Commit Graph

64 Commits

Author SHA1 Message Date
Sergei Trofimovich
0f0faddb8d hdf5: fix non-determinism by removing timestamps from .data
$ diffoscope '...-hdf5-1.12.1' '...-hdf5-1.12.1.check'
    --- ...-hdf5-1.12.1/lib/libhdf5.settings
    +++ ...-hdf5-1.12.1.check/lib/libhdf5.settings
     -1,17 +1,17 @@
                      HDF5 Version: 1.12.1
    -                Configured on: Thu Oct 28 17:42:30 UTC 2021
    +                Configured on: Sat Nov  6 19:02:02 UTC 2021
                     Configured by: nixbld@
                       Host system: x86_64-unknown-linux-gnu
    -            Uname information: Linux localhost 5.10.76 #1-NixOS SMP Wed Oct 27 07:56:57 UTC 2021 x86_64 GNU/Linux
    +            Uname information: Linux localhost 5.14.15 #1-NixOS SMP Wed Oct 27 07:59:56 UTC 2021 x86_64 GNU/Linux

The patch removes `Configured on`, `Configured by` and `Uname information` fields.
2021-11-06 19:28:55 +00:00
Doron Behar
72a4341129 hdf5: consistently use *Support arguments 2021-10-05 00:19:56 +08:00
Markus Kowalewski
550ffc4513
misc: move gfortran to nativeBuildInputs 2021-09-03 13:33:34 +02:00
R. RyanTM
a22fd3f4bb hdf5-cpp: 1.12.0 -> 1.12.1 2021-07-24 15:19:28 +02:00
Sandro
ef9a1d4c57
Merge pull request #119258 from drewrisinger/dr-pr-fix-python-tables 2021-05-25 03:38:59 +02:00
Stefan Frijters
36cce52a78 hdf5_1_10: Add java support 2021-05-07 10:48:26 -07:00
Drew Risinger
19acc797c7 hdf5_1_10: rollback 1.10.7 -> 1.10.6
This package only exists for compatibility with
``python3Packages.tables``, as far as I can tell based on usage in
nixpkgs.

``tables`` tests fail on hdf5 > v1.10.5, so we are reverting this to
the last "good" version of hdf5 that works with ``tables``.
``hdf5_1_10`` should hopefully be unpinned on the next release of
``python3Packages.tables``.
https://github.com/PyTables/PyTables/issues/845
2021-04-28 10:43:04 -04:00
Thomas Gerbet
b9fcaefeb3 hdf5_1_10: init at 1.10.7
Introduce hdf5_1_10 so it can be used by packages encountering issues
hdf5 1.12.0.
2021-04-08 08:35:45 +02:00
Thomas Gerbet
7187949817 hdf5: make possible to use the v1.10 API 2021-04-04 13:27:51 +02:00
Thomas Gerbet
6696362562 hdf5: 1.10.7 -> 1.12.0
Fixes CVE-2020-10809, CVE-2020-10810, CVE-2020-10811 and CVE-2020-10812.
Changes: https://github.com/HDFGroup/hdf5/blob/hdf5-1_12_0/release_docs/RELEASE.txt
2021-03-25 13:03:33 +01:00
Astro
a419187458 hdf4, hdf5: add javaSupport flag 2021-02-17 22:34:49 +01:00
Astro
d1ca6bd23e hdf5: 1.10.6 -> 1.10.7 2021-02-17 22:34:49 +01:00
Markus Kowalewski
6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
 {
   mpi = super.mpich;
 }

All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
2021-01-23 12:15:13 +01:00
Ben Siraphob
8c5d37129f pkgs/tools: stdenv.lib -> lib 2021-01-15 17:12:36 +07:00
John Ericson
f52263ced0 treewide: Start to break up static overlay
We can use use `stdenv.hostPlatform.isStatic` instead, and move the
logic per package. The least opionated benefit of this is that it makes
it much easier to replace packages with modified ones, as there is no
longer any issue of overlay order.

CC @FRidh @matthewbauer
2021-01-03 19:18:16 +00:00
Ben Darwin
95439a7e7d hdf5_1_8: remove
- no longer needed as `libminc` has been updated to use the default hdf5
2020-10-06 15:31:20 -04:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
tviti
2cfad8fa28
Revert "hdf5-fortran: Mark broken on Darwin" (#80419)
This reverts commit 8836c4d71b.

Closes #79952
2020-02-18 14:52:22 -05:00
R. RyanTM
7f8fb20f57 hdf5: 1.10.5 -> 1.10.6 2020-01-06 05:59:41 -08:00
Thomas Tuegel
734979f794 hdf5: Fix flavored builds with multiple outputs 2019-09-29 11:23:58 +02:00
Thomas Tuegel
6cbf0b4bd2
hdf5: Use multiple outputs to reduce closure size 2019-09-25 13:07:20 -05:00
volth
46420bbaa3 treewide: name -> pname (easy cases) (#66585)
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
2019-08-15 13:41:18 +01:00
Markus Kowalewski
015888ce7f hdf5: 1.10.4 -> 1.10.5 2019-04-10 18:53:51 +02:00
Markus Kowalewski
99ca454f23
hdf5: add openmpi-4 compatibility patches 2019-02-21 15:08:33 +01:00
R. RyanTM
8684ef15a1 hdf5: 1.10.3 -> 1.10.4 (#50100)
* hdf5: 1.10.3 -> 1.10.4

Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/hdf5-threadsafe/versions

* hdf5: update meta.license

HDF5 is licensed under a BSD 3-clause variant
2018-11-15 17:04:24 +01:00
R. RyanTM
fb70ad3d60 hdf5-threadsafe: 1.10.2 -> 1.10.3
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/hdf5-threadsafe/versions.
2018-08-24 03:57:05 -07:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
R. RyanTM
e9dbe1a2a3 hdf5-threadsafe: 1.10.1 -> 1.10.2
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/hdf5-threadsafe/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5diff -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5diff --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5diff -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5diff --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5ls -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5ls --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5ls -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5ls --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5dump -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5dump --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5dump -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5dump --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5mkgrp -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5mkgrp --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5mkgrp -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5mkgrp --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5clear -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5clear --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5clear -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5clear --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5import -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5import -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5repack -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5repack --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5repack -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5repack --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5jam -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5jam --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5jam -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5unjam -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5unjam --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5unjam -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5copy -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5copy --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5copy -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5copy --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5format_convert -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5format_convert --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5format_convert -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5format_convert --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5stat -h’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5stat --help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5stat -V’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5stat --version’ and found version 1.10.2
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5perf_serial help’ got 0 exit code
- ran ‘/nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2/bin/h5cc --help’ got 0 exit code
- found 1.10.2 with grep in /nix/store/29yg9dx5p3ppcvyz7fk2lb14hmmy2slj-hdf5-1.10.2
- directory tree listing: https://gist.github.com/aedb29e367d0b709b77bbdc794b96dd6
2018-04-07 08:36:04 -07:00
Roberto Di Remigio
eb43cc569a
hdf5: 1.8.18 -> 1.10.1 2017-11-21 22:08:07 +01:00
Roberto Di Remigio
98a748485e
hdf5_1_8: add fortran2003 option 2017-11-21 22:08:06 +01:00
Roberto Di Remigio
443faefdfb
hdf5_1_8: 1.8.18 -> 1.8.19 2017-11-21 22:08:06 +01:00
Roberto Di Remigio
e4ac6f6ab2
hdf5_1_8: init at 1.8.18 2017-11-21 22:08:06 +01:00
Tuomas Tynkkynen
8836c4d71b hdf5-fortran: Mark broken on Darwin
Never succeeded.

https://hydra.nixos.org/build/62044922
2017-09-30 21:29:50 +03:00
Sukant Hajra
82667fee37 hdf5: remove references to stdenv.cc
The build provides as text a summary of the build, including the
absolute path of the compiler used for compilation.  Unfortunately, this
pulls in stdenv.cc as a transitive closure.

So this change just calls remove-references-to as a postInstall step for
the one stdenv.cc dependency.

See #29889 for details.
2017-09-28 10:41:38 +02:00
Tuomas Tynkkynen
a7440aa7c6 hdf5: Re-enable on darwin
Oops, ab71280823 intended to only disable hdf5-fortran but also
disabled the others that are fine.
2017-09-22 19:56:49 +03:00
Tuomas Tynkkynen
ab71280823 darwin: Disable some packages that have never built successfully
mate.mate-desktop: https://hydra.nixos.org/build/61110037
gdmap: https://hydra.nixos.org/build/61144743
redsocks: https://hydra.nixos.org/build/61123106
resolv_wrapper: https://hydra.nixos.org/build/61121132
ogmtools: https://hydra.nixos.org/build/61108726
mp3info: https://hydra.nixos.org/build/61139015
lxappearance-gtk3: https://hydra.nixos.org/build/61126327
hdf5-fortran: https://hydra.nixos.org/build/61146631
pqiv: https://hydra.nixos.org/build/61124724
2017-09-22 17:25:38 +03:00
Dmitry Kalinkin
8b8e363979 hdfview: init at 2.14
hdf_java: init at 3.3.2
2017-08-22 18:31:39 -04:00
mimadrid
09e0cc7cc7
Update homepage attributes: http -> https
Homepage link "http://.../" is a permanent redirect to "https://.../" and should be updated
https://repology.org/repository/nix_stable/problems
2017-08-03 11:56:15 +02:00
Frederik Rietdijk
3d2cfabad6 hdf5: add comment about multiple outputs 2017-05-29 21:25:42 +02:00
John Ericson
4c0d7da183 Get rid of all with { inherit... } and just used let inherit...
The old forms presumably predates, or were made in ignorance of,
`let inherit`. This way is better style as the scoping as more lexical,
something which Nix can (or might already!) take advantage of.
2017-03-30 03:05:05 -04:00
Lancelot SIX
16eb67ac9c
hdf5: 1.8.16 -> 1.8.18
For release announcement, see
https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18-RELEASE.txt
2016-12-01 17:23:15 +01:00
Frederik Rietdijk
9d25dc12d9 Revert "hdf5: 1.8.16 -> 1.10.0-patch1"
This reverts commit 1c1a03f0d3.

hdf5 1.10 is not yet supported by all tools/libraries (e.g pytables, a dependency of pandas, requires hdf5 1.8).
2016-08-28 19:28:31 +02:00
David Guibert
1c1a03f0d3 hdf5: 1.8.16 -> 1.10.0-patch1 2016-08-28 11:42:21 +02:00
Tuomas Tynkkynen
21f17d69f6 treewide: Add lots of meta.platforms
Build-tested on x86_64 Linux & Mac.
2016-08-02 21:42:43 +03:00
Frederik Rietdijk
46378eb128 hdf5: propagate optional zlib dependency 2016-07-19 14:12:13 +02:00
Lancelot SIX
afa9e26130 pkgs.hdf5: Fix mpi build
@vcunat fixed the assertion (which was his wrong suggestion).
2015-11-20 11:25:47 +01:00
Lancelot SIX
4d28d46c45 hdf5: 1.8.15-patch1 -> 1.8.16 (close #11153) 2015-11-20 11:25:47 +01:00
Vladimír Čunát
6a2a2f4ad5 hdf5: refactor the expression
It's possible enableShared has little impact,
as we pass --disable-static to all packages by default.
2015-11-11 15:17:40 +01:00
Lancelot SIX
27eeb48cd8 pkgs.hdf5: 1.8.14 -> 1.8.15-patch1 2015-10-19 13:07:53 +00:00
Lancelot SIX
924c38214d pkgs.hdf5: Add c++ and fortran variants 2015-10-19 12:57:24 +00:00