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Author SHA1 Message Date
luc65r 8edd400bfb
rofi-calc: init at 1.6 (#83136) 
Also:
* maintainers: add albakhamj
* maintainers: add luc65r
* rofi: add plugins argument to wrapper

Co-authored-by: Maciej Krüger <mkg20001@gmail.com>
 2020-03-30 01:18:56 +02:00
Maximilian Bosch 9e7c54325e
stellarium: 0.19.3 -> 0.20.0 
https://github.com/Stellarium/stellarium/releases/tag/v0.20.0
 2020-03-29 17:56:35 +02:00
Jörg Thalheim d04396da8b
Merge pull request #82852 from Mic92/cross-build-rust-package 
[WIP] buildRustPackage: enable strictDeps
 2020-03-29 14:07:07 +01:00
Guanpeng Xu d2702c915f mathematica: 12.0.0 -> 12.1.0 2020-03-29 14:38:33 +02:00
Jörg Thalheim e841dce44a
rink: fix strict deps build 2020-03-29 12:37:25 +01:00
Constantine Glen Evans 59fbc7acba gwyddion: 2.48 -> 2.55 (and add options) 
Gwyddion has a large number of optional dependencies. In this update,
those dependencies have been added with options set mostly to true,
and an option (default false) for working Python 2.7 support in the
program and in Python has been added. I have also added myself as a
maintainer as no maintainer is currently set.
 2020-03-27 10:56:00 -07:00
Ryan Mulligan c669d2991b
Merge pull request #83464 from r-ryantm/auto-update/last 
last: 1047 -> 1060
 2020-03-27 07:34:18 -07:00
R. RyanTM bd3fbef804 last: 1047 -> 1060 2020-03-27 04:12:41 +00:00
Ryan Mulligan 8c5f9d0200
Merge pull request #83390 from r-ryantm/auto-update/seaview 
seaview: 5.0 -> 5.0.2
 2020-03-26 03:10:56 -07:00
R. RyanTM 4a3ea14b5b seaview: 5.0 -> 5.0.2 2020-03-26 00:25:29 +00:00
Austin Seipp 517fd073fc
xcircuit: 3.9.73 -> 3.10.12, maintain 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-25 17:46:15 -05:00
Austin Seipp 765b2fd866
mcy: 2020.03.16 -> 2020.03.21 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-25 06:46:01 -05:00
Austin Seipp 4808bef486
symbiyosys: 2020.02.11 -> 2020.03.24 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-25 06:46:01 -05:00
Vincent Laporte 618bca7054 alt-ergo: 2.3.0 → 2.3.1 2020-03-24 20:43:06 -04:00
Mario Rodas b2df6d541d
lean: 3.7.0 -> 3.7.2 2020-03-22 04:20:00 -05:00
Mario Rodas baeb670ce2
Merge pull request #82610 from r-ryantm/auto-update/eagle 
eagle: 9.5.2 -> 9.6.0
 2020-03-20 06:21:30 -05:00
Vincent Laporte 8dddd8a07f ocamlPackages.camlp5: 7.10 → 7.11 2020-03-19 18:04:14 -07:00
Claudio Bley 39767f8ae5
foldingathome: Make FAHControl be able to start the FAHViewer (#82925) 
The command to run when clicking the button is configurable, but by default it
tries to run `FAHViewer`.
 2020-03-19 13:05:54 +00:00
Austin Seipp 2ef42e07fd
mcy: 2020.02.05 -> 2020.03.16 
Now with working web UI dashboard -- but no working GUI (yet!)

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-17 17:19:40 -05:00
Austin Seipp 5cd4fd5bc5
symbiyosys: 2020.02.08 -> 2020.02.11 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-17 17:19:40 -05:00
Austin Seipp 9b43cf3a00
yosys: 2020.02.25 -> 2020.03.16 
- Bump `abc-verifier` (2020.03.05)
  - Install `yosys-abc` symlink for tool compatbility
  - Various `yosys` expression cleanups

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-03-17 17:19:37 -05:00
Dmitry Kalinkin ebe5f10794
kicad: don't build versions with 3d on Hydra 
The hydraPlatforms have to be set on the kicad package itself, that can be
checked using:

  echo ":p { inherit kicad kicad-small kicad-unstable; }" | nix repl ./pkgs/top-level/release.nix

This commit disables build of all kicad variants that require downloading
packages3d, which currently fail on hydra with the "Output limit exceeded"
status. This leaves Hydra with only building the kicad-small, which will allow
us to cache the build of kicad-base as well as all libraries except of
packages3d.
 2020-03-16 19:45:04 -04:00
Dmitry Kalinkin 68db99ad97 snakemake: 5.9.1 -> 5.10.0 2020-03-14 15:58:24 -07:00
R. RyanTM bafbfc5a06 eagle: 9.5.2 -> 9.6.0 2020-03-14 20:19:26 +00:00
zimbatm 001be890f7 folding@home: 6.02 -> 7.5.1 
The v7 series is very different.

This commit introduces the 3 packages: fahclient, fahcontrol and
fahviewer. It also rebuilds the NixOS module to map better with the new
client.
 2020-03-14 13:01:26 -07:00
Frederik Rietdijk 5175c35a99
Merge pull request #81611 from r-ryantm/auto-update/R 
R: 3.6.2 -> 3.6.3
 2020-03-14 14:29:05 +01:00
Josef Kemetmüller 3a8d05747b qgroundcontrol: Fix build 
This silences some warnings to not run into "Log limit exceeded" on
hydra.
 2020-03-14 03:18:39 +00:00
Mario Rodas c935567de6 lean: 3.6.1 -> 3.7.0 2020-03-14 01:32:58 +00:00
wucke13 c24b9a57c4 getdp: 3.0.4 -> 3.3.0 2020-03-13 04:10:20 +00:00
R. RyanTM a58d091d8d verilator: 4.028 -> 4.030 2020-03-12 20:57:34 -05:00
Maximilian Bosch 76821e6f43
geogebra: 5-0-573-0 -> 5-0-574-0 2020-03-12 18:12:57 +01:00
Timo Kaufmann ba589e24c9 sage: patch for pari 2.11.3 2020-03-12 12:24:41 +01:00
Timo Kaufmann c4ab541443 pari: backport bug fix 
https://trac.sagemath.org/ticket/29313#comment:4
 2020-03-12 12:24:35 +01:00
xaverdh 5ac085c3cc
wxmaxima: 18.02.0 -> 20.02.4 (#82323) 
The commit description is 18.02.0 -> 20.02.4, because in the last version bump (1c6a193b3e), the version string was changed, but the hash was not.

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2020-03-11 12:07:53 -04:00
Timo Kaufmann 1a6b1fb32a symmetrica: add timokau to maintainers 2020-03-10 18:10:28 +01:00
Timo Kaufmann 0c875c28c6 symmetrica: 2.0 -> 3.0.1 
This switches to the sagemath fork, since the original upstream is no
longer maintained and sagemath has effectively maintained symmetrica
through patches for a while now. The update fixes one bug in particular
that has caused failures in the sagemath test suite:

https://github.com/NixOS/nixpkgs/issues/81449
https://trac.sagemath.org/ticket/15312
https://trac.sagemath.org/ticket/29061

Regarding the licensing change:

7cf91b3800
 2020-03-10 18:10:25 +01:00
Timo Kaufmann e05e219b31
Merge pull request #82240 from timokau/sage-docutils-0.15-fix 
sage: fix test suite with docutils 0.15
 2020-03-10 15:25:22 +00:00
Timo Kaufmann 7133577405 sage: fix test suite with docutils 0.15 
The better way to fix this would be to backport the upstream sphinx
patch:

faedcc48cc

Unfortunately it doesn't apply cleanly and isn't worth the effort
of backporting. Let's hope we can switch to python3 sage and the recent
sphinx version that comes with it before this becomes a problem.
 2020-03-10 13:15:41 +01:00
Timo Kaufmann 63ed2bf3c3
Merge pull request #81950 from r-ryantm/auto-update/pari 
pari: 2.11.2 -> 2.11.3
 2020-03-09 17:31:14 +00:00
Michael Raskin bbab73266d
Merge pull request #80719 from mucaho/feature/clingcon_init 
clingcon: init at 3.3.0
 2020-03-09 07:42:38 +00:00
mucaho 202c2a8eff clingcon: init at 3.3.0 2020-03-08 19:21:55 +01:00
Maximilian Bosch 84f862ed91
Merge pull request #81796 from JohnAZoidberg/satallax-gcc9 
satallax: Fix build with GCC9
 2020-03-08 16:12:40 +01:00
Gabriel Ebner d7a68e9bce
Merge pull request #82028 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 3.7.0 -> 3.8.0
 2020-03-08 13:31:00 +01:00
Frederik Rietdijk 0eb0ddc4db Merge staging-next into master 2020-03-08 08:11:01 +01:00
R. RyanTM e6f5bb8dc4 qalculate-gtk: 3.7.0 -> 3.8.0 2020-03-08 00:14:22 +00:00
Vincent Laporte dcfccdfc33
acgtk: 1.5.0 → 1.5.1 (#81539) 
Co-authored-by: Jon <jonringer@users.noreply.github.com>
 2020-03-07 09:56:18 +01:00
R. RyanTM 6528554396 pari: 2.11.2 -> 2.11.3 2020-03-07 02:43:40 +00:00
Gabriel Ebner 8428f5bb4a elan: v0.8.0 tag was force-pushed by upstream 2020-03-06 15:35:37 +01:00
Gabriel Ebner 70e5428d66 elan: 0.7.5 -> 0.8.0 2020-03-06 14:28:36 +01:00
Joachim Breitner 2d2a5a9b63
js_of_ocaml: 3.4.0 -> 3.5.2 (#75766) 
drive-by contributions, as I was playing around with this (it has better
support for the `num` library, it seems.)

js_of_ocaml: 3.4.0 -> 3.5.2
ocamlPackages.js_of_ocaml-ppx_deriving_json: use ppxlib-0.12.0
ocamlPackages.eliom: 6.8.0 → 6.10.1
ocamlPackages.ocsigen-toolkit: 2.2.0 → 2.5.0
ocamlPackages.ocsigen-start: 2.7.0 → 2.16.1

Co-authored-by: Vincent Laporte <Vincent.Laporte@gmail.com>
 2020-03-06 07:42:04 +01:00
Frederik Rietdijk 188c3a4d03 Merge staging-next into staging 2020-03-06 07:09:30 +01:00
Mario Rodas 7597bdd59b
Merge pull request #81783 from r-ryantm/auto-update/gmsh 
gmsh: 4.5.2 -> 4.5.4
 2020-03-05 08:31:38 -05:00
Mario Rodas 1196a5c7a7
Merge pull request #81722 from r-ryantm/auto-update/workcraft 
workcraft: 3.2.5 -> 3.2.6
 2020-03-05 07:42:25 -05:00
Daniel Schaefer bc56175034 satallax: Fix build with GCC9 2020-03-05 05:16:49 +01:00
R. RyanTM 9974067129 gmsh: 4.5.2 -> 4.5.4 2020-03-05 00:20:08 +00:00
R. RyanTM adcdd7b0a7 gromacs: 2020 -> 2020.1 2020-03-04 23:10:39 +00:00
Jan Tojnar 1a44e325d2
Merge branch 'staging-next' into staging 2020-03-04 21:24:05 +01:00
R. RyanTM 86e6080daf workcraft: 3.2.5 -> 3.2.6 2020-03-04 13:41:09 +00:00
Mario Rodas 5760e001ca
Merge pull request #81706 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.8 -> 2.22.0
 2020-03-04 07:26:05 -05:00
R. RyanTM 343ec80712 picard-tools: 2.21.8 -> 2.22.0 2020-03-04 09:58:40 +00:00
Gabriel Ebner 0d470dc5ea
Merge pull request #81692 from r-ryantm/auto-update/lean 
lean: 3.6.0 -> 3.6.1
 2020-03-04 10:32:38 +01:00
R. RyanTM 5b833c08ef lean: 3.6.0 -> 3.6.1 2020-03-04 06:26:01 +00:00
Aiken Cairncross 3db82f6fc3 python3Packages.monosat: Fix hash 
PR #81562 inadvertently broke these builds
 2020-03-03 11:02:23 -08:00
markuskowa dbb9fab27f
Merge pull request #81604 from markuskowa/upd-octopus 
octopus: 9.1 -> 9.2
 2020-03-03 12:45:16 +01:00
R. RyanTM faa5c3bde3 R: 3.6.2 -> 3.6.3 2020-03-03 11:34:22 +00:00
markuskowa 4822d61252
Merge pull request #80977 from r-ryantm/auto-update/quantum-espresso 
quantum-espresso: 6.4.1 -> 6.5
 2020-03-03 11:09:30 +01:00
Markus Kowalewski eebd6fe75a
octopus: 9.1 -> 9.2 2020-03-03 10:54:23 +01:00
Aiken Cairncross 2148a154c6 python3Packages.monosat: Fix Python 3.8 build 2020-03-03 07:40:57 +01:00
Brenton Horne b07eb54048 marvin: 20.4.0 -> 20.6.0 2020-03-02 21:50:25 +01:00
Jan Tojnar f27031f48f
Merge pull request #81063 from NixOS/netpbm 
netpbm: 10.82.01 → 10.89.1
 2020-03-02 19:26:25 +01:00
scalavision dbb4826457 truvari:1.3.2->1.3.4 2020-03-02 09:15:58 +01:00
Jan Tojnar 9555834399
netpbm: split into multiple outputs 2020-03-01 15:13:03 +01:00
Frederik Rietdijk 21b808cd76 Merge staging-next into staging 2020-02-29 15:29:45 +01:00
Benjamin Hipple ad30a30488 rustPlatform.fetchCargo: handle custom Cargo.lock patchfiles with validation 
Previously, we would asssert that the lockfiles are consistent during the
unpackPhase, but if the pkg has a patch for the lockfile itself then we must
wait until the patchPhase is complete to check.

This also removes an implicity dependency on the src attribute coming from
`fetchzip` / `fetchFromGitHub`, which happens to name the source directory
"source". Now we glob for it, so different fetchers will work consistently.
 2020-02-28 18:54:23 -08:00
Matthieu Coudron 05b6836816 torchPackages, torch-repl: remove 
See https://github.com/NixOS/nixpkgs/issues/71888
and https://github.com/NixOS/nixpkgs/issues/56398

To sump up, development has moved on to other technologies than lua:
https://github.com/torch/torch7#development-status
and the current packages are broken anyway.
 2020-02-28 20:56:42 +01:00
Austin Seipp 7e66ce29bf
mcy: init at 2020.02.05 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-02-27 21:52:15 -06:00
Austin Seipp 3d8efecda1
symbiyosys: fix calls to external programs 
48085826f broke symbiyosys when it needed to call `yosys-abc`: when
`ABCEXTERNAL` is set in the Makefile, then `yosys-abc` is not built.

But in general `sby` was just calling programs out of the ambient
environment. Fix that for most programs it can invoke: it now has a
direct dependency on boolector, aiger, abc, yosys, etc.

This also does some other minor clean up.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-02-27 21:52:15 -06:00
Mario Rodas 79f057e2eb
lean: 3.5.1 -> 3.6.0 2020-02-26 18:00:00 -05:00
Dmitry Kalinkin b9ee6cd85c
Merge pull request #80640 from smaret/gildas-20200201a 
gildas: 20200101_a -> 20200201_a
 2020-02-25 10:26:18 -05:00
R. RyanTM 56d58ecb24 quantum-espresso: 6.4.1 -> 6.5 2020-02-24 19:40:14 +00:00
R. RyanTM 4080e7976e gtkwave: 3.3.103 -> 3.3.104 2020-02-24 11:43:54 -06:00
Linus Heckemann 0cc83f884a
Merge pull request #80292 from bcdarwin/mrtrix 
mrtrix: init at 3.0_RC3_latest
 2020-02-24 13:52:38 +01:00
Timo Kaufmann f4dbf4402b
Merge pull request #80759 from Thra11/fix-r 
Fix R
 2020-02-23 23:48:21 +00:00
Tom Hall ae9e09a2e1 R: fix build on aarch64 by removing a failing test 
I believe this test is currently incorrect on aarch64 and expects a
warning about loss of precision with much smaller numbers than the
platform's long doubles can handle.
 2020-02-22 13:17:40 +00:00
Edward Tjörnhammar 9b6faedb18
shogun: 6.0.0 -> 6.1.4 
Also migrate to opencv3 to address #72739, the PR didn't build for me.
Disable testing and ccache since they were broken.

Co-authored-by: Robert Scott <code@humanleg.org.uk>
 2020-02-21 11:05:09 +01:00
Sébastien Maret 7667207f3d
gildas: 20200101_a -> 20200201_a 
- Upgrade gildas to the latest version

 - Remove a patch that has been included upstream

 - Re-enable parallel building (fixed upstream)
 2020-02-20 15:28:57 +01:00
Gabriel Ebner f098b0dd2c
Merge pull request #80576 from bhipple/u/rust-cargo-elan 
elan: upgrade cargo fetcher and cargoSha256
 2020-02-20 09:53:49 +01:00
Maximilian Bosch 7bdc103ac8
geogebra: 5-0-570-0 -> 5-0-573-0 2020-02-20 03:09:06 +01:00
Benjamin Hipple ed85c9981a elan: upgrade cargo fetcher and cargoSha256 
Infra upgrade as part of #79975; ran `nixpkgs-review wip` successfully.
 2020-02-19 18:17:27 -05:00
Tom Hall 4e5aeca90b R: Enable java support on all platforms 2020-02-19 22:57:41 +00:00
Ben Darwin 9a2cd20478 mrtrix: init at 3.0_RC3_latest 
This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.

Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
 2020-02-16 22:25:25 -05:00
Daniel Schaefer 1e613230d2
Merge pull request #80122 from r-ryantm/auto-update/kallisto 
kallisto: 0.46.1 -> 0.46.2
 2020-02-15 22:41:15 +01:00
R. RyanTM 4c6c40d96a kallisto: 0.46.1 -> 0.46.2 
Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
 2020-02-15 22:39:58 +01:00
Junyoung Clare Jang b71c03e483
lean: 3.4.2 -> 3.5.1 
3.4.2 is not compilable with GCC >= 9.1
 2020-02-15 02:29:12 -05:00
R. RyanTM d54a58a2cd verilator: 4.026 -> 4.028 2020-02-14 12:13:04 -06:00
Benjamin Hipple eb11feaa0b treewide: change fetchCargoTarball default to opt-out 
Changes the default fetcher in the Rust Platform to be the newer
`fetchCargoTarball`, and changes every application using the current default to
instead opt out.

This commit does not change any hashes or cause any rebuilds. Once integrated,
we will start deleting the opt-outs and recomputing hashes.

See #79975 for details.
 2020-02-13 22:41:37 -08:00
Dmitry Kalinkin 5f2a3bef33
Merge pull request #79778 from jbedo/delly 
delly: 0.8.1 -> 0.8.2
 2020-02-11 03:54:02 -05:00
Justin Bedo a8fe9e7aff
delly: 0.8.1 -> 0.8.2 
Backported patch required for htslib 1.10.2
 2020-02-11 19:21:59 +11:00
Ryan Mulligan b99e12f4fe
Merge pull request #79534 from r-ryantm/auto-update/last 
last: 1045 -> 1047
 2020-02-10 18:10:08 -08:00
Brenton Horne 567be48707 marvin: 20.3.0 -> 20.4.0 2020-02-10 19:55:13 +01:00
Evils d3a9e634bf kicad-unstable: update update.sh && update 
use /tmp instead of XDG_RUNTIME_DIR
  which is /run/user/1000, which defaults to 10% of RAM
  and kicad-packages3d needs ~6gb
 2020-02-10 19:54:38 +01:00
Evils a9942b0226 kicad: simplify component names 2020-02-10 19:54:38 +01:00
Ben Darwin 39f0e3b32b minc_tools: enable building conversion tools 2020-02-10 19:53:25 +01:00
Ben Darwin bcad453bcf minc_tools: 2017-09-11 -> unstable-2019-12-04 2020-02-10 19:53:25 +01:00
luc65r 94c60990fc cemu: init at 1.3 2020-02-10 19:26:25 +01:00
R. RyanTM e988c072be clp: 1.17.3 -> 1.17.5 2020-02-10 13:24:22 +01:00
R. RyanTM 1d4fd7f5f2 verifast: 18.02 -> 19.12 2020-02-09 14:29:31 -06:00
R. RyanTM 3a1098e3e2 pcb: 4.2.1 -> 4.2.2 2020-02-09 16:49:13 +01:00
Frederik Rietdijk 3846896084 Merge pull request #79293 from NixOS/staging-next 
Staging next (with glibc 2.30)
 2020-02-09 16:40:16 +01:00
Ryan Mulligan c9cf351871 Merge pull request #79479 from r-ryantm/auto-update/workcraft 
workcraft: 3.1.9 -> 3.2.5
 2020-02-09 06:37:47 -08:00
Frederik Rietdijk 531a48ebdb Merge master into staging-next 2020-02-09 11:00:29 +01:00
Jannik Vierling 6ea5cd21ab iprover: 2018_Jul_24_11h -> 3.1 2020-02-09 09:38:57 +01:00
Frederik Rietdijk 03755ed59a Merge master into staging-next 2020-02-09 09:17:51 +01:00
Luz 0522b3347e librepcb: 0.1.2 -> 0.1.3 (#74786) 2020-02-09 01:07:31 -05:00
Dmitry Kalinkin 1872e69450
Merge pull request #79301 from Abdillah/patch-2 
librepcb: Fix platform plugin xcb not found
 2020-02-09 00:28:49 -05:00
Emily a14a32fd75 symbiyosys: 2019.10.11 -> 2020.02.08 2020-02-08 23:00:07 -06:00
Ryan Mulligan 537f07555f Merge pull request #79557 from r-ryantm/auto-update/marvin 
marvin: 19.27.0 -> 20.3.0
 2020-02-08 12:42:18 -08:00
R. RyanTM 20f22f681f marvin: 19.27.0 -> 20.3.0 2020-02-08 19:34:35 +00:00
markuskowa 8261fc4980
Merge pull request #79511 from r-ryantm/auto-update/gmsh 
gmsh: 4.5.1 -> 4.5.2
 2020-02-08 14:21:27 +01:00
R. RyanTM dae266aa66 last: 1045 -> 1047 2020-02-08 13:04:53 +00:00
R. RyanTM 7c58b6437b gmsh: 4.5.1 -> 4.5.2 2020-02-08 07:25:27 +00:00
Ryan Mulligan 555ca166ec
Merge pull request #79467 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.6 -> 2.21.8
 2020-02-07 18:10:16 -08:00
R. RyanTM 5bf0de57ad workcraft: 3.1.9 -> 3.2.5 2020-02-07 21:09:41 +00:00
Frederik Rietdijk 30f0909e3a Merge master into staging-next 2020-02-07 19:27:52 +01:00
R. RyanTM d5404eebe9 picard-tools: 2.21.6 -> 2.21.8 2020-02-07 17:20:58 +00:00
R. RyanTM 78d6e74427 eagle: 9.5.1 -> 9.5.2 2020-02-06 20:17:53 +01:00
R. RyanTM ce5b0406db labelImg: 1.6.0 -> 1.8.1 2020-02-06 20:11:53 +01:00
Hernawan Faïz Abdillah 2d4ee40176
librepcb: Fix platform plugin xcb not found 2020-02-06 08:44:16 +07:00
Frederik Rietdijk 292fd97f67 Merge staging-next into staging 2020-02-05 20:48:28 +01:00
Frederik Rietdijk 419bc0a4cd Revert "Revert "Merge master into staging-next"" 
In 87a19e9048 I merged staging-next into master using the GitHub gui as intended.
In ac241fb7a5 I merged master into staging-next for the next staging cycle, however, I accidentally pushed it to master.
Thinking this may cause trouble, I reverted it in 0be87c7979. This was however wrong, as it "removed" master.

This reverts commit 0be87c7979.
 2020-02-05 19:41:25 +01:00
Frederik Rietdijk 0be87c7979 Revert "Merge master into staging-next" 
I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048.

This reverts commit ac241fb7a5, reversing
changes made to 76a439239e.
 2020-02-05 19:18:35 +01:00
Ryan Mulligan 67143ec938
Merge pull request #79231 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.13.1 -> 3.14.0
 2020-02-05 06:54:45 -08:00
Vladimír Čunát 48a997cd76
Merge #66528: glibc: 2.27 -> 2.30 (into staging) 
Includes update of stdenv bootstap tools (for three main platforms)
and many package fixes with new glibc.
 2020-02-05 13:41:09 +01:00
R. RyanTM 3c54ae5679 SPAdes: 3.13.1 -> 3.14.0 2020-02-04 16:40:50 +00:00
Millian Poquet 150f4a967c simgrid: 3.24 -> 3.25 2020-02-03 10:37:03 -08:00
Maximilian Bosch ea8ae88f04
Merge branch 'staging' into glibc230 2020-02-01 17:42:03 +01:00
Florian Klink 570afbcb5b abc-verifier: passthru rev 
Some consumers of abc-verifier require certain abc versions.
For that reason, expose the exact rev via a passtrhru.
 2020-02-01 12:49:45 +01:00
Florian Klink 351f47da57 abc-verifier: 2018-07-08 -> 2020-01-11 2020-02-01 12:49:45 +01:00
markuskowa d9209250e5
Merge pull request #78981 from r-ryantm/auto-update/jmol 
jmol: 14.30.1 -> 14.30.2
 2020-02-01 11:07:38 +01:00
Mario Rodas c8af1bef6e
Merge pull request #78833 from r-ryantm/auto-update/snakemake 
snakemake: 5.8.1 -> 5.9.1
 2020-02-01 04:11:11 -05:00
Mario Rodas 611971f9a5
Merge pull request #78849 from r-ryantm/auto-update/tetgen 
tetgen: 1.5.0 -> 1.5.1
 2020-02-01 04:10:16 -05:00
R. RyanTM 097737b5a4 jmol: 14.30.1 -> 14.30.2 2020-02-01 03:50:56 +00:00
Vincent Laporte 13dd5844fd coqPackages_8_11.coq: 8.11+β1 → 8.11.0 2020-01-31 14:09:51 +01:00
Vincent Laporte 659a7ae963 coq: disable CoqIDE on Darwin for Coq ≥ 8.10 2020-01-31 14:09:51 +01:00
Luka Blaskovic fd614a8e8f saw-tools: use default llvm 2020-01-30 18:35:30 -05:00
Jörg Thalheim 6eb23e0721
verilator: 4.024 -> 4.026 (#78891) 
verilator: 4.024 -> 4.026
 2020-01-30 20:43:40 +00:00
Jörg Thalheim 37286820f2
verilator: shebangs patch is not needed anymore 2020-01-30 20:42:51 +00:00
R. RyanTM ab63f72b23
sherpa: 2.2.6 -> 2.2.8 (#78852) 2020-01-30 13:08:47 -05:00
R. RyanTM cd526d844b verilator: 4.024 -> 4.026 2020-01-30 18:06:40 +00:00
Ryan Mulligan c179ec8a64
Merge pull request #78823 from r-ryantm/auto-update/seaview 
seaview: 4.7 -> 5.0
 2020-01-30 06:59:41 -08:00
Maximilian Bosch abefd4f78a
pspp: 1.0.1 -> 1.2.0, fix build w/glibc-2.30 2020-01-30 15:19:44 +01:00
R. RyanTM 53706054ba tetgen: 1.5.0 -> 1.5.1 2020-01-30 12:47:50 +00:00
R. RyanTM a94c66bc88 snakemake: 5.8.1 -> 5.9.1 2020-01-30 09:44:26 +00:00
R. RyanTM 42fff82421 seaview: 4.7 -> 5.0 2020-01-30 08:26:52 +00:00
Mario Rodas a20b7cff7c
Merge pull request #78521 from r-ryantm/auto-update/ott 
ott: 0.29 -> 0.30
 2020-01-29 21:47:20 -05:00
Frederik Rietdijk dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Silvan Mosberger 80a2740991
Merge pull request #78265 from Synthetica9/https-homepages 
treewide: fix redirected urls
 2020-01-27 15:00:53 +01:00
Gabriel Ebner 3809627321
Merge pull request #78511 from r-ryantm/auto-update/libqalculate 
libqalculate: 3.6.0 -> 3.7.0
 2020-01-26 18:47:18 +01:00
Gabriel Ebner 8161fe21e0 qalculate-gtk: 3.6.0 -> 3.7.0 2020-01-26 18:43:29 +01:00
R. RyanTM f1085d02bb ott: 0.29 -> 0.30 2020-01-26 09:43:23 +00:00
samlich 3376628557
pymol: cleanup 2020-01-25 19:58:36 +00:00
samlich 77317774ce
pymol: link desktop icon 2020-01-24 19:51:08 +00:00
samlich 3638755ff3
pymol: add samlich as maintainer 2020-01-24 19:49:38 +00:00
samlich 97410b59f3
pymol: 2.1.0 -> 2.3.0 2020-01-24 19:42:59 +00:00
Justin Bedo 7f142260d3 manta: init 1.6.0 2020-01-24 02:02:19 -08:00
Ryan Mulligan a6dc361cae
Merge pull request #78261 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.3 -> 2.21.6
 2020-01-22 16:18:57 -08:00
Patrick Hilhorst 593e11fd94
treewide: fix redirected urls 
According to https://repology.org/repository/nix_unstable/problems, we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.

The following script was used to make these updates:

```

curl https://repology.org/api/v1/repository/nix_unstable/problems \
    | jq '.[] | .problem' -r \
    | rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
    | sort | uniq > script.sed

find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
 2020-01-22 11:26:22 +01:00
R. RyanTM fff7a7a862 picard-tools: 2.21.3 -> 2.21.6 2020-01-22 10:12:28 +00:00
DwarfMaster 227a3f4383 Renamed maintainer lucas8 -> dwarfmaster 2020-01-21 16:39:52 +10:00
Jonathan Ringer 4de137a77d samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
Frederik Rietdijk bcd8c6b8dc Merge master into staging-next 2020-01-17 17:08:16 +01:00
Dmitry Kalinkin 430dfb8082
Merge pull request #77631 from smaret/gildas-202001a 
gildas: 20191201_a -> 20200101_a
 2020-01-17 10:23:28 -05:00
Anders Kaseorg 3cd8ce3bce treewide: Fix unsafe concatenation of $LD_LIBRARY_PATH 
Naive concatenation of $LD_LIBRARY_PATH can result in an empty
colon-delimited segment; this tells glibc to load libraries from the
current directory, which is definitely wrong, and may be a security
vulnerability if the current directory is untrusted.  (See #67234, for
example.)  Fix this throughout the tree.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2020-01-15 09:47:03 +01:00
Frederik Rietdijk 2a88c3c302 Merge staging-next into staging 2020-01-15 09:23:28 +01:00
Will Dietz afe905246d nota: init at 1.0 
Fixes #77590.
 2020-01-14 15:16:21 -08:00
Sébastien Maret 0956fcab16
gildas: 20191201_a -> 20200101_a 2020-01-14 11:22:53 +01:00
Luka Blaskovic 991a7e041f pcalc: build with bison3 2020-01-13 21:35:19 +00:00
lewo 4ea7d13c5c
Merge pull request #77041 from filalex77/rink-0.4.5 
rink: 0.4.4 -> 0.4.5
 2020-01-11 09:35:16 +01:00
Jonathan Ringer 5961f211f3 python.pkgs wide: fix problematic urls 2020-01-10 21:02:12 -08:00
Jörg Thalheim 01d93cbbe1
kicad: split version.nix & add update.sh (#77003) 
kicad: split version.nix & add update.sh
 2020-01-10 14:19:14 +00:00
Bruno Bzeznik f7a4e4a93a bayescan: init at 2.1 (#68191) 
Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2020-01-09 12:38:53 -05:00
markuskowa 2aecfca22c
Merge pull request #77083 from r-ryantm/auto-update/gmsh 
gmsh: 4.4.1 -> 4.5.1
 2020-01-09 12:27:11 +01:00
Mario Rodas 2148e53664
Merge pull request #77160 from r-ryantm/auto-update/ngspice 
ngspice: 30 -> 31
 2020-01-09 05:13:15 -05:00
Mario Rodas 6f79952429
Merge pull request #77169 from r-ryantm/auto-update/pcb 
pcb: 4.2.0 -> 4.2.1
 2020-01-09 05:09:50 -05:00
Daniel Albert d5dc2cc7ba xflr5: init at 6.47 2020-01-08 23:35:11 +01:00
Evils 2607c4b9f9 kicad: split version.nix & add update.sh 
update.sh generates version.nix
  by default only updates kicad-unstable
  several options (can be combined)
    all, update to latest tag and master
    clean, generate versions.sh from scratch
    commit, make a git commit
 2020-01-08 23:04:54 +01:00
Maximilian Bosch 8a6baaecb5
geogebra: 5-0-569-0 -> 5-0-570-0 2020-01-07 23:26:31 +01:00
Luis Pedro Coelho fdfebafc10 blast: init at 2.10.0 (#61430) 
Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
 2020-01-07 20:14:18 +01:00
Markus Kowalewski a74b248f06
openmolcas: 18.09 -> 19.11 2020-01-07 15:36:59 +01:00
R. RyanTM cc98c9fbb2 pcb: 4.2.0 -> 4.2.1 2020-01-06 19:47:54 -08:00
Ryan Mulligan 8e0b0d08c2
Merge pull request #77125 from r-ryantm/auto-update/last 
last: 1042 -> 1045
 2020-01-06 18:51:09 -08:00
R. RyanTM 501f79aa9b ngspice: 30 -> 31 2020-01-06 17:40:29 -08:00
R. RyanTM 4bc4c70bc6 last: 1042 -> 1045 2020-01-06 11:46:28 -08:00
R. RyanTM 66156e04d5 gmsh: 4.4.1 -> 4.5.1 2020-01-06 06:33:28 -08:00
R. RyanTM 60fd879921 gromacs: 2019.4 -> 2020 2020-01-06 04:30:02 -08:00
Oleksii Filonenko bc8dc2bd0a
rink: add filalex77 to maintainers 2020-01-06 12:41:19 +02:00
Oleksii Filonenko 8d8ce109cb
rink: 0.4.4 -> 0.4.5 2020-01-06 12:39:32 +02:00
markuskowa b06114f078
Merge pull request #76311 from r-ryantm/auto-update/marvin 
marvin: 19.23.0 -> 19.27.0
 2020-01-04 12:24:48 +01:00
Gabriel Ebner 3604ae8394
Merge pull request #74259 from Evils-Devils/kicad-unstable 
kicad: cleanup, fix and update
 2020-01-03 20:14:07 +01:00
Frederik Rietdijk 7aa2b0215b Merge master into staging-next 2020-01-03 10:25:14 +01:00
Ryan Mulligan ec29bb50bf
Merge pull request #76208 from r-ryantm/auto-update/bcftools 
bcftools: 1.9 -> 1.10.2
 2020-01-02 16:42:27 -08:00
Evils e4786f3a1c kicad: update & cleanup 
minor simplification, fix base version

split i18n and get from gitlab

correct wrapper pythonpath, cleanup build output

update & fake git describe

correct base.nix to fit contributing.md
 2020-01-02 03:45:34 +01:00
Evils 6119ca27bb kicad: split wrapping and building 2020-01-02 03:45:34 +01:00
Evils d96992a21b kicad: unite unstable.nix with default.nix 
use latest libraries for unstable
move all revs and hashes to default.nix

thanks TQ for getting me through this blockage
 2020-01-02 03:45:34 +01:00
Evils 958d745fec kicad: use separated libraries 
switch source to gitlab as that's the new upstream source

use wrapper variables for everything but i18n
  add sym and fp templates to template path

update meta to reflect kicad's own language
  set license to AGPLv3, according to the source's LICENSE.README

reduce diff between default and unstable in preparation of merging

on debian gets "no module named 'math'"
  pcbnew 3d viewer is unusable (at least on my T410)
 2020-01-02 03:45:34 +01:00
Evils c61170168d kicad: switch to best try from unstable and 5.1.5 
make unstable use kicad-libraries
  still using a link in $out..., not sure that's a bad thing
  this allows setting that path in makeWrapperArgs
    can't use $out there

kicad-with-packages3d -> kicad and kicad-small

default to OCCT, OCE is outdated
  enforce OCCT on aarch64, where OCE is broken
  withOCE flag allows using OCE on non-aarch64
 2020-01-02 03:45:34 +01:00
Evils 6477f717e3 kicad-unstable: wrap 
use wxGTK31
  brings hiDPI support
  no python shell...
 2020-01-02 03:45:34 +01:00
Matt Huszagh d40747ed2c kicad: add python six package as dep 
This is needed for python scripting support.
 2020-01-02 03:45:34 +01:00
Matt Huszagh 1eb1b067dd kicad: python2 -> python3 2020-01-02 03:45:34 +01:00
Robin Gloster 95526382be
polymake: fix for structured attrs 2019-12-31 00:49:42 +01:00
Robin Gloster 5f2b92e3ec
treewide: NIX_*_COMPILE -> string 2019-12-31 00:13:29 +01:00
Robin Gloster ab0cfd9e03
treewide: NIX_*_COMPILE -> string 2019-12-31 00:10:18 +01:00
Frederik Rietdijk 6d059becd3 Merge gcc-9 into staging (#68029) 2019-12-30 16:38:38 +01:00
Robin Gloster 65395a7105
treewide: installTargets is a list 2019-12-30 13:29:27 +01:00
Merijn Broeren 133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Robin Gloster 1065d80dd3
simgrid: *Flags are lists 2019-12-30 12:15:25 +01:00
Jan Tojnar ea4da9b5fa
Merge pull request #76674 from jtojnar/structured-attrs-masterable 
treewide: structured-attrs fixes
 2019-12-30 04:52:45 +01:00
Robin Gloster ac8eaa8507
treewide: fix *Flags 2019-12-30 04:50:37 +01:00
Franz Pletz 1a871b4382
minisat: 2.2.0 -> 2.2.1 2019-12-30 03:50:35 +01:00
Franz Pletz a88fc6be6d
strelka: fix build w/ gcc9 2019-12-30 03:18:19 +01:00
R. RyanTM 3d740ef586 verilator: 4.022 -> 4.024 2019-12-29 15:48:39 -06:00
Frederik Rietdijk eda01862c4
Merge pull request #75900 from jbedo/tebreak 
Tebreak, minia, last, bx-python, python-lzo
 2019-12-29 10:24:31 +01:00
Justin Bedo 11460d4cac
tebreak: init at 1.0 2019-12-29 17:16:10 +11:00
Ben Wolsieffer 660345d9fe mavproxy: 1.8.17 -> 1.8.18 2019-12-27 16:23:20 -08:00
Franz Pletz 81248e703c
xfitter: 2.0.0 -> 2.0.1, fix build w/ gcc9 2019-12-27 03:48:21 +01:00
Dmitry Kalinkin 984ceb1092
Merge pull request #76541 from veprbl/pr/root_python_wrap 
root: wrap python executables
 2019-12-26 12:29:12 -05:00
Dmitry Kalinkin 0b28198f23
root: wrap python executables 
In normal use of ROOT the PYTHONPATH is intended to be set when user
sources the thisroot.{,s}sh. We do that in the setupHook. This covers
the case when thisroot.sh was not sourced.
 2019-12-26 11:49:12 -05:00
Maximilian Bosch 9842c4b107
treewide: update which packages I'm currently maintaining 
Idea shamelessly stolen from 4e60b0efae.

I realized that I don't really know anymore where I'm listed as maintainer and what
I'm actually (co)-maintaining which means that I can't proactively take
care of packages I officially maintain.

As I don't have the time, energy and motivation to take care of stuff I
was interested in 1 or 2 years ago (or packaged for someone else in the
past), I decided that I make this explicit by removing myself from several
packages and adding myself in some other stuff I'm now interested in.

I've seen it several times now that people remove themselves from a
package without removing the package if it's unmaintained after that
which is why I figured that it's fine in my case as the affected pkgs
are rather low-prio and were pretty easy to maintain.
 2019-12-26 15:27:47 +01:00
Franz Pletz 77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9 2019-12-26 14:17:36 +01:00
Timo Kaufmann 8ac53ed0b1 python.pkgs.sympy: 1.4 -> 1.5 
Sage needs some doctest changes. The patch was included upstream.
Modelled after https://trac.sagemath.org/ticket/28911.
 2019-12-26 11:46:42 +01:00
Markus Kowalewski 63d62699e0
marvin: 19.25.0 -> 19.27.0 2019-12-25 15:11:16 +01:00
Jan Tojnar b1b26f8cf6
Merge pull request #76412 from jtojnar/pangox-compat-drop 
pangox_compat: drop
 2019-12-24 20:04:10 +01:00
Jan Tojnar aee453e5c9
openmodelica: remove pangox dependency 
It was probably just a dependency of `gtkglext` since I cannot find any reference to `pangox` in the repo.

But cannot verify build since it is broken.
 2019-12-24 16:13:13 +01:00
markuskowa 64b6fa927e
Merge pull request #76285 from r-ryantm/auto-update/jmol 
jmol: 14.30.0 -> 14.30.1
 2019-12-24 02:05:48 +01:00
R. RyanTM cf6d80a89d marvin: 19.23.0 -> 19.25.0 2019-12-23 13:15:32 -08:00
R. RyanTM 398f11945e jmol: 14.30.0 -> 14.30.1 2019-12-23 09:16:44 -08:00
R. RyanTM c905a6da5a bcftools: 1.9 -> 1.10.2 2019-12-22 20:00:29 -08:00
Maximilian Bosch 65061ab2ae
stellarium: 0.19.2 -> 0.19.3 
https://github.com/Stellarium/stellarium/releases/tag/v0.19.3
 2019-12-22 13:57:13 +01:00
Alyssa Ross 7887a81193
treewide: fix cargoSha256 (again) 
cargo-vendor output was changed in a4fc84de44.
 2019-12-20 20:08:53 +00:00
Justin Bedo 2191912274
minia: init at 3.2.1 2019-12-20 11:27:04 +11:00
Justin Bedo 6741cff527
last: init at 1042 2019-12-20 11:27:02 +11:00
Jan Tojnar 048faed66a
pcb: 20140316 → 4.2.0 
* Long overdue update
* Clean up the expression
* Drop unneeded pangox_compat – it was probably needed before gtkglext propagated it.
 2019-12-19 00:47:20 +01:00
Justin Bedo 28a057a56b
bedtools: 2.29.1 -> 2.29.2 2019-12-18 10:39:25 +11:00
Mario Rodas 5e5ce79db4
Merge pull request #75807 from jbedo/strelka 
strelka: fix broken build
 2019-12-16 23:52:35 -05:00
Justin Bedo c3f09c33eb
strelka: fix broken build 2019-12-17 11:20:32 +11:00
Alex Branham 7af84afa2a R: 3.6.1 -> 3.6.2 
Closes https://github.com/NixOS/nixpkgs/pull/75587.
 2019-12-16 18:56:49 +01:00
Florian Klink 0380ed20db
Merge pull request #75657 from flokli/gtkwave-gtk3 
gtkwave: build with gtk3
 2019-12-15 15:07:07 +01:00
Renaud 2a1a4cad38
Merge pull request #75388 from Lassulus/xplanet 
xplanet: 1.3.0 -> 1.3.1
 2019-12-15 14:57:48 +01:00
lassulus 3772d04e1c xplanet: 1.3.0 -> 1.3.1 2019-12-15 14:02:36 +01:00
Florian Klink ac1a5ac2db gtkwave: build with gtk3 
gtkwave ships a gtk3 flavour on sourceforge. let's use that one.
 2019-12-15 03:54:35 +01:00