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3330 Commits

Author SHA1 Message Date
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
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
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