve
547071ee63
sage: expose sage-with-env 2023-05-08 14:40:26 +02:00
Markus Kowalewski
d6b6fd9544
nwchem: enable new features (dftd3, libxc, plumed) 2023-05-08 14:24:07 +02:00
Renato Garcia
9d1a27e2fd
snakemake: 7.14.2 -> 7.25.3 (#230524) 2023-05-08 02:05:40 -04:00
Sandro
33f9eb206e
Merge pull request #223411 from apraga/kent-with-include 
Kent: add headers to the package
 2023-05-07 16:29:16 +02:00
Weijia Wang
9b3763d117
Merge pull request #230393 from r-ryantm/auto-update/_4ti2 
_4ti2: 1.6.9 -> 1.6.10
 2023-05-07 10:44:33 +03:00
Robert Scott
8f4308a432
Merge pull request #229364 from jleightcap/jl/verilog-12.0 
verilog: 11.0 -> 12.0
 2023-05-06 21:47:30 +01:00
R. Ryantm
b9216e3e4f _4ti2: 1.6.9 -> 1.6.10 2023-05-06 20:43:07 +00:00
Weijia Wang
589e345207
Merge pull request #230330 from r-ryantm/auto-update/gnuastro 
gnuastro: 0.19 -> 0.20
 2023-05-06 21:01:30 +03:00
Alexis Praga
e027a5d836 kent: package headers too. 
This is needed for perlPackages.BioBigFile.
Removing NIX_BUILD_TOP.
 2023-05-06 19:48:14 +02:00
Jack Leightcap
4fdd191d65
verilog-12.0: installCheckPhase on supported arch 
Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-06 13:06:47 -04:00
Jack Leightcap
03ad8569fd
verilog-12.0: temp disable regression test suite 
Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-06 12:35:27 -04:00
Ilya
32fc1ceac6
qucs-s: 0.0.22 -> 1.0.2 (#223378) 
* qucs-s: 0.0.22->1.0.1 (including Qt4=>Qt5)

* qucs-s: Qt5->Qt6

* qucs-s: add qtwayland input as recommended for Qt6

Co-authored-by: Tungsten842 <quantmint@protonmail.com>

* qucs-s 1.0.1->1.0.2

---------

Co-authored-by: Tungsten842 <quantmint@protonmail.com>
 2023-05-06 16:28:29 +02:00
R. Ryantm
7ef62c2132 gnuastro: 0.19 -> 0.20 2023-05-06 12:26:20 +00:00
Markus Kowalewski
621e086136 nwchem: 7.0.2 -> 7.2.0 2023-05-05 12:43:59 +02:00
Weijia Wang
830fb9f17b
Merge pull request #229863 from r-ryantm/auto-update/sherpa 
sherpa: 2.2.14 -> 2.2.15
 2023-05-04 14:37:34 +03:00
R. Ryantm
48fe29f726 sherpa: 2.2.14 -> 2.2.15 2023-05-04 09:55:53 +00:00
R. Ryantm
be4b60bf4f minimap2: 2.25 -> 2.26 2023-05-03 19:38:48 +00:00
Jörg Thalheim
255c9a8b83
Merge pull request #229536 from lopsided98/mission-planner-update 
mission-planner: 1.3.76 -> 1.3.80
 2023-05-03 16:29:13 +01:00
R. Ryantm
b74708700e verilator: 5.008 -> 5.010 2023-05-03 07:37:25 -05:00
Sandro
93640c56d1
Merge pull request #227420 from GaetanLepage/torchbin-update 
python3Packages.torch-bin: 1.13.1 -> 2.0.0
 2023-05-03 09:58:56 +02:00
R. Ryantm
d18c6089de clp: 1.17.7 -> 1.17.8 2023-05-03 05:21:09 +00:00
Weijia Wang
2992b28922
Merge pull request #229494 from bcdarwin/update-ants 
ants: 2.4.3 -> 2.4.4
 2023-05-03 00:25:01 +03:00
Ben Wolsieffer
9034073d25 mission-planner: 1.3.76 -> 1.3.80 2023-05-02 15:48:27 -04:00
Ben Darwin
cf573698b1 ants: 2.4.3 -> 2.4.4 2023-05-02 12:29:21 -04:00
Daniel Nagy
8372789e47
qgroundcontrol: 4.2.4 -> 4.2.6 
Diff: https://github.com/mavlink/qgroundcontrol/compare/v4.2.4...v4.2.6
 2023-05-02 16:45:00 +02:00
Weijia Wang
ea4289e1f9 nvc: 1.9.1 -> 1.9.2 2023-05-02 11:02:08 +03:00
Luflosi
e97667163e
verilog: 11.0 -> 12.0 
https://github.com/steveicarus/iverilog/releases/tag/v12_0

Bump `iverilog` to 12.0, fixing two build failures:

1. autoconf now picks up on the unwrapped `x86_64-unknown-gnu-gcc` in
   path that fails at configurePhase to link executables.
   See: https://github.com/NixOS/nixpkgs/issues/21751
   fix/hack: define the `{CC,CXX}_FOR_BUILD` variables.
2. buildPhase generates a `-Werror=format-security` error. Backport
   the the upstream patch that fixed the warning very shortly after the
   release was cut.

And in the process,

- use post-install tests from `.github/test.sh` and as a result,
  remove the now unneeded clone of `ivtest`
- un-pin the verilog autoconf version

Signed-off-by: Jack Leightcap <jack@leightcap.com>
 2023-05-01 17:46:06 -04:00
Weijia Wang
f2bef820c8
Merge pull request #228994 from r-ryantm/auto-update/minimap2 
minimap2: 2.24 -> 2.25
 2023-05-01 07:13:09 +03:00
R. Ryantm
6300f3bfb2 elan: 1.4.2 -> 1.4.5 2023-04-30 15:35:03 +00:00
Weijia Wang
41bfa33de5
Merge pull request #229083 from sikmir/pulseview 
pulseview: enable on darwin
 2023-04-30 14:39:16 +03:00
Nikolay Korotkiy
11b65fea77
pulseview: enable on darwin 2023-04-30 14:34:10 +04:00
Nikolay Korotkiy
5b9065da7e
pulseview: refactor 
* Remove Qt's mkDerivation in favour of stdenv.mkDerivation to fix https://github.com/NixOS/nixpkgs/issues/180841
* Move qttools to nativeBuildInputs
 2023-04-30 14:33:24 +04:00