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3781 commits

Author SHA1 Message Date
Mario Rodas c89c819abd
Merge pull request #98672 from r-ryantm/auto-update/bcftools 
bcftools: 1.10.2 -> 1.11
 2020-10-02 23:57:06 -05:00
Ryan Mulligan 6aadae67de
Merge pull request #81550 from scalavision/add-kent-utils-to-bioinf 
kent: init at 394
 2020-10-02 09:05:51 -07:00
Patrick Hilhorst f7e390e6d4 treewide: fix redirected urls (run 3) 
Related:
 - 9fc5e7e473
 - 593e11fd94
 - 508ae42a0f

Since the last time I ran this script, the Repology API changed, so I had to
adapt the script used in the previous PR. The new API should be more robust, so
overall this is a positive (no more grepping the error messages for our relevant
data but just a nice json structure).

Here's the new script I used:

```sh
curl https://repology.org/api/v1/repository/nix_unstable/problems \
   | jq -r '.[] | select(.type == "homepage_permanent_https_redirect") | .data | "s@\(.url)@\(.target)@"' \
   | sort | uniq | tee script.sed
find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```

I will also add this script to `maintainers/scripts`.
 2020-10-02 09:01:35 -07:00
Scalavision a6f124f57b kent: init at 404 2020-10-01 19:50:37 +02:00
Anderson Torres 5e99485b3d
Merge pull request #99214 from bcdarwin/update-mrtrix 
mrtrix: 3.0.0 -> 3.0.2
 2020-10-01 01:14:54 -03:00
Ben Darwin a94d0fe675 mrtrix: 3.0.0 -> 3.0.2 2020-09-30 22:13:18 -04:00
Vincent Laporte cc739e1c67 ocamlPackages.z3: init at 4.8.9 2020-09-30 22:03:17 +02:00
Dmitry Kalinkin dd57dcf2a5
stellarium: enable on darwin 2020-09-27 17:00:10 -04:00
Maximilian Bosch b8d1e39a28
stellarium: 0.20.2 -> 0.20.3 
https://github.com/Stellarium/stellarium/releases/tag/v0.20.3
 2020-09-27 22:09:36 +02:00
Matt Huszagh 6b9481607b openems: init at unstable-2020-02-15 2020-09-27 11:32:27 -07:00
Robert Scott 8db3ea1ef1
Merge pull request #98614 from r-burns/aragorn 
aragorn: fix build on darwin
 2020-09-25 19:58:10 +01:00
Dmitry Kalinkin 7867aafa51
Merge pull request #97613 from drewrisinger/zhf/verilog 
verilog: cleanup & test
 2020-09-25 10:37:34 -04:00
R. RyanTM e66a7e2fb7 cytoscape: 3.8.0 -> 3.8.1 2020-09-25 04:38:49 +00:00
R. RyanTM f4d3204486 bcftools: 1.10.2 -> 1.11 2020-09-24 18:53:07 +00:00
R. RyanTM 0765b507f9 jmol: 14.31.2 -> 14.31.3 2020-09-23 23:36:41 -07:00
Ryan Burns 6cc2d3e6f2 aragorn: fix build on darwin 
Use environment-specified $CC for C compiler
 2020-09-23 20:45:21 -07:00
Ryan Mulligan dfd2eeabd6
Merge pull request #69644 from bzizou/obitools 
obitools3: init at 3.0.0-beta14
 2020-09-23 19:04:11 -07:00
Doron Behar 0307d0e82b
Merge pull request #98441 from vbgl/why3-1.3.3 
why3: 1.3.1 -> 1.3.3
 2020-09-23 10:35:57 +03:00
Daniël de Kok af5b1a9f94
Merge pull request #98427 from jbedo/octopus 
octopus-caller: 0.6.3 -> 0.7.0
 2020-09-23 08:24:10 +02:00
Jon c7fdc43709
Merge pull request #98283 from risicle/ris-truvari-2.0.2 
truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build
 2020-09-22 23:10:58 -07:00
Robert Scott fc709e6dfe cvc3: enable for darwin 
it may be possible to get it building under clang with some work, but
switching it to gcc for now allows us to enable it
 2020-09-22 23:06:45 -07:00
Robert Scott 53a8a415ac cvc3: fix build against bison 3.7 
for some reason bison 3.7 output references $x_defs.h files under the name
$x.hpp. create symlinks to make this work.
 2020-09-22 23:06:45 -07:00
Austin Seipp daaa0e3350
Merge pull request #98239 from Sohalt/avy 
avy: 2017.10.16 -> cav19
 2020-09-22 23:19:05 -05:00
Vincent Laporte 64b68b30e9
why3: 1.3.1 -> 1.3.3 2020-09-23 03:24:02 +02:00
Drew Risinger ba886f7b1a verilog: add tests 
Run recommended self-tests from iverilog's CI.

Tests add about a minute to the build time on local machine
(2 -> 3 mins).
 2020-09-22 13:58:15 -04:00
Drew Risinger 0d9a6e2da5 verilog: cleanup 
Meta attributes were out of date or not in current style,
and some attributes of derivation were redundant.
 2020-09-22 13:58:06 -04:00
Justin Bedo 4bbdb75f22
octopus-caller: 0.6.3 -> 0.7.0 2020-09-22 08:43:04 +10:00
sohalt 40722346b8 avy: 2017.10.16 -> 2019.05.01 2020-09-20 16:13:29 +02:00
Robert Scott ecd5886830 truvari: 1.3.4 -> 2.0.2, fixing build 
seeing it has no tests, use pythonImportsCheck in an attempt to detect
total breakage, even though it's not intended to be used as an importable
module
 2020-09-20 12:25:17 +01:00
Robert Scott f1d2491057 bwa: include static library and some key headers in output 2020-09-20 12:23:18 +01:00
Gabriel Ebner efa2089077
Merge pull request #89731 from doronbehar/jdk_rename 2020-09-20 11:07:55 +02:00
Robert Scott 4637721bc1 truvari: fix build 
be less strict about versions
 2020-09-19 20:25:08 -07:00
Gabriel Ebner 67ff41201f leo3: fix executable 2020-09-19 15:05:02 +02:00
Gabriel Ebner 1c576d0b37 sage: use jdk8 2020-09-19 14:22:43 +02:00
Hannes Weisbach 9c73e34d18 kicad: remove gettext from buildInputs, add to nativeBuildInputs 
The i18n "library" does not link against gettext. It only requires the
msgfmt utility from gettext, hence gettext should be a nativeBuildInput
 2020-09-17 19:48:50 +02:00
Vladyslav M 9147432d5f
Merge pull request #98062 from jonringer/fix-streamlit 
streamlit: fix build
 2020-09-16 23:45:32 +03:00
Austin Seipp f1f1396167
Merge pull request #98109 from Pamplemousse/verilator 
verilator: 4.040 -> 4.100
 2020-09-16 14:25:25 -05:00
Pamplemousse 9839c0b292 verilator: 4.040 -> 4.100 
Signed-off-by: Pamplemousse <xav.maso@gmail.com>
 2020-09-16 08:40:01 -07:00
Anderson Torres 811709ff94
Merge pull request #95734 from trepetti/flatcam 
flatcam: init at 8.5
 2020-09-15 23:17:59 -03:00
Jonathan Ringer 07660b28bc streamlit: fix build 2020-09-15 11:19:26 -07:00
Vincent Laporte cc4a33d78c ott: 0.30 → 0.31 2020-09-14 21:42:22 +02:00
Sébastien Maret 234b39a6d4
gildas: 20200601_b -> 20200901_a (#97968) 2020-09-14 11:18:06 -04:00
Robert Scott 35ca475f8b
Merge pull request #97757 from freezeboy/fix-lp_solve 
lp_solve: fix build
 2020-09-13 11:00:26 +01:00
freezeboy 3fc3fd14cf lp_solve: fix buildCommand some binaries moved 2020-09-13 03:51:51 +02:00
Thomas Tuegel 87c7d1d4f8
z3: 4.8.8 -> 4.8.9 2020-09-11 14:38:43 -05:00
Maximilian Bosch 56708c3bf3
Merge pull request #97555 from badmutex/badi/maintainers-update 
maintainers: updates for badi/badmutex
 2020-09-09 23:03:52 +02:00
Badi Abdul-Wahid f3ce1df79a
tlaplus: remove myself from maintainers list 2020-09-09 10:40:46 -05:00
Cole Helbling 339f6248f6
verilog: unstable-2019-08-01 -> unstable-2020-08-24 
The build would previously fail due to a change in bison's behavior (see
5b699c1be7
for more information). Updating to a more recent version fixes this
issue.
 2020-09-09 00:47:52 -07:00
Emery Hemingway dc09e3edfc nim: wrap compiler for cross-compilation support 2020-09-07 16:16:55 +02:00
Emery Hemingway 06ac3c1d2a nim: patch to fix dynamic library loading 2020-09-07 16:16:55 +02:00