Commit graph

2211 commits

Author SHA1 Message Date
Will Dietz c417342cd2
Merge pull request #48579 from dtzWill/update/z3-4.8.1
z3: 4.7.1 -> 4.8.1
2018-11-02 04:02:24 -05:00
royneary bb2bae6986 mosdeph: fix compilation with nim 0.19 2018-10-31 22:03:27 +01:00
Jörg Thalheim 8df0ca2bbc
coq_8_4: remove
verasco was its only user
2018-10-30 13:31:11 +00:00
Timo Kaufmann 2513747356 sage: fix attrname
This is a minimal change mainly to make sure repology recognizes this
package as sage. I plan a bit more refactoring later, but this is
intentionally kept minimally invasive so that it won't break anything
and can be backported to 18.09.
2018-10-27 14:18:08 +02:00
Timo Kaufmann 7970a5a475
Merge pull request #49225 from timokau/arb-2.15.1
arb: 2.14.0 -> 2.15.1
2018-10-27 12:36:51 +02:00
Timo Kaufmann fbea2cd77a arb: 2.14.0 -> 2.15.1 2018-10-27 11:27:03 +02:00
Joachim F b6a5cd8970
Merge pull request #48812 from mpickering/cedille
cedille bug fixes
2018-10-24 15:29:47 +00:00
R. RyanTM c759273e2e star: 2.6.1a -> 2.6.1c
Semi-automatic update generated by
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2018-10-24 15:22:22 +02:00
Timo Kaufmann db75fe7313 sage: fix doctest
The test is depending on the "py2" tag always being added. I patched
that recently to make it possible to test sagedoc individually. Somehow
I missed this doctest.
2018-10-22 14:52:19 +02:00
Matthew Pickering 08e5ef20d8 cedille: Make a seperate output for the base library
For now, for normal usage you need to add `${cedille.lib}` to
the `~/.cedille/options` file so that cedille will find the base
libraries. There is no option to pass options by the command line.
2018-10-22 08:43:07 +00:00
Matthew Pickering f7d4bc2c71 cedille: Apply patch which unbreaks the options file
See https://github.com/cedille/cedille/issues/29
2018-10-22 08:42:01 +00:00
Timo Kaufmann b39142cd1f sage: fix dochtml tests 2018-10-21 19:17:07 +02:00
Timo Kaufmann 38c2be5ffe sage: fix docbuild
This is only a hotfix without really knowing the issue. See
https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ
2018-10-21 14:16:06 +02:00
Timo Kaufmann a413dedde1
Merge pull request #44527 from timokau/sage-8.4
[WIP] sage: 8.3 -> 8.4
2018-10-20 01:34:34 +02:00
Vincent Laporte c091e93b99
Merge pull request #48617 from Zimmi48/passthru-ocamlPackages-in-coq-package
coq: add ocamlPackages in passthru
2018-10-19 09:38:07 +00:00
Jörg Thalheim a595b872c8
Merge pull request #48509 from r-ryantm/auto-update/gtkwave
gtkwave: 3.3.94 -> 3.3.95
2018-10-19 09:29:23 +01:00
Jörg Thalheim 02405cfe83
Merge pull request #48565 from rprospero/sasview-4.2.0
Sasview: unstable -> 4.2.0
2018-10-18 21:44:25 +01:00
Jörg Thalheim 84890ac196
Merge pull request #48653 from vbgl/why3-1.1.0
why3: 1.0.0 -> 1.1.0
2018-10-18 18:55:10 +01:00
Timo Kaufmann 7ca1c31dfa sage: 8.4.rc1 -> 8.4 2018-10-18 09:58:36 +02:00
Vincent Laporte bc8d25c1ef
why3: 1.0.0 -> 1.1.0 2018-10-18 05:43:36 +00:00
Jörg Thalheim 4057f2107a
Merge pull request #48511 from r-ryantm/auto-update/gmsh
gmsh: 4.0.1 -> 4.0.2
2018-10-17 16:02:01 +01:00
Adam Washington 6be90bf8d7
sasmodels: unstable -> 4.2.0 2018-10-17 14:36:46 +01:00
Théo Zimmermann fa12476755
coq: add ocamlPackages in passthru
We might need OCaml packages that are not the one Coq is depending on
but they still need to come from the same package set (same OCaml version).
2018-10-17 13:26:43 +02:00
Will Dietz 51e511130a z3: 4.7.1 -> 4.8.1 2018-10-16 12:28:06 -05:00
Timo Kaufmann d2b5518e1e
Merge pull request #48507 from r-ryantm/auto-update/jmol
jmol: 14.29.22 -> 14.29.26
2018-10-16 10:36:39 +02:00
R. RyanTM eeb2ee296c gmsh: 4.0.1 -> 4.0.2
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2018-10-15 21:54:45 -07:00
R. RyanTM a721411239 gtkwave: 3.3.94 -> 3.3.95
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2018-10-15 21:21:29 -07:00
R. RyanTM fedc17a99d jmol: 14.29.22 -> 14.29.26
Semi-automatic update generated by
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2018-10-15 21:05:03 -07:00
Chris Ostrouchov 397e15f89e
lammps: patch_2Aug2018 -> stable_22Aug2018
nix derivation was cleaned significantly to follow nixpkgs better
2018-10-15 08:43:57 -04:00
Chris Ostrouchov 7717a2b844
dl-poly-classic: init 1.10
only mpi version provided
2018-10-15 08:43:50 -04:00
Matthew Pickering 43ae33728b cedille: init at 1.0.0 2018-10-14 19:17:23 +00:00
R. RyanTM d074fb1940 verilator: 4.002 -> 4.004
Semi-automatic update generated by
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2018-10-14 09:01:56 +02:00
Moritz Kiefer 6738033727
alt-ergo: 1.30->2.2.0, ocplib-simplex: 0.3->0.4 2018-10-13 17:45:45 +00:00
Timo Kaufmann f89df0b556 sage: 8.4.rc0 -> 8.4.rc1 2018-10-13 13:27:10 +02:00
Sebastien Maret 4f3c13b84f gildas: 20181001_a -> 20181001_b (#48200) 2018-10-11 11:37:38 +02:00
Vincent Laporte 6113d95235
prooftree: cleaning 2018-10-11 05:59:21 +00:00
Théo Zimmermann 2fdd38ed2d
camlp5_transitional: remove in favor of camlp5 (strict) 2018-10-10 19:44:54 +02:00
Théo Zimmermann 7ac0a23194
prooftree: 0.12 -> 0.13 2018-10-10 19:42:50 +02:00
Théo Zimmermann c76ffb9253
matita: remove broken package
As requested by Vincent Laporte.
2018-10-09 09:47:31 +02:00
Théo Zimmermann 34394a38ef
ocamlPackages_3_11_2: remove
This requires removing also the Coq 8.3 and Matita 0.5.8 packages.

Coq 8.3 was released 8 years ago (2010) and there is no trace left
of users of this version (contrary to Coq 8.4, released 2012).
It is well over time to remove it.

Matita 0.5.8 was released in 2010 and because this version was still
used for teaching according to the official website, a legacy release
(0.5.9) was released in 5 years later to compile with more recent
OCaml libraries.
Updating to 0.5.9 (or a more recent version like 0.99.3) should allow
getting rid of the dependency on older OCaml but it is hard to test
given that the package is already broken before this update.
2018-10-08 21:10:05 +02:00
Timo Kaufmann 27919e06f1 sage: 8.4.beta7 -> 8.4.rc0 2018-10-07 12:23:10 +02:00
Marco Maggesi 9a5f7b1630 hol_light: 2017-07-06 -> 2018-09-30
Also handle compatibility with newer version of OCaml (depend on num
library as needed).
2018-10-06 15:49:09 +00:00
Matthew Bauer c4f344ac44
Merge pull request #47291 from veprbl/pr/xfitter_init
xfitter: init at 2.0.0
2018-10-05 22:38:09 -05:00
Jörg Thalheim 5200167f12
Merge pull request #47831 from r-ryantm/auto-update/calc
calc: 2.12.6.6 -> 2.12.6.8
2018-10-04 23:31:38 +01:00
Jörg Thalheim a24cf5c4f7
Merge pull request #47845 from r-ryantm/auto-update/bowtie2
bowtie2: 2.3.4.2 -> 2.3.4.3
2018-10-04 20:19:35 +01:00
Gabriel Ebner 0a7e258012 elan: 0.5.0 -> 0.7.1 2018-10-04 16:33:36 +02:00
R. RyanTM 269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3
Semi-automatic update generated by
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2018-10-03 21:49:10 -07:00
R. RyanTM 904fd99bb4 calc: 2.12.6.6 -> 2.12.6.8
Semi-automatic update generated by
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2018-10-03 16:01:08 -07:00
R. RyanTM 98092f7a67 nauty: 26r10 -> 26r11
Semi-automatic update generated by
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2018-10-03 05:54:07 -07:00
R. RyanTM 609f9198f2 verilator: 3.926 -> 4.002
Semi-automatic update generated by
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2018-10-02 09:56:10 -05:00
Sebastien Maret 34ac35dfc6 gildas: 20180901_a -> 20181001_a (#47657)
- Update gildas to the latest version
 - Remove a patch that has been applied upstream
2018-10-02 12:49:33 +02:00
Austin Seipp 919a3b7f9c symbiyosys: 2018.07.26 -> 2018.09.12
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-10-01 22:32:54 -05:00
Timo Kaufmann a13eb29485 sage: 8.4.beta6 -> 8.4.beta7 2018-10-01 17:38:20 +02:00
Timo Kaufmann bcc066b569 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-10-01 14:20:33 +02:00
R. RyanTM 77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978)
Semi-automatic update generated by
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2018-09-29 21:03:17 +02:00
R. RyanTM 7ecc7c9220 gtkwave: 3.3.93 -> 3.3.94 (#47048)
Semi-automatic update generated by
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2018-09-28 23:47:58 +02:00
R. RyanTM b65fbe8fcd gmsh: 4.0.0 -> 4.0.1 (#47060)
Semi-automatic update generated by
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2018-09-28 22:17:32 +02:00
Will Dietz eb91037e7b tree-wide: patchelf used during build -> nativeBuildInputs
In a few cases it wasn't clear so I left them as-is.

While visiting these moved other things to nativeBuildInputs
when it was clear they were one of these cases:

* makeWrapper
* archive utilities (in order to unpack src)
  * a few of these might no longer be needed but leaving for another day
2018-09-28 11:43:16 -05:00
Timo Kaufmann 87ca34b895
Merge pull request #47043 from r-ryantm/auto-update/jmol
jmol: 14.29.19 -> 14.29.22
2018-09-27 12:09:01 +02:00
Timo Kaufmann 0be6ca9e71 sage: 8.4.beta5 -> 8.4.beta6 2018-09-27 12:08:15 +02:00
Timo Kaufmann 2f6b13950e Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-27 12:07:37 +02:00
markuskowa 6f6222c40f openmolcas: 20180529 -> 18.09 (#47410) 2018-09-27 10:47:02 +02:00
Vincent Laporte 23900febe7 coq: 8.8.1 -> 8.8.2 (#47388) 2018-09-26 22:26:39 +02:00
Sebastien Maret 1e67ff3f05 gildas: 20180801_a -> 20180901_a (#46159)
* gildas: 20180801_a -> 20180801_b

  - Update gildas
  - Remove a patch that has been applied upstream

* gildas: 20180801_b -> 20180901_a
2018-09-25 16:18:53 +02:00
Dmitry Kalinkin 39c85c3bf9 xfitter: init at 2.0.0 2018-09-24 14:34:49 -04:00
Dmitry Kalinkin 3187db6e8d root5: init at 5.34.36 2018-09-24 14:34:49 -04:00
Frederik Rietdijk 56853dc6d8
Merge pull request #45941 from NixOS/staging-next
Staging next
2018-09-23 09:31:28 +02:00
Orivej Desh 7545b7dcf3 platypus: 2017-03-07 -> 2018-07-22 2018-09-21 22:42:28 +00:00
Orivej Desh cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
R. RyanTM 730eb9f5f2 jmol: 14.29.19 -> 14.29.22
Semi-automatic update generated by
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2018-09-20 12:30:18 -07:00
Frederik Rietdijk de419917a3 Merge master into staging-next 2018-09-18 18:44:48 +02:00
Timo Kaufmann 1217882907 sage: 8.4.beta4 -> 8.4.beta5 2018-09-15 17:23:14 +02:00
Timo Kaufmann c3f652d5a8 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-15 17:22:11 +02:00
Chris Ostrouchov a2bc529f22
siesta: init at 4.0.2 2018-09-14 15:40:25 -04:00
Chris Ostrouchov 2c7295ebe0
quantum-espresso: init at 6.3 2018-09-14 15:40:14 -04:00
Maximilian Bosch 2cfc0bb7ee tamarin-prover: fix ghc 8.4 build (#46597)
See https://hydra.nixos.org/build/81125645

`tamarin-prover' upstream has a patch to fix GHC 8.4 compilation (and
uses stack lts-12.1 now), but it's not released yet:

a08f6e4007

The build is divided in several derivations, therefore the patch had to
be splitted and rebased for `lib/term', `lib/theory' and `lib/utils' to
ensure that the patch applies properly during the `patchPhase'.

Addresses #45960
2018-09-13 14:11:09 +02:00
Markus J. Ankenbrand e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
Uli Baum 1df2560dde Merge branch 'master' into staging-next 2018-09-13 10:08:53 +02:00
R. RyanTM e94947af0a gromacs: 2018.2 -> 2018.3 (#46275)
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2018-09-12 23:07:27 +02:00
R. RyanTM c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176)
Semi-automatic update generated by
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star
2018-09-12 22:49:12 +02:00
Matthew Bauer 40d19d8e7c
Merge pull request #45102 from jbedo/hisat2
hisat2: init 2.1.0
2018-09-10 15:11:58 -05:00
Matthew Bauer 05d379f3cf
Merge pull request #46211 from r-ryantm/auto-update/picard-tools
picard-tools: 2.18.11 -> 2.18.12
2018-09-10 14:58:59 -05:00
Silvan Mosberger 10a412f251
almonds: update license 2018-09-09 02:04:34 +02:00
Markus Kowalewski 70e254d6bd
root: add license 2018-09-08 14:51:28 +02:00
Markus Kowalewski 1cff2dd135
pynac: add license 2018-09-08 14:48:19 +02:00
Markus Kowalewski 258c202565
prooftree: add license 2018-09-08 14:44:43 +02:00
Markus Kowalewski 2ed07fdb2b
drgeo: add license + homepage 2018-09-08 14:42:12 +02:00
Timo Kaufmann db784d883c sage: re-add pkg-config aliases
Those were removed because they were added to openblas itself. There was
an error with that however and it will take some time until the fix
makes its way through staging. For the time being, reverting this part
of 26d5d030fe will fix the sage build.
This commit should be reverted once
408eacbc89 is in master.
2018-09-07 21:55:41 +02:00
Timo Kaufmann 770c5b8a69 sage: 8.4.beta3 -> 8.4.beta4 2018-09-07 20:56:37 +02:00
Timo Kaufmann 4ab832d6e7 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-07 20:54:09 +02:00
Timo Kaufmann 7521f2863d sage: fix numpy and scipy integration 2018-09-07 18:36:52 +02:00
Timo Kaufmann 759e495881
Merge pull request #46268 from r-ryantm/auto-update/jmol
jmol: 14.29.17 -> 14.29.19
2018-09-07 11:32:26 +02:00
R. RyanTM baf51804f0 jmol: 14.29.17 -> 14.29.19
Semi-automatic update generated by
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2018-09-06 19:54:40 -07:00
R. RyanTM f72cba212c picard-tools: 2.18.11 -> 2.18.12
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2018-09-06 14:22:26 -07:00
Profpatsch 3e45b61a99 lib/trivial: add a few examples of usage of assertMsg/assertOneOf 2018-09-06 18:14:27 +02:00
Sebastien Maret 5b58c6ac76 gildas: add alternative url for the source code (#46145)
For each new release, the upstream developers of Gildas move the
source code of the previous release to a different directory. Add this
directory to the list of url to avoid build failure at each new
release.
2018-09-06 15:10:21 +01:00
Renato Garcia 318c9296fa snakemake: add maintainers (#46117) 2018-09-05 21:46:17 +02:00
xeji bf2a90298a
Merge pull request #46053 from danieldk/mxnet-fixes
pythonPackages.mxnet: fix build
2018-09-05 16:07:56 +02:00
Sebastien Maret b76cf0b54c gildas: ignore clang warnings for unused command line arguments
See #46044
2018-09-05 12:17:05 +02:00
Daniël de Kok 590ce7d1ae mxnet: fix library dependencies.
- mxnet now builds the open source MKL DNN library. However, this
  was not included with the build.
- mxnet builds its own OpenMP library, even when OpenMP is provided
  by the system. This leads to problems, so remove the included
  OpenMP implementation:

  https://github.com/apache/incubator-mxnet/pull/12160
2018-09-04 20:27:25 +02:00