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2020 Commits

Author SHA1 Message Date
Silvan Mosberger
e710f80018
sad: fix build 2018-08-09 22:13:44 +02:00
Frederik Rietdijk
d9fa74ba78 Merge master into staging 2018-08-09 18:28:15 +02:00
Austin Seipp
752284680b symbiyosys: 2018.05.03 -> 2018.07.26 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-08 19:49:42 -05:00
R. RyanTM
f5f55e4727 vcftools: 0.1.15 -> 0.1.16 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions.
 2018-08-08 00:48:04 -07:00
Timo Kaufmann
291018b34e arb: 2.13.0 -> 2.14.0 (#44600) 2018-08-07 16:38:34 +02:00
symphorien
0ca40a51c7 gwyddion, ripser: fix derivation name (#44577) 2018-08-07 01:21:53 +02:00
Michael Raskin
75cb04672f
Merge pull request #44508 from timokau/cddlib-0.94j 
cddlib: 0.94i -> 0.94j
 2018-08-05 19:03:47 +00:00
Timo Kaufmann
0a44ff7676 cddlib: 0.94i -> 0.94j 
cddlib was autotoolized, incorporated equivalents to the sage patches
and moved to GitHub.
 2018-08-05 19:02:45 +02:00
Michael Raskin
6b0234942b
Merge pull request #44501 from timokau/sage-native-pari 
sage: don't override pari
 2018-08-05 15:14:00 +00:00
Timo Kaufmann
30c822189d sage: don't override pari 
Sage assumes that pari does not use threads. However instead of
disabling them at compile time, we can diable them at runtime instead.
As a result, sage doesn't need its own version of pari anymore. That
means less rebuilds, less complexity and easier debugging.
 2018-08-05 13:48:14 +02:00
Michael Raskin
58384b1dd0 scilab-bin: 5.5.2 -> 6.0.1 2018-08-05 11:27:35 +03:00
Michael Raskin
b79dbfe482
Merge pull request #43281 from timokau/sage-8.3 
sage: 8.2 -> 8.3
 2018-08-04 13:02:06 +00:00
Timo Kaufmann
834a24e0ff sage: don't pin ntl 
Now possible because of the lcalc c++11 patch.
 2018-08-04 14:22:58 +02:00
Timo Kaufmann
e550e5d0c7 lcalc: apply c++11 patch 2018-08-04 14:22:29 +02:00
Timo Kaufmann
fa34f6d41c sage: don't pin pari 2018-08-04 14:22:28 +02:00
Timo Kaufmann
e82c26af9b sage: don't pin singular 2018-08-04 14:22:28 +02:00
Timo Kaufmann
289173366b singular: backport ntl error handling patch 2018-08-04 14:22:27 +02:00
Timo Kaufmann
840b64fdb8 sage: 8.2 -> 8.3 2018-08-04 14:22:21 +02:00
Tuomas Tynkkynen
008fd5fcf5 Merge remote-tracking branch 'upstream/master' into staging 2018-08-04 15:17:42 +03:00
John Ericson
db965063b3 treewide: Make configureFlags lists 2018-08-03 17:06:03 -04:00
John Ericson
85a9913edd treewide: Make more complicated configureFlags lists 2018-08-03 17:06:03 -04:00
John Ericson
632d24f11f scilab: Make configureFlags a list 2018-08-03 17:05:58 -04:00
Robert Schütz
ae3bbf2958 almonds: use python3 2018-08-03 18:04:46 +02:00
Johannes Frankenau
79cd841713 bcal: 1.8 -> 1.9 2018-08-03 09:08:26 +02:00
Uli Baum
052e4baf0a somatic-sniper: disable parallel building 
to fix non-deterministic failure
 2018-08-03 08:27:41 +02:00
xeji
9e52696649
Merge pull request #44325 from markuskowa/molcas 
openmolcas: init at 20180529
 2018-08-02 10:32:04 +02:00
Markus Kowalewski
484473b184
openmolcas: init at 20180529 2018-08-02 10:18:17 +02:00
Justin Bedő
51fc0ef8d2 somatic-sniper: init 1.0.5.0 (#43403) 2018-08-01 22:11:13 +02:00
Jörg Thalheim
9cff865230
Merge pull request #44122 from bgamari/kicad-0.5 
kicad: 4.0.7 -> 5.0.0
 2018-07-31 15:12:27 +01:00
Jörg Thalheim
71b579f9d4 kicad: remove scripting flag for simplicity 2018-07-31 14:44:49 +01:00
Jörg Thalheim
611f0ed188 kicad: properly wrap wxPython 2018-07-31 14:37:59 +01:00
R. RyanTM
38c8be3726 gp2c: 0.0.10pl1 -> 0.0.11 (#43941) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gp2c/versions.
 2018-07-31 00:30:21 +02:00
R. RyanTM
d7c3926352 bcftools: 1.8 -> 1.9 (#43950) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/bcftools/versions.
 2018-07-30 22:36:27 +02:00
Timo Kaufmann
ae821e09e7 glpk: adopt error recovery patch (#44201) 
This makes it possible to use "vanilla" glpk for sage and shouldn't
affect anything else.
 2018-07-29 20:53:56 +02:00
Frederik Rietdijk
e46e7f44c2
Merge staging-next into master 2018-07-29 09:13:54 +02:00
Lluís Batlle i Rossell
f54b387b63 Merge remote-tracking branch 'central/master' into viric_clean 2018-07-28 19:25:14 +02:00
Frederik Rietdijk
8db716d9f3 Merge master into staging-next 2018-07-28 12:31:35 +02:00
Frederik Rietdijk
1fe2a0f81e
Merge pull request #44129 from timokau/pari-2.11.0 
pari: 2.9.5 -> 2.11.0
 2018-07-27 11:57:57 +02:00
Timo Kaufmann
330c501be0 pari: 2.9.5 -> 2.11.0 
The pari update makes it necessary to disable a giac test that only
fails because it directly tests the pari interface.
 2018-07-26 18:42:17 +02:00
Ben Gamari
a4c932fa51 kicad: 4.0.7 -> 5.0.0 2018-07-26 12:27:27 -04:00
Frederik Rietdijk
f59e6f4037 Merge master into staging 2018-07-26 16:18:53 +02:00
Robert Schütz
daabcc3b9a spyder: use python3 
Dependency pylint is no longer supported on Python 2.
 2018-07-26 12:43:18 +02:00
Matthew Bauer
6d880d2d5b
Merge pull request #42149 from timjrd/openspace-rebase 
openspace: init at 0.11.1
 2018-07-23 11:38:06 -04:00
Timo Kaufmann
024c23503c singular: 4.1.1p1 -> 4.1.1p2 2018-07-23 12:17:25 +02:00
Lluís Batlle i Rossell
66d7126255 Take me (viric) out of most maintenance 
Since years I'm not maintaining anything of the list below other
than some updates when I needed them for some reason. Other people
is doing that maintenance on my behalf so I better take me out but
for very few packages. Finally!
 2018-07-22 21:50:19 +02:00
Frederik Rietdijk
f3088832df
Merge pull request #43899 from r-ryantm/auto-update/tla-toolbox 
tlaplusToolbox: 1.5.6 -> 1.5.7
 2018-07-22 08:44:58 +02:00
Frederik Rietdijk
5dcb1febac
Merge pull request #43913 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.9 -> 2.18.10
 2018-07-22 08:42:32 +02:00
Frederik Rietdijk
935a54f300
Merge pull request #43940 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.91 -> 3.3.92
 2018-07-22 08:23:25 +02:00
R. RyanTM
a7a3526f71 gtkwave: 3.3.91 -> 3.3.92 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gtkwave/versions.
 2018-07-21 17:57:51 -07:00
Ricardo M. Correia
0cf09556eb
why3: 0.88.3 -> 1.0.0 2018-07-21 22:53:44 +00:00
R. RyanTM
668047ca55 picard-tools: 2.18.9 -> 2.18.10 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/picard-tools/versions.
 2018-07-21 12:28:41 -07:00
R. RyanTM
9882d5635c tlaplusToolbox: 1.5.6 -> 1.5.7 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/tla-toolbox/versions.
 2018-07-21 08:39:53 -07:00
Jörg Thalheim
218298b30f
Merge branch 'master' into unused5 2018-07-21 15:41:22 +01:00
Sebastien Maret
9092083e9e gildas: fix architecture detection for aarch64 2018-07-21 13:21:06 +02:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
volth
6d2857a311 [bot] treewide: remove unused 'inherit' in let blocks 2018-07-20 19:38:19 +00:00
Frederik Rietdijk
1a6af9f88e
Merge pull request #43857 from volth/unused 
[bot] treewide: remove unreferenced code
 2018-07-20 21:06:32 +02:00
volth
87f5930c3f [bot]: remove unreferenced code 2018-07-20 18:48:37 +00:00
Matthew Bauer
fddd90e9ea
Merge pull request #43538 from timokau/fetchpatch-fix 
fetchpatch: quote excludes
 2018-07-19 00:35:09 -04:00
Matthew Bauer
76999cc40e treewide: remove aliases in nixpkgs 
This makes the command ‘nix-env -qa -f. --arg config '{skipAliases =
true;}'’ work in Nixpkgs.

Misc...

- qtikz: use libsForQt5.callPackage

  This ensures we get the right poppler.

- rewrites:

  docbook5_xsl -> docbook_xsl_ns
  docbook_xml_xslt -> docbook_xsl

diffpdf: fixup
 2018-07-18 23:25:20 -04:00
Michael Raskin
877899fdb9
Merge pull request #43679 from timokau/ntl-11.2.1 
ntl: 9.11.0 -> 11.2.1
 2018-07-18 15:08:43 +00:00
Jan Tojnar
a4443ef859
nasc: 0.4.6 → 0.4.7 2018-07-18 15:38:52 +02:00
Timo Kaufmann
cad446513e ntl: 9.11.0 -> 11.2.1 
ntl hasn't been updated in a while. So I'm doing that and adding myself
as the maintainer. I'm also adding some options and pinning the sage
dependency, since it is unfortunately not compatible with the latest ntl
yet.

I've also enabled the tests, since they don't take terribly long and are
worth the time in my opinion.
 2018-07-18 14:58:38 +02:00
Timo Kaufmann
3058513941 fetchpatch: add option to revert a patch 2018-07-16 22:46:54 +02:00
Jan Malakhovski
e80ca2182c clp: cleanup expression 2018-07-16 16:33:14 +00:00
Gabriel Ebner
862e4e4fdb cvc4: fix homepage url 2018-07-16 15:58:22 +01:00
fragamus
794a60a2fb bliss: fix header location (#43170) 2018-07-16 04:12:07 +00:00
Shea Levy
ed23255c5a
Merge branch 'init-gurobi' of git://github.com/jfrankenau/nixpkgs 2018-07-15 18:25:07 -04:00
Timo Kaufmann
c77d1e5b31 eclib: 20171219 -> 20180710 
Also includes the necessary sage compatibility patch, borrowed from
ArchLinux.
 2018-07-15 14:59:28 +02:00
Johannes Frankenau
d6874a7e1e gurobi: init at 8.0.1 2018-07-14 23:52:48 +02:00
Mario Rodas
1c88d0c6bd z3: fix darwin build (#43526) 2018-07-14 21:49:47 +02:00
markuskowa
7f1bcb1ebf octopus: 7.2 -> 8.1 (libxc 3.0.1 -> 4.2.3) (#43484) 2018-07-14 00:37:30 +02:00
Timo Kaufmann
85f7fa93bc pythonPackages.cypari2: 1.1.4 -> 1.2.1 (#43496) 2018-07-14 00:17:55 +02:00
Frederik Rietdijk
d0446a5c76
Merge pull request #43436 from timokau/sage-new-flask 
sage: replace flask-babel version pin by patch
 2018-07-13 18:52:26 +02:00
Frederik Rietdijk
59163c9c1c
Merge pull request #43471 from r-ryantm/auto-update/igv 
igv: 2.4.11 -> 2.4.13
 2018-07-13 18:47:57 +02:00
Michael Raskin
9932071581
Merge pull request #43472 from r-ryantm/auto-update/golly 
golly: 3.1 -> 3.2
 2018-07-13 15:51:31 +00:00
Will Dietz
efdf4711d8
Merge pull request #43445 from dtzWill/fix/yices-symlink 
yices: fix symlink created to match version
 2018-07-13 10:11:49 -05:00
R. RyanTM
d25ec8df03 golly: 3.1 -> 3.2 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/golly/versions.
 2018-07-13 03:02:59 -07:00
R. RyanTM
ab535c2757 igv: 2.4.11 -> 2.4.13 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/igv/versions.
 2018-07-13 02:49:22 -07:00
Will Dietz
f731c99e7d abc-verifier: 20160818 -> 2018-07-08 
Now hosted on github.
 2018-07-12 21:44:56 -05:00
Will Dietz
946a65ca5c yices: use lib.splitString, not everyone has builtins.splitVersion 2018-07-12 19:11:06 -05:00
Will Dietz
237c8f4148 yices: simplify ln command 2018-07-12 18:52:10 -05:00
Will Dietz
6ff8685057 yices: fix symlink to match version of package 
To help avoid this happening again, derive the string to use
from the version directly instead of embedding it in installPhase.
 2018-07-12 18:46:28 -05:00
Will Dietz
d3a595f190 libpoly: 0.1.5 -> 0.1.7 (noop), cleanup a bit to modern style 2018-07-12 17:06:57 -05:00
Timo Kaufmann
35896e3506 sage: replace flask-babel version pin by patch 2018-07-12 22:55:16 +02:00
Austin Seipp
54e9f7dcbe z3: move to multiple output packages 
The Z3 source code is effectively compiled into two completely separate
objects: the z3 binary file, and the libz3.so library -- but the binary is not
linked against the shared library, it simply incorporates all of the object
files. The Z3 code base results in an ~25MB object on x86_64-linux. As a
result, splitting bin/ and lib/ results in a 50% reduction in closure size.

(The include/ directory is also surprisingly large at .5MB...)

This also splits the python API into a completely separate .python attribute,
as well.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-07-12 15:48:48 -05:00
Timo Kaufmann
d37c23c699 jmol: 14.29.12 -> 14.29.17 (#43429) 2018-07-12 22:31:52 +02:00
Frederik Rietdijk
04cae0e5fb
Merge pull request #43333 from r-ryantm/auto-update/libpoly 
libpoly: 0.1.4 -> 0.1.5
 2018-07-11 19:01:02 +02:00
R. RyanTM
40e648b7ab yices: 2.5.4 -> 2.6.0 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/yices/versions.
 2018-07-11 08:45:45 -05:00
R. RyanTM
a89b538f0b libpoly: 0.1.4 -> 0.1.5 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/libpoly/versions.
 2018-07-11 02:29:13 -07:00
R. RyanTM
ade3e571a1 qalculate-gtk: 2.6.0 -> 2.6.1 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/qalculate-gtk/versions.
 2018-07-11 00:45:08 -07:00
R. RyanTM
99cb9de551 fricas: 1.3.3 -> 1.3.4 (#43023) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/fricas/versions.

These checks were done:

- built on NixOS
- /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4/bin/fricas passed the binary check.
- /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4/bin/efricas passed the binary check.
- 2 of 2 passed binary check by having a zero exit code.
- 0 of 2 passed binary check by having the new version present in output.
- found 1.3.4 with grep in /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4
- directory tree listing: https://gist.github.com/75d751d9733f6b0a7b582ab838a71963
- du listing: https://gist.github.com/4c6fe5f342430a2b36568da3229d3dc4
 2018-07-09 16:02:58 +02:00
R. RyanTM
6ec4be7ec5 igv: 2.4.10 -> 2.4.11 (#43003) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/igv/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11/bin/igv had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.4.11 with grep in /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11
- directory tree listing: https://gist.github.com/ca4cf484aab1c1590806c47c4fdde1d7
- du listing: https://gist.github.com/f7ff80a2429cf0a942195db4944659b1
 2018-07-09 16:02:34 +02:00
Silvan Mosberger
8e2c3b93ba
Merge pull request #43096 from jbedo/mosdepth 
mosdepth: init 0.2.3
 2018-07-09 04:55:24 +02:00
Dan Peebles
1dd7bc7dfc monosat: update build to use handy new environment variable 2018-07-08 22:04:05 -04:00
Dan Peebles
0372c87481 monosat: cbaf79cf -> 2deeadef 
Upstream fixed a few things I needed to work around
 2018-07-08 21:57:00 -04:00
Justin Bedo
59141de608
mosdepth: init 0.2.3 2018-07-09 08:51:49 +10:00
Dan Peebles
631dd7a4e9 monosat: init at 1nx3wh34 
Also includes the python and java bindings (although java is only
currently enabled on Linux)
 2018-07-08 12:43:29 -04:00
R. RyanTM
cb85999b6b picard-tools: 2.18.7 -> 2.18.9 (#42967) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
 2018-07-06 20:24:57 +02:00
Sebastien Maret
8ae9e7ef10 gildas: apply upstream fix and restore parallel building 2018-07-06 14:02:37 +02:00