2013-08-24 10:51:56 +02:00
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;;; GNU Guix --- Functional package management for GNU
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2016-04-05 18:48:02 +02:00
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;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
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2013-11-04 19:58:54 +01:00
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;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
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2017-03-07 07:51:51 +01:00
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;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
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2018-01-31 23:56:10 +01:00
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;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
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2014-09-23 16:20:02 +02:00
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;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
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2014-09-28 01:29:56 +02:00
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;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
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2018-02-12 14:45:34 +01:00
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;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
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2015-03-04 09:01:30 +01:00
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;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
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2015-05-26 05:29:53 +02:00
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;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
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2018-02-28 13:41:42 +01:00
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;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
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2015-12-15 21:00:38 +01:00
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;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
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2016-04-08 10:48:58 +02:00
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;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
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2018-01-26 16:08:52 +01:00
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;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
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2018-03-12 16:06:17 +01:00
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;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
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2016-07-20 08:17:30 +02:00
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;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
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2017-10-04 17:17:03 +02:00
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;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
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2017-01-18 11:01:36 +01:00
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;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
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Correct name and Email for ng0.
* .mailmap: Correct name and Email for ng0.
* Makefile.am, doc/guix.texi, etc/completion/fish/guix.fish
gnu/packages/accessibility.scm, gnu/packages/admin.scm,
gnu/packages/audio.scm, gnu/packages/autotools.scm,
gnu/packages/cdrom.scm, gnu/packages/check.scm,
gnu/packages/cinnamon.scm, gnu/packages/compression.scm,
gnu/packages/crypto.scm, gnu/packages/databases.scm,
gnu/packages/django.scm, gnu/packages/dns.scm,
gnu/packages/emacs.scm, gnu/packages/enlightenment.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm,
gnu/packages/forth.scm, gnu/packages/fvwm.scm,
gnu/packages/games.scm, gnu/packages/gl.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm,
gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm,
gnu/packages/guile.scm, gnu/packages/haskell-check.scm,
gnu/packages/haskell-crypto.scm, gnu/packages/haskell.scm,
gnu/packages/image-viewers.scm, gnu/packages/image.scm,
gnu/packages/irc.scm, gnu/packages/language.scm,
gnu/packages/libcanberra.scm, gnu/packages/linux.scm,
gnu/packages/lisp.scm, gnu/packages/lolcode.scm,
gnu/packages/lxde.scm, gnu/packages/lxqt.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm,
gnu/packages/mate.scm, gnu/packages/maths.scm,
gnu/packages/mc.scm, gnu/packages/messaging.scm,
gnu/packages/music.scm, gnu/packages/ncurses.scm,
gnu/packages/networking.scm, gnu/packages/nickle.scm,
gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl-check.scm, gnu/packages/perl.scm,
gnu/packages/python-crypto.scm, gnu/packages/python-web.scm,
gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/ruby.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/serialization.scm,
gnu/packages/shells.scm, gnu/packages/ssh.scm,
gnu/packages/suckless.scm, gnu/packages/tbb.scm,
gnu/packages/telephony.scm, gnu/packages/text-editors.scm,
gnu/packages/textutils.scm, gnu/packages/time.scm,
gnu/packages/tls.scm, gnu/packages/tor.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vim.scm, gnu/packages/web.scm,
gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xfce.scm, gnu/packages/xml.scm,
gnu/packages/xorg.scm, gnu/services/certbot.scm,
gnu/services/desktop.scm, gnu/services/version-control.scm,
gnu/services/web.scm, guix/import/hackage.scm,
guix/licenses.scm: Likewise.
Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
2018-03-20 16:39:45 +01:00
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;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
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2017-03-17 12:23:21 +01:00
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;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
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2017-09-29 12:36:20 +02:00
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;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
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2017-08-07 12:43:17 +02:00
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;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
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2018-01-26 22:43:06 +01:00
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;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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2017-12-24 20:51:48 +01:00
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;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
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2018-02-08 08:50:06 +01:00
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;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
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2018-02-17 22:47:57 +01:00
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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2018-03-28 02:42:15 +02:00
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;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
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2018-05-02 05:49:40 +02:00
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;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
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2018-05-02 18:22:33 +02:00
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;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
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2013-08-24 10:51:56 +02:00
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages maths)
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2014-10-26 11:03:02 +01:00
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#:use-module (ice-9 regex)
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2013-08-24 10:51:56 +02:00
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#:use-module (gnu packages)
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Use #:prefix instead of #:renamer with 'symbol-prefix-proc'.
* gnu/packages/abiword.scm, gnu/packages/admin.scm, gnu/packages/aidc.scm,
gnu/packages/backup.scm, gnu/packages/bittorrent.scm,
gnu/packages/boost.scm, gnu/packages/compression.scm,
gnu/packages/cryptsetup.scm, gnu/packages/curl.scm,
gnu/packages/cyrus-sasl.scm, gnu/packages/dc.scm, gnu/packages/emacs.scm,
gnu/packages/fonts.scm, gnu/packages/fontutils.scm, gnu/packages/geeqie.scm,
gnu/packages/ghostscript.scm, gnu/packages/gimp.scm,
gnu/packages/gkrellm.scm, gnu/packages/gl.scm, gnu/packages/glib.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm, gnu/packages/gnupg.scm,
gnu/packages/gnutls.scm, gnu/packages/gnuzilla.scm, gnu/packages/gsasl.scm,
gnu/packages/gtk.scm, gnu/packages/gv.scm, gnu/packages/image.scm,
gnu/packages/indent.scm, gnu/packages/inkscape.scm,
gnu/packages/lesstif.scm, gnu/packages/links.scm, gnu/packages/lisp.scm,
gnu/packages/lsh.scm, gnu/packages/lsof.scm, gnu/packages/maths.scm,
gnu/packages/mp3.scm, gnu/packages/openssl.scm, gnu/packages/ots.scm,
gnu/packages/pciutils.scm, gnu/packages/pcre.scm, gnu/packages/pdf.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python.scm, gnu/packages/slim.scm,
gnu/packages/ssh.scm, gnu/packages/texlive.scm, gnu/packages/vim.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wv.scm,
gnu/packages/xiph.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm,
gnu/packages/yasm.scm, gnu/packages/zip.scm,
guix/build/cmake-build-system.scm, guix/build/perl-build-system.scm,
guix/build/python-build-system.scm, guix/download.scm: Replaces uses of
#:renamer and 'symbol-prefix-proc' with #:prefix.
2014-09-23 22:44:22 +02:00
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#:use-module ((guix licenses) #:prefix license:)
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2013-08-24 10:51:56 +02:00
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#:use-module (guix packages)
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#:use-module (guix download)
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2017-01-30 07:27:53 +01:00
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#:use-module (guix git-download)
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2014-05-04 11:15:30 +02:00
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#:use-module (guix utils)
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2015-06-16 14:10:51 +02:00
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#:use-module (guix build utils)
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2013-11-04 19:58:54 +01:00
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#:use-module (guix build-system cmake)
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2013-08-24 11:04:12 +02:00
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#:use-module (guix build-system gnu)
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2017-03-17 12:23:21 +01:00
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#:use-module (guix build-system ocaml)
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2018-05-02 18:22:33 +02:00
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#:use-module (guix build-system python)
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2016-04-08 10:48:58 +02:00
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#:use-module (guix build-system r)
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2015-12-31 13:46:49 +01:00
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#:use-module (guix build-system ruby)
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2014-04-24 22:13:59 +02:00
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#:use-module (gnu packages algebra)
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2018-01-26 16:08:52 +01:00
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#:use-module (gnu packages audio)
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2017-07-08 04:58:27 +02:00
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#:use-module (gnu packages autotools)
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2014-04-24 22:13:59 +02:00
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#:use-module (gnu packages bison)
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2015-06-23 11:05:11 +02:00
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#:use-module (gnu packages boost)
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2015-03-17 12:24:45 +01:00
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#:use-module (gnu packages check)
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2014-04-24 22:13:59 +02:00
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#:use-module (gnu packages cmake)
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2013-08-24 11:04:12 +02:00
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#:use-module (gnu packages compression)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages curl)
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2016-05-18 02:36:17 +02:00
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#:use-module (gnu packages cyrus-sasl)
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2016-03-17 15:15:18 +01:00
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#:use-module (gnu packages documentation)
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2014-04-09 06:08:30 +02:00
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#:use-module (gnu packages elf)
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2014-04-24 22:13:59 +02:00
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#:use-module (gnu packages flex)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages fltk)
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2013-11-17 18:30:50 +01:00
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#:use-module (gnu packages fontutils)
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gnu: gettext: Rename binding to 'gnu-gettext'.
* gnu/packages/gettext.scm (gettext): Rename to...
(gnu-gettext): ... this. This is used to work around the circular
dependency introduced in commit c42a4b7, which users with a #:renamer
cannot cope with.
* gnu/packages/acl.scm, gnu/packages/attr.scm, gnu/packages/cdrom.scm,
gnu/packages/fdisk.scm, gnu/packages/gkrellm.scm, gnu/packages/glib.scm,
gnu/packages/gnunet.scm, gnu/packages/grub.scm, gnu/packages/linux.scm,
gnu/packages/maths.scm, gnu/packages/nano.scm, gnu/packages/parted.scm,
gnu/packages/system.scm, gnu/packages/version-control.scm,
gnu/packages/vpn.scm, gnu/packages/w3m.scm, gnu/packages/wget.scm:
Adjust accordingly.
2013-11-20 22:12:49 +01:00
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#:use-module (gnu packages gettext)
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2013-11-04 19:58:54 +01:00
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#:use-module (gnu packages gcc)
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2014-01-26 10:09:21 +01:00
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#:use-module (gnu packages gd)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages ghostscript)
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2016-04-12 17:04:01 +02:00
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#:use-module (gnu packages graphviz)
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2013-11-17 18:30:50 +01:00
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#:use-module (gnu packages gtk)
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2015-12-15 21:00:38 +01:00
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#:use-module (gnu packages image)
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2017-10-04 17:17:03 +02:00
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#:use-module (gnu packages java)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages less)
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2014-07-05 14:31:49 +02:00
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#:use-module (gnu packages lisp)
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2018-01-26 16:08:52 +01:00
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#:use-module (gnu packages linux)
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2016-06-29 12:01:05 +02:00
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#:use-module (gnu packages logging)
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2017-03-25 18:37:17 +01:00
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#:use-module (gnu packages lua)
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gnu: Add gsegrafix and dependent libraries.
* gnu/packages/math.scm (gsegrafix): New variable.
* gnu/packages/gtk.scm (pangox-compat): New variable.
* gnu/packages/gnome.scm (libidl, orbit2, libbonobo, gconf, gnome-mime-data,
gnome-vfs, libgnome, libart-lgpl, libgnomecanvas, libgnomeui, libglade,
libgnomeprint, libgnomeprintui, libbonoboui): New variables.
2014-05-25 07:29:30 +02:00
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#:use-module (gnu packages gnome)
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2016-05-03 14:30:25 +02:00
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#:use-module (gnu packages guile)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages xorg)
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#:use-module (gnu packages gl)
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2017-03-08 21:11:44 +01:00
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#:use-module (gnu packages imagemagick)
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2014-07-05 14:31:49 +02:00
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#:use-module (gnu packages m4)
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2014-05-08 19:33:47 +02:00
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#:use-module (gnu packages mpi)
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2013-10-22 20:24:33 +02:00
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#:use-module (gnu packages multiprecision)
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2016-03-17 15:15:18 +01:00
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#:use-module (gnu packages netpbm)
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2017-03-17 12:23:21 +01:00
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#:use-module (gnu packages ocaml)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages pcre)
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gnu: Add gsegrafix and dependent libraries.
* gnu/packages/math.scm (gsegrafix): New variable.
* gnu/packages/gtk.scm (pangox-compat): New variable.
* gnu/packages/gnome.scm (libidl, orbit2, libbonobo, gconf, gnome-mime-data,
gnome-vfs, libgnome, libart-lgpl, libgnomecanvas, libgnomeui, libglade,
libgnomeprint, libgnomeprintui, libbonoboui): New variables.
2014-05-25 07:29:30 +02:00
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#:use-module (gnu packages popt)
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2013-08-24 11:04:12 +02:00
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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2018-01-26 16:08:52 +01:00
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#:use-module (gnu packages pulseaudio)
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2013-11-04 19:58:54 +01:00
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#:use-module (gnu packages python)
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gnu: Move more packages from python to python-web.
* gnu/packages/python.scm (python-requests, python2-requests)
(python-requests-2.7, python-oauthlib, python2-oauthlib)
(python-furl, python2-furl, python-wsgi-intercept)
(python-publicsuffix, python2-publicsuffix)
(python-publicsuffix2, python2-publicsuffix2): Move to...
* gnu/packages/python-web.scm: ... here.
* gnu/packages/bioinformatics.scm, gnu/packages/finance.scm:
gnu/packages/maths.scm, gnu/packages/terminals.scm,
gnu/packages/video.scm, gnu/packages/virtualization.scm: Adjust
accordingly.
2017-11-15 14:59:31 +01:00
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#:use-module (gnu packages python-web)
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2018-02-08 08:50:06 +01:00
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#:use-module (gnu packages qt)
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2013-08-24 11:04:12 +02:00
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#:use-module (gnu packages readline)
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2015-12-31 13:46:49 +01:00
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#:use-module (gnu packages ruby)
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2015-03-10 11:32:48 +01:00
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#:use-module (gnu packages tbb)
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2017-02-26 20:28:48 +01:00
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#:use-module (gnu packages scheme)
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2016-08-03 11:01:56 +02:00
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#:use-module (gnu packages shells)
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2014-09-23 16:20:02 +02:00
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#:use-module (gnu packages tcl)
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2014-01-30 14:22:49 +01:00
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#:use-module (gnu packages texinfo)
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2016-05-24 21:18:53 +02:00
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#:use-module (gnu packages tex)
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2016-05-18 02:36:17 +02:00
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#:use-module (gnu packages tls)
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2018-02-08 08:50:06 +01:00
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#:use-module (gnu packages version-control)
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2015-05-26 05:29:53 +02:00
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#:use-module (gnu packages wxwidgets)
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2015-03-14 17:36:07 +01:00
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#:use-module (gnu packages xml)
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2015-06-23 11:05:11 +02:00
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#:use-module (srfi srfi-1))
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2013-08-24 10:51:56 +02:00
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2017-02-17 18:24:35 +01:00
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(define-public aris
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(package
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2017-02-17 18:50:35 +01:00
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(name "aris")
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(version "2.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
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(sha256 (base32
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"1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
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(build-system gnu-build-system)
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(inputs `(("gtk+" ,gtk+)
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("libxml2" ,libxml2)))
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(native-inputs `(("pkg-config" ,pkg-config)))
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(synopsis "Natural deduction first-order logic interface")
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|
(description "Aris is a program for performing logical proofs. It supports
|
|
|
|
|
propositional and predicate logic, as well as Boolean algebra and
|
|
|
|
|
arithmetical logic. In addition to its predefined inference and equivalence
|
|
|
|
|
rules, Aris also supports references to older proofs. Its use of standard
|
|
|
|
|
logical symbols and its natural deduction interface make it easy to use for
|
|
|
|
|
beginners.")
|
|
|
|
|
(license license:gpl3+)
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/aris/")))
|
2017-02-17 18:24:35 +01:00
|
|
|
|
|
2016-04-08 21:33:59 +02:00
|
|
|
|
(define-public c-graph
|
|
|
|
|
(package
|
|
|
|
|
(name "c-graph")
|
|
|
|
|
(version "2.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/c-graph/c-graph-" version
|
|
|
|
|
".tar.gz"))
|
|
|
|
|
(sha256 (base32
|
|
|
|
|
"1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("fortran" ,gfortran)))
|
2016-07-29 10:13:12 +02:00
|
|
|
|
(synopsis "Visualizing and demonstrating convolution")
|
2016-04-08 21:33:59 +02:00
|
|
|
|
(description
|
2016-07-29 10:13:12 +02:00
|
|
|
|
"GNU C-Graph is a tool for demonstrating the theory of convolution.
|
|
|
|
|
Thus, it can serve as an excellent aid to students of signal and systems
|
|
|
|
|
theory in visualizing the convolution process. Rather than forcing the
|
|
|
|
|
student to write code, the program offers an intuitive interface with
|
|
|
|
|
interactive dialogs to guide them.")
|
2016-04-08 21:33:59 +02:00
|
|
|
|
(license license:gpl3+)
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/c-graph/")))
|
2016-04-08 21:33:59 +02:00
|
|
|
|
|
2016-10-19 11:44:33 +02:00
|
|
|
|
(define-public coda
|
|
|
|
|
(package
|
|
|
|
|
(name "coda")
|
2017-11-27 23:56:08 +01:00
|
|
|
|
(version "2.18.3")
|
2016-10-19 11:44:33 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
|
|
|
|
|
version "/coda-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
2017-11-27 23:56:08 +01:00
|
|
|
|
(base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
|
2016-10-25 10:56:46 +02:00
|
|
|
|
(patches (search-patches "coda-use-system-libs.patch"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Make sure we don't use the bundled software.
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(for-each (lambda (d)
|
|
|
|
|
(delete-file-recursively (string-append "libcoda/" d)))
|
|
|
|
|
'("zlib" "pcre" "expat"))
|
|
|
|
|
#t))))
|
2016-10-19 11:44:33 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("fortran" ,gfortran)
|
|
|
|
|
("python" ,python)
|
|
|
|
|
("python-numpy" ,python-numpy)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
2016-10-25 10:56:46 +02:00
|
|
|
|
("pcre" ,pcre)
|
|
|
|
|
("expat" ,expat)
|
2016-10-19 11:44:33 +02:00
|
|
|
|
("hdf4" ,hdf4-alt)
|
|
|
|
|
("hdf5" ,hdf5)))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2016-10-25 10:56:46 +02:00
|
|
|
|
'(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
|
|
|
|
|
"LIBS= -lz -lpcre -lexpat")))
|
2016-10-19 11:44:33 +02:00
|
|
|
|
(synopsis "A common interface to various earth observation data formats")
|
|
|
|
|
(description
|
|
|
|
|
"The Common Data Access toolbox (CODA) provides a set of interfaces for
|
|
|
|
|
reading remote sensing data from earth observation data files. It consists of
|
|
|
|
|
command line applications and interfaces to the C, Fortran, Python, and Java
|
|
|
|
|
programming languages.")
|
|
|
|
|
(home-page "https://stcorp.nl/coda")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2018-07-17 18:49:20 +02:00
|
|
|
|
(define-public qhull
|
|
|
|
|
(package
|
|
|
|
|
(name "qhull")
|
|
|
|
|
(version "2015.2")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.qhull.org/download/qhull-"
|
|
|
|
|
(car (string-split version #\.))
|
|
|
|
|
"-src-7.2.0.tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(synopsis "Calculate convex hulls and related structures")
|
|
|
|
|
(description
|
|
|
|
|
"@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
|
|
|
|
|
diagram, halfspace intersection about a point, furthest-site Delaunay
|
|
|
|
|
triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
|
|
|
|
|
3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
|
|
|
|
|
algorithm for computing the convex hull. It handles roundoff errors from
|
|
|
|
|
floating point arithmetic. It computes volumes, surface areas, and
|
|
|
|
|
approximations to the convex hull.
|
|
|
|
|
|
|
|
|
|
@code{Qhull} does not support triangulation of non-convex surfaces, mesh
|
|
|
|
|
generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
|
|
|
|
|
shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
|
|
|
|
|
triangulations.")
|
|
|
|
|
(home-page "http://qhull.org")
|
|
|
|
|
(license (license:non-copyleft "file://COPYING.txt"
|
|
|
|
|
"See COPYING in the distribution."))))
|
|
|
|
|
|
2013-08-24 10:51:56 +02:00
|
|
|
|
(define-public units
|
|
|
|
|
(package
|
|
|
|
|
(name "units")
|
2018-07-03 03:12:15 +02:00
|
|
|
|
(version "2.17")
|
2013-08-24 10:51:56 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/units/units-" version
|
|
|
|
|
".tar.gz"))
|
|
|
|
|
(sha256 (base32
|
2018-07-03 03:12:15 +02:00
|
|
|
|
"1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz"))))
|
2013-08-24 10:51:56 +02:00
|
|
|
|
(build-system gnu-build-system)
|
2017-11-01 23:12:06 +01:00
|
|
|
|
(inputs
|
2017-11-01 23:17:01 +01:00
|
|
|
|
`(("readline" ,readline)
|
|
|
|
|
("python" ,python-wrapper) ;for 'units_cur' script
|
2017-11-01 23:12:06 +01:00
|
|
|
|
("python-requests" ,python-requests)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-after 'install 'wrap-units_cur
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin")))
|
|
|
|
|
(wrap-program (string-append bin "/units_cur")
|
|
|
|
|
`("PYTHONPATH" ":" prefix
|
|
|
|
|
,(search-path-as-string->list (getenv "PYTHONPATH"))))
|
|
|
|
|
#t))))))
|
2013-08-24 10:51:56 +02:00
|
|
|
|
(synopsis "Conversion between thousands of scales")
|
|
|
|
|
(description
|
2014-04-06 21:17:42 +02:00
|
|
|
|
"GNU Units converts numeric quantities between units of measure. It
|
2015-07-16 11:14:13 +02:00
|
|
|
|
can handle scale changes through adaptive usage of standard scale
|
|
|
|
|
prefixes (micro-, kilo-, etc.). It can also handle nonlinear
|
|
|
|
|
conversions such as Fahrenheit to Celsius. Its interpreter is powerful
|
|
|
|
|
enough to be used effectively as a scientific calculator.")
|
2013-08-24 10:51:56 +02:00
|
|
|
|
(license license:gpl3+)
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/units/")))
|
2013-08-24 11:04:12 +02:00
|
|
|
|
|
2015-03-20 12:11:35 +01:00
|
|
|
|
(define-public double-conversion
|
|
|
|
|
(package
|
|
|
|
|
(name "double-conversion")
|
2018-07-20 15:37:49 +02:00
|
|
|
|
(version "3.0.0")
|
2018-07-20 15:14:12 +02:00
|
|
|
|
(home-page "https://github.com/google/double-conversion")
|
2015-03-20 12:11:35 +01:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2018-07-20 15:14:12 +02:00
|
|
|
|
(uri (string-append home-page "/archive/v" version ".tar.gz"))
|
2015-03-20 12:11:35 +01:00
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-07-20 15:37:49 +02:00
|
|
|
|
"059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
|
2015-03-20 12:11:35 +01:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:test-target "test"
|
|
|
|
|
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
|
|
|
|
|
"-DBUILD_TESTING=ON")))
|
|
|
|
|
(synopsis "Conversion routines for IEEE doubles")
|
|
|
|
|
(description
|
|
|
|
|
"The double-conversion library provides binary-decimal and decimal-binary
|
|
|
|
|
routines for IEEE doubles. The library consists of efficient conversion
|
|
|
|
|
routines that have been extracted from the V8 JavaScript engine.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
2014-09-28 01:29:56 +02:00
|
|
|
|
(define-public dionysus
|
|
|
|
|
(package
|
|
|
|
|
(name "dionysus")
|
2018-02-28 13:41:42 +01:00
|
|
|
|
(version "1.4.0")
|
2014-09-28 01:29:56 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/dionysus/dionysus-" version
|
2018-02-28 13:41:42 +01:00
|
|
|
|
".tar.xz"))
|
2014-09-28 01:29:56 +02:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-02-28 13:41:42 +01:00
|
|
|
|
"194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
|
2014-09-28 01:29:56 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs `(("tcl" ,tcl))) ;for 'tclsh'
|
|
|
|
|
(synopsis "Local search for universal constants and scientific values")
|
|
|
|
|
(description
|
|
|
|
|
"GNU Dionysus is a convenient system for quickly retrieving the values of
|
|
|
|
|
mathematical constants used in science and engineering. Values can be
|
|
|
|
|
searched using a simple command-line tool, choosing from three databases:
|
|
|
|
|
universal constants, atomic numbers, and constants related to
|
|
|
|
|
semiconductors.")
|
|
|
|
|
(license license:gpl3+)
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/dionysus/")))
|
2014-09-28 01:29:56 +02:00
|
|
|
|
|
2013-08-29 15:42:52 +02:00
|
|
|
|
(define-public gsl
|
|
|
|
|
(package
|
|
|
|
|
(name "gsl")
|
2018-06-17 01:25:35 +02:00
|
|
|
|
(version "2.5")
|
2016-10-05 14:52:47 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/gsl/gsl-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-06-17 01:25:35 +02:00
|
|
|
|
"1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
|
2016-10-05 14:52:47 +02:00
|
|
|
|
(patches (search-patches "gsl-test-i686.patch"))))
|
2013-08-29 15:42:52 +02:00
|
|
|
|
(build-system gnu-build-system)
|
2013-08-31 12:18:53 +02:00
|
|
|
|
(arguments
|
2017-06-19 22:38:25 +02:00
|
|
|
|
`(;; Currently there are numerous tests that fail on "exotic"
|
2017-03-27 08:39:48 +02:00
|
|
|
|
;; architectures such as aarch64 and ppc64le.
|
|
|
|
|
,@(if (string-prefix? "aarch64-linux"
|
|
|
|
|
(or (%current-target-system) (%current-system)))
|
|
|
|
|
'(#:tests? #f)
|
|
|
|
|
'())))
|
|
|
|
|
(home-page "https://www.gnu.org/software/gsl/")
|
2013-08-29 15:42:52 +02:00
|
|
|
|
(synopsis "Numerical library for C and C++")
|
|
|
|
|
(description
|
Synchronize package descriptions with the Womb.
* gnu/packages/algebra.scm,
gnu/packages/aspell.scm,
gnu/packages/autotools.scm,
gnu/packages/base.scm,
gnu/packages/bash.scm,
gnu/packages/bison.scm,
gnu/packages/cdrom.scm,
gnu/packages/cflow.scm,
gnu/packages/compression.scm,
gnu/packages/cpio.scm,
gnu/packages/cppi.scm,
gnu/packages/ddrescue.scm,
gnu/packages/dejagnu.scm,
gnu/packages/ed.scm,
gnu/packages/emacs.scm,
gnu/packages/fdisk.scm,
gnu/packages/freeipmi.scm,
gnu/packages/gawk.scm,
gnu/packages/gcal.scm,
gnu/packages/gcc.scm,
gnu/packages/gdb.scm,
gnu/packages/gdbm.scm,
gnu/packages/gettext.scm,
gnu/packages/ghostscript.scm,
gnu/packages/global.scm,
gnu/packages/gnunet.scm,
gnu/packages/gnupg.scm,
gnu/packages/gnutls.scm,
gnu/packages/gperf.scm,
gnu/packages/gprolog.scm,
gnu/packages/groff.scm,
gnu/packages/grub.scm,
gnu/packages/gsasl.scm,
gnu/packages/guile.scm,
gnu/packages/gv.scm,
gnu/packages/help2man.scm,
gnu/packages/idutils.scm,
gnu/packages/indent.scm,
gnu/packages/less.scm,
gnu/packages/libidn.scm,
gnu/packages/libsigsegv.scm,
gnu/packages/libunistring.scm,
gnu/packages/lightning.scm,
gnu/packages/linux.scm,
gnu/packages/lsh.scm,
gnu/packages/m4.scm,
gnu/packages/mail.scm,
gnu/packages/maths.scm,
gnu/packages/multiprecision.scm,
gnu/packages/nano.scm,
gnu/packages/ncurses.scm,
gnu/packages/nettle.scm,
gnu/packages/ocrad.scm,
gnu/packages/oggvorbis.scm,
gnu/packages/parted.scm,
gnu/packages/plotutils.scm,
gnu/packages/pth.scm,
gnu/packages/readline.scm,
gnu/packages/recutils.scm,
gnu/packages/rush.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/shishi.scm,
gnu/packages/smalltalk.scm,
gnu/packages/system.scm,
gnu/packages/texinfo.scm,
gnu/packages/time.scm,
gnu/packages/unrtf.scm,
gnu/packages/version-control.scm,
gnu/packages/wdiff.scm,
gnu/packages/wget.scm,
gnu/packages/which.scm,
gnu/packages/xnee.scm,
gnu/packages/zile.scm: Change value of the 'description' field to that
of the Womb.
2013-10-09 16:14:23 +02:00
|
|
|
|
"The GNU Scientific Library is a library for numerical analysis in C
|
|
|
|
|
and C++. It includes a wide range of mathematical routines, with over 1000
|
|
|
|
|
functions in total. Subject areas covered by the library include:
|
|
|
|
|
differential equations, linear algebra, Fast Fourier Transforms and random
|
|
|
|
|
numbers.")
|
2013-08-29 15:42:52 +02:00
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2017-03-17 12:23:21 +01:00
|
|
|
|
(define-public ocaml-gsl
|
|
|
|
|
(package
|
|
|
|
|
(name "ocaml-gsl")
|
|
|
|
|
(version "1.19.3")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri
|
|
|
|
|
(string-append
|
|
|
|
|
"https://github.com/mmottl/gsl-ocaml/releases/download/v"
|
|
|
|
|
version"/gsl-ocaml-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
|
|
|
|
|
(build-system ocaml-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("gsl" ,gsl)))
|
|
|
|
|
(home-page "https://mmottl.github.io/gsl-ocaml")
|
|
|
|
|
(synopsis "Bindings to the GNU Scientific Library")
|
|
|
|
|
(description
|
|
|
|
|
"GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
|
|
|
|
|
the OCaml language.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2017-03-17 22:15:58 +01:00
|
|
|
|
(define-public ocaml4.01-gsl
|
|
|
|
|
(package-with-ocaml4.01 ocaml-gsl))
|
|
|
|
|
|
2013-10-22 20:24:33 +02:00
|
|
|
|
(define-public glpk
|
|
|
|
|
(package
|
|
|
|
|
(name "glpk")
|
2018-02-16 22:08:03 +01:00
|
|
|
|
(version "4.65")
|
2013-10-22 20:24:33 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/glpk/glpk-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-02-16 22:08:03 +01:00
|
|
|
|
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
|
2013-10-22 20:24:33 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("gmp" ,gmp)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags '("--with-gmp")))
|
2017-01-23 18:54:27 +01:00
|
|
|
|
(home-page "https://www.gnu.org/software/glpk/")
|
2013-12-01 22:33:23 +01:00
|
|
|
|
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
|
2013-10-22 20:24:33 +02:00
|
|
|
|
(description
|
|
|
|
|
"GLPK is a C library for solving large-scale linear programming (LP),
|
|
|
|
|
mixed integer programming (MIP), and other related problems. It supports the
|
|
|
|
|
GNU MathProg modeling language, a subset of the AMPL language, and features a
|
|
|
|
|
translator for the language. In addition to the C library, a stand-alone
|
|
|
|
|
LP/MIP solver is included in the package.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2016-04-05 18:48:02 +02:00
|
|
|
|
(define-public 4ti2
|
|
|
|
|
(package
|
|
|
|
|
(name "4ti2")
|
|
|
|
|
(version "1.6.7")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.4ti2.de/version_" version
|
|
|
|
|
"/4ti2-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("which" ,(@ (gnu packages base) which)))) ; for the tests
|
|
|
|
|
(inputs
|
|
|
|
|
`(("glpk" ,glpk)
|
|
|
|
|
("gmp" ,gmp)))
|
|
|
|
|
(home-page "http://www.4ti2.de/")
|
|
|
|
|
(synopsis "Mathematical tool suite for problems on linear spaces")
|
|
|
|
|
(description
|
|
|
|
|
"4ti2 implements algorithms for solving algebraic, geometric and
|
|
|
|
|
combinatorial problems on linear spaces. Among others, it solves systems
|
|
|
|
|
of linear equations, computes extreme rays of polyhedral cones, solves
|
|
|
|
|
integer programming problems and computes Markov bases for statistics.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2016-04-05 19:22:36 +02:00
|
|
|
|
(define-public cddlib
|
|
|
|
|
(package
|
|
|
|
|
(name "cddlib")
|
|
|
|
|
(version "0.94h")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2017-02-04 06:26:26 +01:00
|
|
|
|
(uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
|
2016-04-05 19:22:36 +02:00
|
|
|
|
(string-delete #\. version) ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("gmp" ,gmp)))
|
|
|
|
|
(home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
|
|
|
|
|
(synopsis "Library for convex hulls and extreme rays of polyhedra")
|
|
|
|
|
(description
|
|
|
|
|
"The C-library cddlib implements the Double Description Method of
|
|
|
|
|
Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
|
|
|
|
|
rays of a general convex polyhedron given by a system of linear inequalities
|
|
|
|
|
in arbitrary dimension. It can also be used for the converse operation of
|
|
|
|
|
computing convex hulls.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(define-public arpack-ng
|
|
|
|
|
(package
|
|
|
|
|
(name "arpack-ng")
|
2018-03-12 16:06:17 +01:00
|
|
|
|
(version "3.5.0")
|
|
|
|
|
(home-page "https://github.com/opencollab/arpack-ng")
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2018-03-12 16:06:17 +01:00
|
|
|
|
(uri (string-append home-page "/archive/" version ".tar.gz"))
|
gnu: Add 'file-name' fields for github source tarballs without a name.
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-27 18:23:27 +01:00
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-03-12 16:06:17 +01:00
|
|
|
|
"0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(build-system gnu-build-system)
|
2018-03-12 16:06:17 +01:00
|
|
|
|
(arguments
|
|
|
|
|
'(#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'autoreconf
|
|
|
|
|
(lambda _
|
|
|
|
|
(invoke "autoreconf" "-vfi"))))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("autoconf" ,autoconf)
|
|
|
|
|
("automake" ,automake)
|
|
|
|
|
("libtool" ,libtool)))
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(inputs
|
|
|
|
|
`(("lapack" ,lapack)
|
2015-06-25 17:56:07 +02:00
|
|
|
|
("fortran" ,gfortran)))
|
2015-02-18 16:08:33 +01:00
|
|
|
|
(synopsis "Fortran subroutines for solving eigenvalue problems")
|
|
|
|
|
(description
|
|
|
|
|
"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
|
|
|
|
|
large scale eigenvalue problems.")
|
gnu: Update packages to use 'non-copyleft' instead of 'bsd-style'.
* gnu/packages/avr.scm, gnu/packages/compression.scm,
gnu/packages/curl.scm, gnu/packages/cyrus-sasl.scm,
gnu/packages/databases.scm, gnu/packages/firmware.scm,
gnu/packages/flex.scm, gnu/packages/fontutils.scm,
gnu/packages/gd.scm, gnu/packages/ghostscript.scm,
gnu/packages/gnunet.scm, gnu/packages/graphics.scm,
gnu/packages/hugs.scm, gnu/packages/image.scm,
gnu/packages/linux.scm, gnu/packages/mail.scm,
gnu/packages/maths.scm, gnu/packages/mit-krb5.scm,
gnu/packages/python.scm, gnu/packages/rdf.scm,
gnu/packages/ssh.scm, gnu/packages/tcl.scm,
gnu/packages/xdisorg.scm, gnu/packages/xiph.scm,
gnu/packages/yasm.scm, gnu/packages/zip.scm: Use 'non-copyleft'
instead of 'bsd-style'.
2015-03-14 19:26:34 +01:00
|
|
|
|
(license (license:non-copyleft "file://COPYING"
|
2015-02-18 16:08:33 +01:00
|
|
|
|
"See COPYING in the distribution."))))
|
|
|
|
|
|
2018-03-12 16:06:17 +01:00
|
|
|
|
(define-public arpack-ng-3.3.0
|
|
|
|
|
(package
|
|
|
|
|
(inherit arpack-ng)
|
|
|
|
|
(version "3.3.0")
|
|
|
|
|
(name (package-name arpack-ng))
|
|
|
|
|
(home-page (package-home-page arpack-ng))
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append home-page "/archive/" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
|
|
|
|
|
|
2015-06-17 11:58:25 +02:00
|
|
|
|
(define-public arpack-ng-openmpi
|
|
|
|
|
(package (inherit arpack-ng)
|
|
|
|
|
(name "arpack-ng-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
,@(package-inputs arpack-ng)))
|
2018-05-11 17:16:12 +02:00
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments arpack-ng)
|
|
|
|
|
((#:configure-flags _ '())
|
|
|
|
|
''("--enable-mpi"))))
|
2015-06-17 11:58:25 +02:00
|
|
|
|
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
|
|
|
|
|
|
2013-11-04 19:58:54 +01:00
|
|
|
|
(define-public lapack
|
|
|
|
|
(package
|
|
|
|
|
(name "lapack")
|
2017-06-26 16:57:19 +02:00
|
|
|
|
(version "3.7.1")
|
2013-11-04 19:58:54 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.netlib.org/lapack/lapack-"
|
|
|
|
|
version ".tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-07-16 21:01:59 +02:00
|
|
|
|
"1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
|
2013-11-04 19:58:54 +01:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(home-page "http://www.netlib.org/lapack/")
|
2015-06-25 17:56:07 +02:00
|
|
|
|
(inputs `(("fortran" ,gfortran)
|
2013-11-04 19:58:54 +01:00
|
|
|
|
("python" ,python-2)))
|
|
|
|
|
(arguments
|
2017-06-29 14:46:07 +02:00
|
|
|
|
`(#:configure-flags (list
|
|
|
|
|
"-DBUILD_SHARED_LIBS:BOOL=YES"
|
|
|
|
|
"-DLAPACKE=ON"
|
|
|
|
|
|
|
|
|
|
;; Build the 'LAPACKE_clatms' functions.
|
|
|
|
|
"-DLAPACKE_WITH_TMG=ON")
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'patch-python
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(let ((python (assoc-ref inputs "python")))
|
|
|
|
|
(substitute* "lapack_testing.py"
|
|
|
|
|
(("/usr/bin/env python") python)))
|
|
|
|
|
#t)))))
|
2013-11-04 19:58:54 +01:00
|
|
|
|
(synopsis "Library for numerical linear algebra")
|
|
|
|
|
(description
|
|
|
|
|
"LAPACK is a Fortran 90 library for solving the most commonly occurring
|
|
|
|
|
problems in numerical linear algebra.")
|
gnu: Update packages to use 'non-copyleft' instead of 'bsd-style'.
* gnu/packages/avr.scm, gnu/packages/compression.scm,
gnu/packages/curl.scm, gnu/packages/cyrus-sasl.scm,
gnu/packages/databases.scm, gnu/packages/firmware.scm,
gnu/packages/flex.scm, gnu/packages/fontutils.scm,
gnu/packages/gd.scm, gnu/packages/ghostscript.scm,
gnu/packages/gnunet.scm, gnu/packages/graphics.scm,
gnu/packages/hugs.scm, gnu/packages/image.scm,
gnu/packages/linux.scm, gnu/packages/mail.scm,
gnu/packages/maths.scm, gnu/packages/mit-krb5.scm,
gnu/packages/python.scm, gnu/packages/rdf.scm,
gnu/packages/ssh.scm, gnu/packages/tcl.scm,
gnu/packages/xdisorg.scm, gnu/packages/xiph.scm,
gnu/packages/yasm.scm, gnu/packages/zip.scm: Use 'non-copyleft'
instead of 'bsd-style'.
2015-03-14 19:26:34 +01:00
|
|
|
|
(license (license:non-copyleft "file://LICENSE"
|
2013-11-04 19:58:54 +01:00
|
|
|
|
"See LICENSE in the distribution."))))
|
2014-01-26 10:09:21 +01:00
|
|
|
|
|
2015-06-15 16:32:07 +02:00
|
|
|
|
(define-public scalapack
|
|
|
|
|
(package
|
|
|
|
|
(name "scalapack")
|
|
|
|
|
(version "2.0.2")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.netlib.org/scalapack/scalapack-"
|
|
|
|
|
version ".tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
("fortran" ,gfortran)
|
|
|
|
|
("lapack" ,lapack))) ;for testing only
|
|
|
|
|
(arguments
|
2018-05-12 17:53:54 +02:00
|
|
|
|
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'set-test-environment
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default, running the test suite would fail because
|
|
|
|
|
;; 'ssh' could not be found in $PATH. Define this
|
|
|
|
|
;; variable to placate Open MPI without adding a
|
|
|
|
|
;; dependency on OpenSSH (the agent isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
#t)))))
|
2015-06-15 16:32:07 +02:00
|
|
|
|
(home-page "http://www.netlib.org/scalapack/")
|
|
|
|
|
(synopsis "Library for scalable numerical linear algebra")
|
|
|
|
|
(description
|
|
|
|
|
"ScaLAPACK is a Fortran 90 library of high-performance linear algebra
|
|
|
|
|
routines on parallel distributed memory machines. ScaLAPACK solves dense and
|
|
|
|
|
banded linear systems, least squares problems, eigenvalue problems, and
|
|
|
|
|
singular value problems.")
|
|
|
|
|
(license (license:bsd-style "file://LICENSE"
|
|
|
|
|
"See LICENSE in the distribution."))))
|
|
|
|
|
|
2014-01-26 10:09:21 +01:00
|
|
|
|
(define-public gnuplot
|
2016-12-19 05:27:43 +01:00
|
|
|
|
(package
|
|
|
|
|
(name "gnuplot")
|
2018-05-02 05:49:40 +02:00
|
|
|
|
(version "5.2.2")
|
2016-12-19 05:27:43 +01:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
|
|
|
|
version "/gnuplot-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-05-02 05:49:40 +02:00
|
|
|
|
"18diyy7aib9mn098x07g25c7jij1x7wbfpicz0z8gwxx08px45m4"))))
|
2016-12-19 05:27:43 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs `(("readline" ,readline)
|
|
|
|
|
("cairo" ,cairo)
|
|
|
|
|
("pango" ,pango)
|
2017-03-25 18:37:17 +01:00
|
|
|
|
("gd" ,gd)
|
|
|
|
|
("lua" ,lua)))
|
2017-06-30 10:12:19 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("pkg-config" ,pkg-config)
|
|
|
|
|
("texlive" ,texlive-tiny)))
|
2018-05-02 05:49:40 +02:00
|
|
|
|
(arguments `(#:configure-flags (list (string-append
|
|
|
|
|
"--with-texdir=" %output
|
|
|
|
|
"/texmf-local/tex/latex/gnuplot"))))
|
2016-12-19 05:27:43 +01:00
|
|
|
|
(home-page "http://www.gnuplot.info")
|
|
|
|
|
(synopsis "Command-line driven graphing utility")
|
|
|
|
|
(description "Gnuplot is a portable command-line driven graphing
|
gnu: Some cleanup based on lint checkers.
* gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm,
gnu/packages/apr.scm, gnu/packages/avahi.scm, gnu/packages/backup.scm,
gnu/packages/base.scm, gnu/packages/calcurse.scm, gnu/packages/cdrom.scm,
gnu/packages/check.scm, gnu/packages/compression.scm, gnu/packages/cook.scm,
gnu/packages/crypto.scm, gnu/packages/cryptsetup.scm, gnu/packages/curl.scm,
gnu/packages/cyrus-sasl.scm, gnu/packages/databases.scm,
gnu/packages/doxygen.scm, gnu/packages/dwm.scm, gnu/packages/elf.scm,
gnu/packages/emacs.scm, gnu/packages/feh.scm, gnu/packages/file.scm,
gnu/packages/fish.scm, gnu/packages/flex.scm, gnu/packages/fltk.scm,
gnu/packages/fontutils.scm, gnu/packages/games.scm, gnu/packages/gcal.scm,
gnu/packages/gcc.scm, gnu/packages/geeqie.scm, gnu/packages/ghostscript.scm,
gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/glib.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm, gnu/packages/gnupg.scm,
gnu/packages/gperf.scm, gnu/packages/grub.scm, gnu/packages/gsasl.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm, gnu/packages/guile.scm,
gnu/packages/hurd.scm, gnu/packages/icu4c.scm, gnu/packages/image.scm,
gnu/packages/imagemagick.scm, gnu/packages/irssi.scm, gnu/packages/kde.scm,
gnu/packages/libdaemon.scm, gnu/packages/libevent.scm,
gnu/packages/libidn.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm,
gnu/packages/lout.scm, gnu/packages/lsh.scm, gnu/packages/lsof.scm,
gnu/packages/lua.scm, gnu/packages/maths.scm, gnu/packages/mcrypt.scm,
gnu/packages/mp3.scm, gnu/packages/netpbm.scm, gnu/packages/noweb.scm,
gnu/packages/ocaml.scm, gnu/packages/openssl.scm, gnu/packages/pcre.scm,
gnu/packages/pdf.scm, gnu/packages/pkg-config.scm,
gnu/packages/pretty-print.scm, gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/rsync.scm, gnu/packages/scheme.scm, gnu/packages/scrot.scm,
gnu/packages/sdl.scm, gnu/packages/skribilo.scm, gnu/packages/ssh.scm,
gnu/packages/stalonetray.scm, gnu/packages/tcl.scm, gnu/packages/tcsh.scm,
gnu/packages/telephony.scm, gnu/packages/texlive.scm, gnu/packages/tor.scm,
gnu/packages/valgrind.scm, gnu/packages/version-control.scm,
gnu/packages/vim.scm, gnu/packages/vpn.scm, gnu/packages/w3m.scm,
gnu/packages/web.scm, gnu/packages/wordnet.scm, gnu/packages/xiph.scm,
gnu/packages/xml.scm, gnu/packages/xorg.scm, gnu/packages/zile.scm,
gnu/packages/zip.scm, gnu/packages/zsh.scm [synopsis, description]: Adjust
according to lint checkers.
* gnu/packages/fltk.scm (fltk)[source]: Wrap long line in uri.
* /gnu/packages/xiph.scm (libogg, libtheora, vorbis-tools)[source]: Same.
2014-10-24 06:46:59 +02:00
|
|
|
|
utility. It was originally created to allow scientists and students to
|
2014-01-26 10:09:21 +01:00
|
|
|
|
visualize mathematical functions and data interactively, but has grown to
|
gnu: Some cleanup based on lint checkers.
* gnu/packages/admin.scm, gnu/packages/aidc.scm, gnu/packages/algebra.scm,
gnu/packages/apr.scm, gnu/packages/avahi.scm, gnu/packages/backup.scm,
gnu/packages/base.scm, gnu/packages/calcurse.scm, gnu/packages/cdrom.scm,
gnu/packages/check.scm, gnu/packages/compression.scm, gnu/packages/cook.scm,
gnu/packages/crypto.scm, gnu/packages/cryptsetup.scm, gnu/packages/curl.scm,
gnu/packages/cyrus-sasl.scm, gnu/packages/databases.scm,
gnu/packages/doxygen.scm, gnu/packages/dwm.scm, gnu/packages/elf.scm,
gnu/packages/emacs.scm, gnu/packages/feh.scm, gnu/packages/file.scm,
gnu/packages/fish.scm, gnu/packages/flex.scm, gnu/packages/fltk.scm,
gnu/packages/fontutils.scm, gnu/packages/games.scm, gnu/packages/gcal.scm,
gnu/packages/gcc.scm, gnu/packages/geeqie.scm, gnu/packages/ghostscript.scm,
gnu/packages/gimp.scm, gnu/packages/gl.scm, gnu/packages/glib.scm,
gnu/packages/gnome.scm, gnu/packages/gnunet.scm, gnu/packages/gnupg.scm,
gnu/packages/gperf.scm, gnu/packages/grub.scm, gnu/packages/gsasl.scm,
gnu/packages/gtk.scm, gnu/packages/guile-wm.scm, gnu/packages/guile.scm,
gnu/packages/hurd.scm, gnu/packages/icu4c.scm, gnu/packages/image.scm,
gnu/packages/imagemagick.scm, gnu/packages/irssi.scm, gnu/packages/kde.scm,
gnu/packages/libdaemon.scm, gnu/packages/libevent.scm,
gnu/packages/libidn.scm, gnu/packages/libusb.scm, gnu/packages/linux.scm,
gnu/packages/lout.scm, gnu/packages/lsh.scm, gnu/packages/lsof.scm,
gnu/packages/lua.scm, gnu/packages/maths.scm, gnu/packages/mcrypt.scm,
gnu/packages/mp3.scm, gnu/packages/netpbm.scm, gnu/packages/noweb.scm,
gnu/packages/ocaml.scm, gnu/packages/openssl.scm, gnu/packages/pcre.scm,
gnu/packages/pdf.scm, gnu/packages/pkg-config.scm,
gnu/packages/pretty-print.scm, gnu/packages/python.scm, gnu/packages/qt.scm,
gnu/packages/rsync.scm, gnu/packages/scheme.scm, gnu/packages/scrot.scm,
gnu/packages/sdl.scm, gnu/packages/skribilo.scm, gnu/packages/ssh.scm,
gnu/packages/stalonetray.scm, gnu/packages/tcl.scm, gnu/packages/tcsh.scm,
gnu/packages/telephony.scm, gnu/packages/texlive.scm, gnu/packages/tor.scm,
gnu/packages/valgrind.scm, gnu/packages/version-control.scm,
gnu/packages/vim.scm, gnu/packages/vpn.scm, gnu/packages/w3m.scm,
gnu/packages/web.scm, gnu/packages/wordnet.scm, gnu/packages/xiph.scm,
gnu/packages/xml.scm, gnu/packages/xorg.scm, gnu/packages/zile.scm,
gnu/packages/zip.scm, gnu/packages/zsh.scm [synopsis, description]: Adjust
according to lint checkers.
* gnu/packages/fltk.scm (fltk)[source]: Wrap long line in uri.
* /gnu/packages/xiph.scm (libogg, libtheora, vorbis-tools)[source]: Same.
2014-10-24 06:46:59 +02:00
|
|
|
|
support many non-interactive uses such as web scripting. It is also used as a
|
2014-01-26 10:09:21 +01:00
|
|
|
|
plotting engine by third-party applications like Octave.")
|
2016-12-19 05:27:43 +01:00
|
|
|
|
;; X11 Style with the additional restriction that derived works may only be
|
|
|
|
|
;; distributed as patches to the original.
|
|
|
|
|
(license (license:fsf-free
|
|
|
|
|
"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
|
2014-01-30 14:22:49 +01:00
|
|
|
|
|
2016-06-17 10:41:50 +02:00
|
|
|
|
(define-public gctp
|
|
|
|
|
(package
|
|
|
|
|
(name "gctp")
|
|
|
|
|
(version "2.0.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("fortran" ,gfortran)))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(synopsis "General Cartographic Transformation Package (GCTP)")
|
|
|
|
|
(description
|
|
|
|
|
"The General Cartographic Transformation Package (GCTP) is a system of
|
|
|
|
|
software routines designed to permit the transformation of coordinate pairs
|
|
|
|
|
from one map projection to another. The GCTP is the standard computer
|
|
|
|
|
software used by the National Mapping Division for map projection
|
|
|
|
|
computations.")
|
|
|
|
|
(home-page "https://github.com/OkoSanto/GCTP")
|
2016-10-03 23:20:23 +02:00
|
|
|
|
(license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
|
2016-06-17 10:41:50 +02:00
|
|
|
|
|
2016-09-28 10:34:58 +02:00
|
|
|
|
(define-public hdf4
|
|
|
|
|
(package
|
|
|
|
|
(name "hdf4")
|
2017-08-01 10:26:39 +02:00
|
|
|
|
(version "4.2.13")
|
2016-09-28 10:34:58 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
|
|
|
|
|
version "/src/hdf-" version ".tar.bz2"))
|
|
|
|
|
(sha256
|
2017-08-01 10:26:39 +02:00
|
|
|
|
(base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
|
2016-10-18 21:15:43 +02:00
|
|
|
|
(patches (search-patches "hdf4-architectures.patch"
|
|
|
|
|
"hdf4-reproducibility.patch"
|
2016-09-28 10:34:58 +02:00
|
|
|
|
"hdf4-shared-fortran.patch"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)
|
|
|
|
|
("bison" ,bison)
|
|
|
|
|
("flex" ,flex)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
|
("libjpeg" ,libjpeg)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:parallel-tests? #f
|
|
|
|
|
#:configure-flags '("--enable-shared")
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
2017-08-16 07:52:35 +02:00
|
|
|
|
;; This is inspired by two of Debian's patches.
|
|
|
|
|
(add-before 'configure 'add-more-aarch64-support
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* '("mfhdf/ncgen/ncgen.l"
|
|
|
|
|
"mfhdf/ncgen/ncgenyy.c"
|
|
|
|
|
"mfhdf/libsrc/netcdf.h.in")
|
|
|
|
|
(("AIX5L64") "__aarch64__"))
|
|
|
|
|
#t))
|
2016-09-28 10:34:58 +02:00
|
|
|
|
(add-before 'configure 'patchbuild
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute*
|
|
|
|
|
'("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
|
|
|
|
|
(("/bin/rm") "rm")
|
|
|
|
|
(("/bin/mkdir") "mkdir"))
|
|
|
|
|
(substitute* (find-files "." "^Makefile\\.in$")
|
|
|
|
|
(("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
|
|
|
|
|
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
|
|
|
|
|
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
|
|
|
|
|
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
|
2017-08-16 07:52:35 +02:00
|
|
|
|
-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
|
2017-08-24 14:27:29 +02:00
|
|
|
|
#t))
|
|
|
|
|
(add-after 'configure 'patch-settings
|
|
|
|
|
(lambda _
|
|
|
|
|
;; libhdf4.settings contains the full path of the
|
|
|
|
|
;; compilers used, and its contents are included in
|
|
|
|
|
;; .so-files. We truncate the hashes to avoid
|
|
|
|
|
;; unnecessary store references to those compilers:
|
|
|
|
|
(substitute* "libhdf4.settings"
|
|
|
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
|
|
|
|
(string-append prefix (string-take hash 10) "...")))
|
|
|
|
|
#t))
|
|
|
|
|
)))
|
2016-09-28 10:34:58 +02:00
|
|
|
|
(home-page "https://www.hdfgroup.org/products/hdf4/")
|
|
|
|
|
(synopsis
|
|
|
|
|
"Library and multi-object file format for storing and managing data")
|
|
|
|
|
(description "HDF4 is a library and multi-object file format for storing
|
|
|
|
|
and managing data between machines. HDF4 is an older hierarchical data format,
|
|
|
|
|
incompatible with HDF5.")
|
|
|
|
|
(license
|
|
|
|
|
(license:non-copyleft
|
|
|
|
|
"https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
|
|
|
|
|
|
|
|
|
|
(define-public hdf4-alt
|
|
|
|
|
(package
|
|
|
|
|
(inherit hdf4)
|
|
|
|
|
(name "hdf4-alt")
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments hdf4)
|
|
|
|
|
((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
|
|
|
|
|
(synopsis
|
|
|
|
|
"HDF4 without netCDF API, can be combined with the regular netCDF library")))
|
|
|
|
|
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(define-public hdf5
|
|
|
|
|
(package
|
|
|
|
|
(name "hdf5")
|
2017-06-19 09:57:32 +02:00
|
|
|
|
(version "1.8.19")
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2017-06-19 09:57:32 +02:00
|
|
|
|
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
|
|
|
|
|
"hdf5-" (version-major+minor version)
|
|
|
|
|
"/hdf5-" version "/src/hdf5-"
|
2016-11-30 16:29:58 +01:00
|
|
|
|
version ".tar.bz2")
|
|
|
|
|
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
|
|
|
|
|
"current"
|
|
|
|
|
(apply string-append
|
|
|
|
|
(take (string-split version #\.) 2))
|
|
|
|
|
"/src/hdf5-" version ".tar.bz2")))
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(sha256
|
2017-06-19 09:57:32 +02:00
|
|
|
|
(base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
|
2016-04-15 17:39:54 +02:00
|
|
|
|
(patches (list (search-patch "hdf5-config-date.patch")))))
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(build-system gnu-build-system)
|
2015-03-13 00:15:47 +01:00
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)))
|
2017-08-24 11:00:59 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(outputs '("out" ; core library
|
|
|
|
|
"fortran")) ; fortran interface
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(arguments
|
2016-11-24 11:55:15 +01:00
|
|
|
|
`(;; Some of the users, notably Flann, need the C++ interface.
|
2017-08-24 11:00:59 +02:00
|
|
|
|
#:configure-flags '("--enable-cxx"
|
|
|
|
|
"--enable-fortran"
|
|
|
|
|
"--enable-fortran2003")
|
2018-02-12 14:45:34 +01:00
|
|
|
|
;; Use -fPIC to allow the R bindings to link with the static libraries
|
|
|
|
|
#:make-flags (list "CFLAGS=-fPIC"
|
|
|
|
|
"CXXFLAGS=-fPIC")
|
2016-11-24 11:55:15 +01:00
|
|
|
|
#:phases
|
2016-04-12 17:02:22 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'patch-configure
|
2017-08-24 11:00:59 +02:00
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2016-04-12 17:02:22 +02:00
|
|
|
|
(substitute* "configure"
|
2016-04-15 17:39:54 +02:00
|
|
|
|
(("/bin/mv") "mv"))
|
2017-08-24 11:00:59 +02:00
|
|
|
|
(substitute* "fortran/src/Makefile.in"
|
|
|
|
|
(("libhdf5_fortran_la_LDFLAGS =")
|
|
|
|
|
(string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
|
|
|
|
|
(assoc-ref outputs "fortran") "/lib")))
|
|
|
|
|
(substitute* "hl/fortran/src/Makefile.in"
|
|
|
|
|
(("libhdf5hl_fortran_la_LDFLAGS =")
|
|
|
|
|
(string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
|
|
|
|
|
(assoc-ref outputs "fortran") "/lib")))
|
2016-04-15 17:39:54 +02:00
|
|
|
|
#t))
|
2017-08-31 17:29:36 +02:00
|
|
|
|
(add-after 'configure 'patch-settings
|
|
|
|
|
(lambda _
|
|
|
|
|
;; libhdf5.settings contains the full path of the
|
|
|
|
|
;; compilers used, and its contents are included in
|
|
|
|
|
;; libhdf5.so. We truncate the hashes to avoid
|
|
|
|
|
;; unnecessary store references to those compilers:
|
|
|
|
|
(substitute* "src/libhdf5.settings"
|
|
|
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
2018-03-09 11:20:22 +01:00
|
|
|
|
(string-append prefix (string-take hash 10) "..."))
|
|
|
|
|
;; Don't record the build-time kernel version to make the
|
|
|
|
|
;; settings file reproducible.
|
|
|
|
|
(("Uname information:.*")
|
|
|
|
|
"Uname information: Linux\n"))
|
2016-04-15 17:39:54 +02:00
|
|
|
|
#t))
|
2016-04-12 17:02:22 +02:00
|
|
|
|
(add-after 'install 'patch-references
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
|
|
|
|
|
(zlib (assoc-ref inputs "zlib")))
|
|
|
|
|
(substitute* (find-files bin "h5p?cc")
|
|
|
|
|
(("-lz" lib)
|
|
|
|
|
(string-append "-L" zlib "/lib " lib)))
|
2017-08-24 11:00:59 +02:00
|
|
|
|
#t)))
|
|
|
|
|
(add-after 'install 'split
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
;; Move all fortran-related files
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin"))
|
|
|
|
|
(lib (string-append out "/lib"))
|
|
|
|
|
(inc (string-append out "/include"))
|
|
|
|
|
(ex (string-append out "/share/hdf5_examples/fortran"))
|
|
|
|
|
(fort (assoc-ref outputs "fortran"))
|
|
|
|
|
(fbin (string-append fort "/bin"))
|
|
|
|
|
(flib (string-append fort "/lib"))
|
|
|
|
|
(finc (string-append fort "/include"))
|
|
|
|
|
(fex (string-append fort "/share/hdf5_examples/fortran")))
|
|
|
|
|
(mkdir-p fbin)
|
|
|
|
|
(mkdir-p flib)
|
|
|
|
|
(mkdir-p finc)
|
|
|
|
|
(mkdir-p fex)
|
|
|
|
|
(rename-file (string-append bin "/h5fc")
|
|
|
|
|
(string-append fbin "/h5fc"))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(rename-file file
|
|
|
|
|
(string-append flib "/" (basename file))))
|
|
|
|
|
(find-files lib ".*fortran.*"))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(rename-file file
|
|
|
|
|
(string-append finc "/" (basename file))))
|
|
|
|
|
(find-files inc ".*mod"))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(rename-file file
|
|
|
|
|
(string-append fex "/" (basename file))))
|
|
|
|
|
(find-files ex ".*"))
|
|
|
|
|
(delete-file-recursively ex))
|
|
|
|
|
#t)))))
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(home-page "http://www.hdfgroup.org")
|
2014-09-19 13:31:19 +02:00
|
|
|
|
(synopsis "Management suite for extremely large and complex data")
|
2014-02-16 23:01:56 +01:00
|
|
|
|
(description "HDF5 is a suite that makes possible the management of
|
|
|
|
|
extremely large and complex data collections.")
|
2014-03-31 01:09:10 +02:00
|
|
|
|
(license (license:x11-style
|
|
|
|
|
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
2014-02-16 23:01:56 +01:00
|
|
|
|
|
2017-10-04 17:17:03 +02:00
|
|
|
|
(define-public hdf-java
|
|
|
|
|
(package
|
|
|
|
|
(name "hdf-java")
|
|
|
|
|
(version "3.3.2")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
|
|
|
|
|
version "/src/CMake-hdfjava-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet ; Make sure we don't use the bundled sources and binaries.
|
|
|
|
|
`(begin
|
|
|
|
|
(for-each delete-file
|
|
|
|
|
(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
|
|
|
|
|
"HDF4.tar.gz" "HDF5.tar.gz"))
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
(delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
|
|
|
|
|
#t))))
|
2017-10-04 17:17:03 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("jdk" ,icedtea "jdk")
|
|
|
|
|
("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
|
|
|
|
|
;; For tests:
|
|
|
|
|
("hamcrest-core" ,java-hamcrest-core)
|
|
|
|
|
("junit" ,java-junit)
|
|
|
|
|
("slf4j-simple" ,java-slf4j-simple)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("hdf4" ,hdf4)
|
|
|
|
|
("hdf5" ,hdf5)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("libjpeg" ,libjpeg)
|
|
|
|
|
("slf4j-api" ,java-slf4j-api)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags
|
|
|
|
|
(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
|
|
|
|
|
(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
|
|
|
|
|
(assoc-ref %build-inputs "jdk") "/lib" )
|
|
|
|
|
(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
|
|
|
|
|
(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
|
|
|
|
|
|
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
|
|
|
|
|
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
|
|
|
|
|
(string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
|
|
|
|
|
(string-append "JPEGLIB="
|
|
|
|
|
(assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
|
|
|
|
|
"LLEXT=so")
|
|
|
|
|
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'chdir-to-source
|
|
|
|
|
(lambda _ (chdir ,(string-append "hdfjava-" version))))
|
|
|
|
|
(add-before 'configure 'patch-build
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(substitute* "configure"
|
|
|
|
|
(("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
|
|
|
|
|
(("/bin/cat") (which "cat")))
|
|
|
|
|
;; Set classpath for compilation
|
|
|
|
|
(substitute* '("hdf/hdf5lib/Makefile.in"
|
|
|
|
|
"hdf/hdf5lib/exceptions/Makefile.in"
|
|
|
|
|
"hdf/hdflib/Makefile.in")
|
|
|
|
|
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
|
|
|
|
|
(string-append (assoc-ref inputs "slf4j-api")
|
|
|
|
|
"/share/java/slf4j-api.jar")))
|
|
|
|
|
;; Replace outdated config.sub and config.guess:
|
|
|
|
|
(with-directory-excursion "config"
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(copy-file
|
|
|
|
|
(string-append (assoc-ref inputs "automake")
|
|
|
|
|
"/share/automake-1.15/" file) file))
|
|
|
|
|
'("config.sub" "config.guess")))
|
|
|
|
|
(mkdir-p (string-append (assoc-ref outputs "out")))
|
|
|
|
|
;; Set classpath for tests
|
|
|
|
|
(let* ((build-dir (getcwd))
|
|
|
|
|
(lib (string-append build-dir "/lib"))
|
|
|
|
|
(jhdf (string-append lib "/jhdf.jar"))
|
|
|
|
|
(jhdf5 (string-append lib "/jhdf5.jar"))
|
|
|
|
|
(testjars
|
|
|
|
|
(map (lambda (i)
|
|
|
|
|
(string-append (assoc-ref inputs i)
|
|
|
|
|
"/share/java/" i ".jar"))
|
|
|
|
|
'("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
|
|
|
|
|
(class-path
|
|
|
|
|
(string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
|
|
|
|
|
|
|
|
|
|
(substitute* '("test/hdf5lib/Makefile.in"
|
|
|
|
|
"test/hdf5lib/junit.sh.in"
|
|
|
|
|
"examples/runExample.sh.in")
|
|
|
|
|
(("/usr/bin/test")
|
|
|
|
|
(string-append (assoc-ref inputs "coreutils")
|
|
|
|
|
"/bin/test"))
|
|
|
|
|
(("/usr/bin/uname")
|
|
|
|
|
(string-append (assoc-ref inputs "coreutils")
|
|
|
|
|
"/bin/uname"))
|
|
|
|
|
(("CLASSPATH=[^\n]*")
|
|
|
|
|
(string-append "CLASSPATH=" class-path)))
|
|
|
|
|
(setenv "CLASSPATH" class-path))
|
|
|
|
|
#t))
|
|
|
|
|
(add-before 'check 'build-examples
|
|
|
|
|
(lambda _
|
|
|
|
|
(zero? (apply system* `("javac"
|
|
|
|
|
,@(find-files "examples" ".*\\.java")))))))
|
|
|
|
|
|
|
|
|
|
#:parallel-build? #f
|
|
|
|
|
|
|
|
|
|
#:parallel-tests? #f ))
|
|
|
|
|
(home-page "https://support.hdfgroup.org/products/java")
|
|
|
|
|
(synopsis "Java interface for the HDF4 and HDF5 libraries")
|
|
|
|
|
(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
|
|
|
|
|
the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
|
|
|
|
|
implemented in C.")
|
|
|
|
|
|
|
|
|
|
;; BSD-style license:
|
|
|
|
|
(license (license:x11-style
|
|
|
|
|
"https://support.hdfgroup.org/ftp/HDF5/hdf-java\
|
|
|
|
|
/current/src/unpacked/COPYING"))))
|
|
|
|
|
|
2016-09-30 09:59:08 +02:00
|
|
|
|
(define-public hdf-eos2
|
|
|
|
|
(package
|
|
|
|
|
(name "hdf-eos2")
|
|
|
|
|
(version "19.1.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri "ftp://edhs1.gsfc.nasa.gov\
|
|
|
|
|
/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
|
|
|
|
|
(patches (search-patches "hdf-eos2-remove-gctp.patch"
|
|
|
|
|
"hdf-eos2-build-shared.patch"
|
|
|
|
|
"hdf-eos2-fortrantests.patch"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("libjpeg" ,libjpeg)
|
|
|
|
|
("gctp" ,gctp)))
|
|
|
|
|
(arguments
|
|
|
|
|
`( #:configure-flags '("--enable-install-include" "--enable-shared"
|
|
|
|
|
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
|
|
|
|
|
#:parallel-tests? #f))
|
|
|
|
|
(home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
|
|
|
|
|
(synopsis "HDF4-based data format for NASA's Earth Observing System")
|
|
|
|
|
(description "HDF-EOS2 is a software library built on HDF4 which supports
|
|
|
|
|
the construction of data structures used in NASA's Earth Observing
|
|
|
|
|
System (Grid, Point and Swath).")
|
|
|
|
|
|
|
|
|
|
;; Source files carry a permissive license header.
|
|
|
|
|
(license (license:non-copyleft home-page))))
|
|
|
|
|
|
2016-06-17 10:51:38 +02:00
|
|
|
|
(define-public hdf-eos5
|
|
|
|
|
(package
|
|
|
|
|
(name "hdf-eos5")
|
|
|
|
|
(version "1.15")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "ftp://edhs1.gsfc.nasa.gov\
|
|
|
|
|
/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
|
|
|
|
|
(patches (search-patches "hdf-eos5-build-shared.patch"
|
|
|
|
|
"hdf-eos5-remove-gctp.patch"
|
|
|
|
|
"hdf-eos5-fix-szip.patch"
|
|
|
|
|
"hdf-eos5-fortrantests.patch"))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("hdf5" ,hdf5)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("gctp" ,gctp)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags '("--enable-install-include" "--enable-shared"
|
|
|
|
|
"CC=h5cc -Df2cFortran" "LIBS=-lgctp")
|
|
|
|
|
#:parallel-tests? #f))
|
|
|
|
|
(synopsis "HDF5-based data format for NASA's Earth Observing System")
|
|
|
|
|
(description
|
|
|
|
|
"HDF-EOS5 is a software library built on HDF5 to support the construction
|
|
|
|
|
of data structures used in NASA's Earth Observing System (Grid, Point and
|
|
|
|
|
Swath).")
|
|
|
|
|
(home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
|
|
|
|
|
|
|
|
|
|
;; Source files carry a permissive license header.
|
|
|
|
|
(license (license:non-copyleft home-page))))
|
|
|
|
|
|
2016-03-17 15:35:38 +01:00
|
|
|
|
(define-public hdf5-parallel-openmpi
|
|
|
|
|
(package (inherit hdf5)
|
|
|
|
|
(name "hdf5-parallel-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
,@(package-inputs hdf5)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
|
|
|
|
|
,@(package-arguments hdf5))
|
|
|
|
|
((#:phases phases)
|
|
|
|
|
`(modify-phases ,phases
|
|
|
|
|
(add-before 'check 'patch-tests
|
|
|
|
|
(lambda _
|
|
|
|
|
;; OpenMPI's mpirun will exit with non-zero status if it
|
|
|
|
|
;; detects an "abnormal termination", i.e. any process not
|
|
|
|
|
;; calling MPI_Finalize(). Since the test is explicitely
|
|
|
|
|
;; avoiding MPI_Finalize so as not to have at_exit and thus
|
|
|
|
|
;; H5C_flush_cache from being called, mpirun will always
|
|
|
|
|
;; complain, so turn this test off.
|
|
|
|
|
(substitute* "testpar/Makefile"
|
|
|
|
|
(("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
|
|
|
|
|
(string-append front back "\n")))
|
|
|
|
|
(substitute* "tools/h5diff/testph5diff.sh"
|
|
|
|
|
(("/bin/sh") (which "sh")))
|
|
|
|
|
#t))))))
|
|
|
|
|
(synopsis "Management suite for data with parallel IO support")))
|
|
|
|
|
|
2016-04-12 17:01:52 +02:00
|
|
|
|
(define-public h5check
|
|
|
|
|
(package
|
|
|
|
|
(name "h5check")
|
|
|
|
|
(version "2.0.1")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
|
|
|
|
|
"h5check/src/h5check-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs `(("hdf5" ,hdf5))) ;h5cc for tests
|
|
|
|
|
(home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
|
|
|
|
|
(synopsis "HDF5 format checker")
|
|
|
|
|
(description "@code{h5check} is a validation tool for verifying that an
|
|
|
|
|
HDF5 file is encoded according to the HDF File Format Specification.")
|
|
|
|
|
(license (license:x11-style "file://COPYING"))))
|
|
|
|
|
|
2017-03-07 07:51:51 +01:00
|
|
|
|
(define-public itpp
|
|
|
|
|
(package
|
|
|
|
|
(name "itpp")
|
|
|
|
|
(version "4.3.1")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/itpp/itpp/"
|
|
|
|
|
version "/itpp-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments `(#:tests? #f)) ; Tests require googletest *sources*
|
|
|
|
|
(inputs `(("lapack" ,lapack)
|
|
|
|
|
("fftw" ,fftw)))
|
2017-06-30 13:55:28 +02:00
|
|
|
|
;; FIXME: Even though the fonts are available dvips complains:
|
|
|
|
|
;; "Font cmmi10 not found; characters will be left blank."
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("texlive" ,texlive-tiny)
|
|
|
|
|
("ghostscript" ,ghostscript)
|
|
|
|
|
("doxygen" ,doxygen)))
|
2017-03-07 07:51:51 +01:00
|
|
|
|
(home-page "http://itpp.sourceforge.net")
|
|
|
|
|
(synopsis "C++ library of maths, signal processing and communication classes")
|
|
|
|
|
(description "IT++ is a C++ library of mathematical, signal processing and
|
|
|
|
|
communication classes and functions. Its main use is in simulation of
|
|
|
|
|
communication systems and for performing research in the area of
|
|
|
|
|
communications. The kernel of the library consists of generic vector and
|
|
|
|
|
matrix classes, and a set of accompanying routines. Such a kernel makes IT++
|
|
|
|
|
similar to MATLAB, GNU Octave or SciPy.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2016-04-12 17:04:01 +02:00
|
|
|
|
(define-public netcdf
|
|
|
|
|
(package
|
|
|
|
|
(name "netcdf")
|
2016-12-01 04:26:01 +01:00
|
|
|
|
(version "4.4.1.1")
|
2016-04-12 17:04:01 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
|
|
|
|
|
"netcdf-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-12-01 04:26:01 +01:00
|
|
|
|
"1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
|
|
|
|
|
(patches (search-patches "netcdf-date-time.patch"
|
|
|
|
|
"netcdf-tst_h_par.patch"))))
|
2016-04-12 17:04:01 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("m4" ,m4)
|
|
|
|
|
("doxygen" ,doxygen)
|
|
|
|
|
("graphviz" ,graphviz)))
|
|
|
|
|
(inputs
|
2016-12-23 14:56:00 +01:00
|
|
|
|
`(("hdf4" ,hdf4-alt)
|
|
|
|
|
("hdf5" ,hdf5)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("libjpeg" ,libjpeg)))
|
2016-04-12 17:04:01 +02:00
|
|
|
|
(arguments
|
2016-12-23 14:56:00 +01:00
|
|
|
|
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
|
2017-08-24 15:13:02 +02:00
|
|
|
|
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'fix-source-date
|
|
|
|
|
(lambda _
|
|
|
|
|
;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
|
|
|
|
|
;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
|
|
|
|
|
;; to '1st hour of the current day', and therefore makes the
|
|
|
|
|
;; package not reproducible.
|
|
|
|
|
(substitute* "./configure"
|
|
|
|
|
(("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
|
|
|
|
|
"date --date='@0'"))
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'configure 'patch-settings
|
|
|
|
|
(lambda _
|
|
|
|
|
;; libnetcdf.settings contains the full filename of the compilers
|
|
|
|
|
;; used to build the library. We truncate the hashes of those
|
|
|
|
|
;; filenames to avoid unnecessary references to the corresponding
|
|
|
|
|
;; store items.
|
|
|
|
|
(substitute* "libnetcdf.settings"
|
|
|
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
|
|
|
|
(string-append prefix (string-take hash 10) "...")))
|
|
|
|
|
#t)))
|
|
|
|
|
|
2016-04-12 17:04:01 +02:00
|
|
|
|
#:parallel-tests? #f)) ;various race conditions
|
|
|
|
|
(home-page "http://www.unidata.ucar.edu/software/netcdf/")
|
|
|
|
|
(synopsis "Library for scientific data")
|
|
|
|
|
(description "NetCDF is an interface for scientific data access and a
|
|
|
|
|
software library that provides an implementation of the interface. The netCDF
|
|
|
|
|
library defines a machine-independent format for representing scientific data.
|
|
|
|
|
Together, the interface, library, and format support the creation, access, and
|
|
|
|
|
sharing of scientific data.")
|
|
|
|
|
(license (license:x11-style "file://COPYRIGHT"))))
|
|
|
|
|
|
|
|
|
|
(define-public netcdf-parallel-openmpi
|
|
|
|
|
(package (inherit netcdf)
|
|
|
|
|
(name "netcdf-parallel-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
|
|
|
|
|
(package-inputs netcdf))))
|
|
|
|
|
;; TODO: Replace pkg-config references in nc-config with absolute references
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments netcdf)
|
|
|
|
|
((#:configure-flags flags)
|
|
|
|
|
`(cons* "CC=mpicc" "CXX=mpicxx"
|
|
|
|
|
"--enable-parallel-tests"
|
|
|
|
|
;; Shared libraries not supported with parallel IO.
|
|
|
|
|
"--disable-shared" "--with-pic"
|
|
|
|
|
,flags))))))
|
|
|
|
|
|
2017-04-27 17:06:53 +02:00
|
|
|
|
(define-public netcdf-fortran
|
|
|
|
|
(package
|
|
|
|
|
(name "netcdf-fortran")
|
|
|
|
|
(version "4.4.4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:parallel-tests? #f))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("netcdf" ,netcdf)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(synopsis "Fortran interface for the netCDF library")
|
|
|
|
|
(description (package-description netcdf))
|
|
|
|
|
(home-page (package-home-page netcdf))
|
|
|
|
|
(license (package-license netcdf))))
|
|
|
|
|
|
2016-05-03 14:30:25 +02:00
|
|
|
|
(define-public nlopt
|
|
|
|
|
(package
|
|
|
|
|
(name "nlopt")
|
|
|
|
|
(version "2.4.2")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(;; Shared libraries are not built by default. They are required to
|
|
|
|
|
;; build the Guile, Octave, and Python bindings.
|
|
|
|
|
#:configure-flags '("--enable-shared")
|
|
|
|
|
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'set-libnlopt-file-name
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; Make sure the Scheme module refers to the library by its
|
|
|
|
|
;; absolute file name (we cannot do that from a snippet
|
|
|
|
|
;; because the expansion of @libdir@ contains
|
|
|
|
|
;; ${exec_prefix}.)
|
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(substitute* "swig/nlopt.scm.in"
|
|
|
|
|
(("libnlopt")
|
|
|
|
|
(string-append out "/lib/libnlopt")))
|
|
|
|
|
#t))))))
|
|
|
|
|
(inputs `(("guile" ,guile-2.0)))
|
|
|
|
|
(native-inputs `(("pkg-config" ,pkg-config)))
|
|
|
|
|
(home-page "http://ab-initio.mit.edu/wiki/")
|
|
|
|
|
(synopsis "Library for nonlinear optimization")
|
|
|
|
|
(description "NLopt is a library for nonlinear optimization, providing a
|
|
|
|
|
common interface for a number of different free optimization routines available
|
|
|
|
|
online as well as original implementations of various other algorithms.")
|
|
|
|
|
(license license:lgpl2.1+)))
|
|
|
|
|
|
2016-06-02 18:22:26 +02:00
|
|
|
|
(define-public ipopt
|
|
|
|
|
(package
|
|
|
|
|
(name "ipopt")
|
|
|
|
|
(version "3.12.5")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://www.coin-or.org/download/source/Ipopt/Ipopt-"
|
|
|
|
|
version".tgz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Make sure we don't use the bundled software.
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(delete-file-recursively "ThirdParty")
|
|
|
|
|
#t))))
|
2016-06-02 18:22:26 +02:00
|
|
|
|
(build-system gnu-build-system)
|
2016-06-03 14:34:32 +02:00
|
|
|
|
(arguments
|
|
|
|
|
'(#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-after 'install 'add--L-flags-in-ipopt.pc
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
;; The '.pc' file lists '-llapack -lblas' in "Libs";
|
|
|
|
|
;; move it to "Libs.private" where it belongs, and add a
|
|
|
|
|
;; '-L' flag for LAPACK.
|
|
|
|
|
(let ((out (assoc-ref outputs "out"))
|
|
|
|
|
(lapack (assoc-ref inputs "lapack")))
|
|
|
|
|
(substitute* (string-append out "/lib/pkgconfig/"
|
|
|
|
|
"ipopt.pc")
|
|
|
|
|
(("Libs: (.*)-llapack -lblas(.*)$" _ before after)
|
|
|
|
|
(string-append "Libs: " before " " after "\n"
|
|
|
|
|
"Libs.private: " before
|
|
|
|
|
"-L" lapack "/lib -llapack -lblas "
|
|
|
|
|
after "\n")))
|
|
|
|
|
#t))))))
|
2016-06-02 18:22:26 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(inputs
|
|
|
|
|
;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
|
2016-06-03 14:34:32 +02:00
|
|
|
|
`(("lapack" ,lapack))) ;for both libblas and liblapack
|
2016-06-02 18:22:26 +02:00
|
|
|
|
(home-page "http://www.coin-or.org")
|
|
|
|
|
(synopsis "Large-scale nonlinear optimizer")
|
|
|
|
|
(description
|
|
|
|
|
"The Interior Point Optimizer (IPOPT) is a software package for
|
|
|
|
|
large-scale nonlinear optimization. It provides C++, C, and Fortran
|
|
|
|
|
interfaces.")
|
|
|
|
|
(license license:epl1.0)))
|
|
|
|
|
|
2016-06-03 13:54:20 +02:00
|
|
|
|
(define-public ceres
|
|
|
|
|
(package
|
|
|
|
|
(name "ceres-solver")
|
2018-03-24 22:36:38 +01:00
|
|
|
|
(version "1.14.0")
|
2016-06-03 13:54:20 +02:00
|
|
|
|
(home-page "http://ceres-solver.org/")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append home-page "ceres-solver-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-03-24 22:36:38 +01:00
|
|
|
|
"13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
|
2016-06-03 13:54:20 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
;; TODO: Build HTML user documentation and install separately.
|
2016-06-29 12:01:05 +02:00
|
|
|
|
'(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
|
2016-06-03 13:54:20 +02:00
|
|
|
|
"-DBUILD_SHARED_LIBS=ON")
|
|
|
|
|
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'set-library-directory
|
|
|
|
|
(lambda _
|
|
|
|
|
;; Install libraries to lib/, not lib64/.
|
|
|
|
|
(substitute* "internal/ceres/CMakeLists.txt"
|
|
|
|
|
(("set\\(LIB_SUFFIX \"64\"\\)")
|
|
|
|
|
"set(LIB_SUFFIX \"\")"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("pkg-config" ,pkg-config)))
|
2016-06-29 16:07:48 +02:00
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("glog" ,glog))) ;for #include <glog/glog.h>
|
2016-06-03 13:54:20 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("eigen" ,eigen)
|
|
|
|
|
("blas" ,openblas)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("suitesparse" ,suitesparse)
|
|
|
|
|
("gflags" ,gflags)))
|
|
|
|
|
(synopsis "C++ library for solving large optimization problems")
|
|
|
|
|
(description
|
|
|
|
|
"Ceres Solver is a C++ library for modeling and solving large,
|
|
|
|
|
complicated optimization problems. It is a feature rich, mature and
|
|
|
|
|
performant library which has been used in production since 2010. Ceres Solver
|
|
|
|
|
can solve two kinds of problems:
|
|
|
|
|
@enumerate
|
|
|
|
|
@item non-linear least squares problems with bounds constraints;
|
|
|
|
|
@item general unconstrained optimization problems.
|
|
|
|
|
@end enumerate\n")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
2014-01-30 14:22:49 +01:00
|
|
|
|
;; For a fully featured Octave, users are strongly recommended also to install
|
2017-08-07 12:43:17 +02:00
|
|
|
|
;; the following packages: less, ghostscript, gnuplot.
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(define-public octave
|
|
|
|
|
(package
|
|
|
|
|
(name "octave")
|
2018-05-05 16:21:38 +02:00
|
|
|
|
(version "4.4.0")
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/octave/octave-"
|
2016-11-15 14:21:15 +01:00
|
|
|
|
version ".tar.lz"))
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-05-05 16:21:38 +02:00
|
|
|
|
"0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp"))))
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("lapack" ,lapack)
|
2018-07-17 21:29:05 +02:00
|
|
|
|
("qhull" ,qhull)
|
2014-01-30 14:22:49 +01:00
|
|
|
|
("readline" ,readline)
|
2017-04-03 17:46:55 +02:00
|
|
|
|
("gl2ps" ,gl2ps)
|
2014-01-30 14:22:49 +01:00
|
|
|
|
("glpk" ,glpk)
|
2015-05-08 21:44:29 +02:00
|
|
|
|
("fftw" ,fftw)
|
|
|
|
|
("fftwf" ,fftwf)
|
|
|
|
|
("arpack" ,arpack-ng)
|
2014-01-30 14:22:49 +01:00
|
|
|
|
("pcre" ,pcre)
|
|
|
|
|
("fltk" ,fltk)
|
|
|
|
|
("fontconfig" ,fontconfig)
|
|
|
|
|
("freetype" ,freetype)
|
2015-03-12 22:16:12 +01:00
|
|
|
|
("hdf5" ,hdf5)
|
2014-01-30 14:22:49 +01:00
|
|
|
|
("libxft" ,libxft)
|
|
|
|
|
("mesa" ,mesa)
|
2015-05-08 21:44:29 +02:00
|
|
|
|
("glu" ,glu)
|
2017-03-08 21:11:44 +01:00
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("curl" ,curl)
|
2017-08-07 12:43:17 +02:00
|
|
|
|
("texinfo" ,texinfo)
|
2018-01-26 16:08:52 +01:00
|
|
|
|
("graphicsmagick" ,graphicsmagick)
|
|
|
|
|
("suitesparse" ,suitesparse)
|
|
|
|
|
("libsndfile" ,libsndfile)
|
|
|
|
|
("portaudio" ,portaudio)
|
|
|
|
|
("alsa-lib" ,alsa-lib)))
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(native-inputs
|
2016-11-15 14:21:15 +01:00
|
|
|
|
`(("lzip" ,lzip)
|
|
|
|
|
("gfortran" ,gfortran)
|
2014-01-30 14:22:49 +01:00
|
|
|
|
("pkg-config" ,pkg-config)
|
|
|
|
|
("perl" ,perl)
|
2015-05-08 21:44:29 +02:00
|
|
|
|
;; The following inputs are not actually used in the build process.
|
|
|
|
|
;; However, the ./configure gratuitously tests for their existence and
|
|
|
|
|
;; assumes that programs not present at build time are also not, and
|
|
|
|
|
;; can never be, available at run time! If these inputs are therefore
|
|
|
|
|
;; not present, support for them will be built out. However, Octave
|
|
|
|
|
;; will still run without them, albeit without the features they
|
2014-01-30 14:22:49 +01:00
|
|
|
|
;; provide.
|
|
|
|
|
("less" ,less)
|
|
|
|
|
("ghostscript" ,ghostscript)
|
|
|
|
|
("gnuplot" ,gnuplot)))
|
|
|
|
|
(arguments
|
2016-05-18 02:36:17 +02:00
|
|
|
|
`(#:configure-flags
|
|
|
|
|
(list (string-append "--with-shell="
|
|
|
|
|
(assoc-ref %build-inputs "bash")
|
2017-08-07 12:43:17 +02:00
|
|
|
|
"/bin/sh"))
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'configure 'configure-makeinfo
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(substitute* "libinterp/corefcn/help.cc"
|
|
|
|
|
(("Vmakeinfo_program = \"makeinfo\"")
|
|
|
|
|
(string-append "Vmakeinfo_program = \""
|
|
|
|
|
(assoc-ref inputs "texinfo")
|
|
|
|
|
"/bin/makeinfo\"")))
|
|
|
|
|
#t)))))
|
2016-11-15 14:21:15 +01:00
|
|
|
|
(home-page "https://www.gnu.org/software/octave/")
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(synopsis "High-level language for numerical computation")
|
2015-05-08 21:44:29 +02:00
|
|
|
|
(description "GNU Octave is a high-level interpreted language that is
|
|
|
|
|
specialized for numerical computations. It can be used for both linear and
|
|
|
|
|
non-linear applications and it provides great support for visualizing results.
|
|
|
|
|
Work may be performed both at the interactive command-line as well as via
|
|
|
|
|
script files.")
|
2014-01-30 14:22:49 +01:00
|
|
|
|
(license license:gpl3+)))
|
2014-04-24 22:13:59 +02:00
|
|
|
|
|
2018-01-27 22:06:13 +01:00
|
|
|
|
(define-public qtoctave
|
|
|
|
|
(package (inherit octave)
|
|
|
|
|
(name "qtoctave")
|
2018-07-01 02:03:42 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(inherit (package-source octave))
|
|
|
|
|
(patches (append (origin-patches (package-source octave))
|
|
|
|
|
(search-patches
|
|
|
|
|
"qtoctave-qt-5.11-fix.patch")))))
|
2018-01-27 22:06:13 +01:00
|
|
|
|
(inputs
|
|
|
|
|
`(("qscintilla" ,qscintilla)
|
|
|
|
|
("qt" ,qtbase)
|
|
|
|
|
,@(package-inputs octave)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("qttools" , qttools) ;for lrelease
|
2018-07-01 02:03:42 +02:00
|
|
|
|
("texlive" ,texlive) ;for texi2dvi
|
2018-01-27 22:06:13 +01:00
|
|
|
|
,@(package-native-inputs octave)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments octave)
|
|
|
|
|
((#:phases phases)
|
|
|
|
|
`(modify-phases ,phases
|
|
|
|
|
(add-before 'configure 'patch-qscintilla-library-name
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
;; The QScintilla library that the Octave configure script tries
|
|
|
|
|
;; to link with should be named libqscintilla-qt5.so, but the
|
|
|
|
|
;; QScintilla input provides the shared library as
|
|
|
|
|
;; libqscintilla2_qt5.so.
|
|
|
|
|
(substitute* "configure"
|
|
|
|
|
(("qscintilla2-qt5")
|
|
|
|
|
"qscintilla2_qt5"))
|
|
|
|
|
#t))))))))
|
|
|
|
|
|
2017-01-18 11:01:36 +01:00
|
|
|
|
(define-public opencascade-oce
|
|
|
|
|
(package
|
|
|
|
|
(name "opencascade-oce")
|
|
|
|
|
(version "0.17.2")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/tpaviot/oce/archive/OCE-"
|
|
|
|
|
version
|
|
|
|
|
".tar.gz"))
|
2018-01-17 00:20:43 +01:00
|
|
|
|
(patches (search-patches "opencascade-oce-glibc-2.26.patch"))
|
2017-01-18 11:01:36 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:configure-flags
|
|
|
|
|
(list "-DOCE_TESTING:BOOL=ON"
|
|
|
|
|
"-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
|
|
|
|
|
"-DOCE_DRAW:BOOL=ON"
|
|
|
|
|
(string-append "-DOCE_INSTALL_PREFIX:PATH="
|
|
|
|
|
(assoc-ref %outputs "out"))
|
|
|
|
|
"-UCMAKE_INSTALL_RPATH")))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("freetype" ,freetype)
|
|
|
|
|
("glu" ,glu)
|
|
|
|
|
("libxmu" ,libxmu)
|
|
|
|
|
("mesa" ,mesa)
|
|
|
|
|
("tcl" ,tcl)
|
|
|
|
|
("tk" ,tk)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python" ,python-wrapper)))
|
|
|
|
|
(home-page "https://github.com/tpaviot/oce")
|
|
|
|
|
(synopsis "Libraries for 3D modeling and numerical simulation")
|
|
|
|
|
(description
|
|
|
|
|
"Open CASCADE is a set of libraries for the development of applications
|
|
|
|
|
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
|
|
|
|
|
C++ class libraries providing services for 3D surface and solid modeling, CAD
|
|
|
|
|
data exchange, and visualization. It is used for development of specialized
|
|
|
|
|
software dealing with 3D models in design (CAD), manufacturing (CAM),
|
|
|
|
|
numerical simulation (CAE), measurement equipment (CMM), and quality
|
|
|
|
|
control (CAQ) domains.
|
|
|
|
|
|
|
|
|
|
This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
|
|
|
|
|
patches, improvements, and experiments contributed by users over the official
|
|
|
|
|
Open CASCADE library.")
|
|
|
|
|
(license (list license:lgpl2.1; OCE libraries, with an exception for the
|
|
|
|
|
; use of header files; see
|
|
|
|
|
; OCCT_LGPL_EXCEPTION.txt
|
|
|
|
|
license:public-domain; files
|
|
|
|
|
; src/Standard/Standard_StdAllocator.hxx and
|
|
|
|
|
; src/NCollection/NCollection_StdAllocator.hxx
|
|
|
|
|
license:expat; file src/OpenGl/OpenGl_glext.h
|
|
|
|
|
license:bsd-3)))); test framework gtest
|
|
|
|
|
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(define-public gmsh
|
|
|
|
|
(package
|
|
|
|
|
(name "gmsh")
|
2017-01-31 16:53:49 +01:00
|
|
|
|
(version "2.16.0")
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2016-11-10 14:25:51 +01:00
|
|
|
|
(uri (string-append "http://gmsh.info/src/gmsh-"
|
2014-04-24 22:13:59 +02:00
|
|
|
|
version "-source.tgz"))
|
|
|
|
|
(sha256
|
2017-01-31 16:53:49 +01:00
|
|
|
|
(base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Remove non-free METIS code
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(delete-file-recursively "contrib/Metis")
|
|
|
|
|
#t))))
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("fltk" ,fltk)
|
2015-06-25 17:56:07 +02:00
|
|
|
|
("gfortran" ,gfortran)
|
2014-04-24 22:13:59 +02:00
|
|
|
|
("gmp" ,gmp)
|
2015-03-12 22:16:12 +01:00
|
|
|
|
("hdf5" ,hdf5)
|
2014-04-24 22:13:59 +02:00
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("mesa" ,mesa)
|
2014-12-27 15:14:09 +01:00
|
|
|
|
("glu" ,glu)
|
2017-02-01 16:12:59 +01:00
|
|
|
|
("opencascade-oce" ,opencascade-oce)
|
2014-04-24 22:13:59 +02:00
|
|
|
|
("libx11" ,libx11)
|
|
|
|
|
("libxext" ,libxext)))
|
2016-05-16 09:18:16 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("fontconfig" ,fontconfig)
|
|
|
|
|
("libxft" ,libxft)))
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
|
|
|
|
|
"-DENABLE_BUILD_SHARED:BOOL=ON"
|
2017-02-01 16:12:59 +01:00
|
|
|
|
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(home-page "http://www.geuz.org/gmsh/")
|
|
|
|
|
(synopsis "3D finite element grid generator")
|
2014-04-30 21:56:52 +02:00
|
|
|
|
(description "Gmsh is a 3D finite element grid generator with a built-in
|
|
|
|
|
CAD engine and post-processor. Its design goal is to provide a fast, light
|
|
|
|
|
and user-friendly meshing tool with parametric input and advanced
|
|
|
|
|
visualization capabilities. Gmsh is built around four modules: geometry,
|
|
|
|
|
mesh, solver and post-processing. The specification of any input to these
|
|
|
|
|
modules is done either interactively using the graphical user interface or in
|
|
|
|
|
ASCII text files using Gmsh's own scripting language.")
|
2014-04-24 22:13:59 +02:00
|
|
|
|
(license license:gpl2+)))
|
2014-04-30 21:01:43 +02:00
|
|
|
|
|
2017-03-08 19:24:31 +01:00
|
|
|
|
(define-public maxflow
|
|
|
|
|
(package
|
|
|
|
|
(name "maxflow")
|
|
|
|
|
(version "3.04")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/gerddie/maxflow.git")
|
|
|
|
|
(commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
|
|
|
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(home-page "http://pub.ist.ac.at/~vnk/software.html")
|
|
|
|
|
(synopsis "Library implementing Maxflow algorithm")
|
|
|
|
|
(description "An implementation of the maxflow algorithm described in
|
|
|
|
|
@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
|
|
|
|
|
Energy Minimization in Computer Vision.\n
|
|
|
|
|
Yuri Boykov and Vladimir Kolmogorov.\n
|
|
|
|
|
In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
|
|
|
|
|
September 2004}")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(define-public petsc
|
|
|
|
|
(package
|
|
|
|
|
(name "petsc")
|
2017-10-24 22:33:38 +02:00
|
|
|
|
(version "3.8.0")
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
;; The *-lite-* tarball does not contain the *large* documentation
|
|
|
|
|
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
|
|
|
|
|
"petsc-lite-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
2017-10-24 22:33:38 +02:00
|
|
|
|
(base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
2017-10-24 22:33:38 +02:00
|
|
|
|
`(("python" ,python-2)))
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(inputs
|
2015-06-25 17:56:07 +02:00
|
|
|
|
`(("gfortran" ,gfortran)
|
2014-04-30 21:01:43 +02:00
|
|
|
|
("lapack" ,lapack)
|
2014-05-02 21:11:37 +02:00
|
|
|
|
("superlu" ,superlu)
|
2014-04-30 21:01:43 +02:00
|
|
|
|
;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
|
|
|
|
|
;; leaving out opengl, as configuration seems to only be for mac
|
|
|
|
|
))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:test-target "test"
|
2015-06-16 19:39:42 +02:00
|
|
|
|
#:parallel-build? #f ;build is parallel by default
|
2014-04-30 21:01:43 +02:00
|
|
|
|
#:configure-flags
|
|
|
|
|
`("--with-mpi=0"
|
2014-05-02 21:11:37 +02:00
|
|
|
|
"--with-openmp=1"
|
|
|
|
|
"--with-superlu=1"
|
|
|
|
|
,(string-append "--with-superlu-include="
|
|
|
|
|
(assoc-ref %build-inputs "superlu") "/include")
|
|
|
|
|
,(string-append "--with-superlu-lib="
|
|
|
|
|
(assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
|
2017-08-08 07:21:20 +02:00
|
|
|
|
#:make-flags
|
|
|
|
|
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
|
|
|
|
|
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
|
|
|
|
|
(list (format #f "MAKE_NP=~a" (parallel-job-count)))
|
2014-04-30 21:01:43 +02:00
|
|
|
|
#:phases
|
2016-07-08 00:03:44 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(replace 'configure
|
|
|
|
|
;; PETSc's configure script is actually a python script, so we can't
|
|
|
|
|
;; run it with bash.
|
|
|
|
|
(lambda* (#:key outputs (configure-flags '())
|
|
|
|
|
#:allow-other-keys)
|
|
|
|
|
(let* ((prefix (assoc-ref outputs "out"))
|
|
|
|
|
(flags `(,(string-append "--prefix=" prefix)
|
|
|
|
|
,@configure-flags)))
|
|
|
|
|
(format #t "build directory: ~s~%" (getcwd))
|
|
|
|
|
(format #t "configure flags: ~s~%" flags)
|
2018-06-30 02:22:23 +02:00
|
|
|
|
(apply invoke "./configure" flags))))
|
2016-07-08 00:03:44 +02:00
|
|
|
|
(add-after 'configure 'clean-local-references
|
2017-08-08 07:21:20 +02:00
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2016-07-08 00:03:44 +02:00
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
|
2016-07-08 17:29:02 +02:00
|
|
|
|
;; Prevent build directory from leaking into compiled code
|
|
|
|
|
(((getcwd)) out)
|
|
|
|
|
;; Scrub timestamp for reproducibility
|
2016-07-08 17:31:34 +02:00
|
|
|
|
((".*Libraries compiled on.*") ""))
|
2017-08-08 07:21:20 +02:00
|
|
|
|
(substitute* (find-files "." "petscvariables")
|
|
|
|
|
;; Do not expose build machine characteristics, set to defaults.
|
|
|
|
|
(("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
|
|
|
|
|
(("NPMAX = [:digit:]+") "NPMAX = 2"))
|
2016-07-08 17:31:34 +02:00
|
|
|
|
#t)))
|
2016-07-08 00:03:44 +02:00
|
|
|
|
(add-after 'install 'clean-install
|
2014-05-08 18:39:59 +02:00
|
|
|
|
;; Try to keep installed files from leaking build directory names.
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
2016-07-08 00:03:44 +02:00
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
2014-05-08 18:39:59 +02:00
|
|
|
|
(substitute* (map (lambda (file)
|
2015-06-16 19:39:42 +02:00
|
|
|
|
(string-append out "/lib/petsc/conf/" file))
|
2016-07-08 17:31:34 +02:00
|
|
|
|
'("petscvariables"))
|
2014-05-08 18:39:59 +02:00
|
|
|
|
(((getcwd)) out))
|
|
|
|
|
;; Make compiler references point to the store
|
2015-06-16 19:39:42 +02:00
|
|
|
|
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
|
2016-03-16 17:29:49 +01:00
|
|
|
|
(("= (gcc|g\\+\\+|gfortran)" _ compiler)
|
|
|
|
|
(string-append "= " (which compiler))))
|
2014-05-08 18:39:59 +02:00
|
|
|
|
;; PETSc installs some build logs, which aren't necessary.
|
|
|
|
|
(for-each (lambda (file)
|
2015-06-16 19:39:42 +02:00
|
|
|
|
(let ((f (string-append out "/lib/petsc/conf/" file)))
|
2014-05-08 18:39:59 +02:00
|
|
|
|
(when (file-exists? f)
|
|
|
|
|
(delete-file f))))
|
2015-06-16 19:39:42 +02:00
|
|
|
|
'("configure.log" "make.log" "gmake.log"
|
|
|
|
|
"test.log" "error.log" "RDict.db"
|
2016-07-08 17:31:34 +02:00
|
|
|
|
"PETScBuildInternal.cmake"
|
2014-05-08 18:39:59 +02:00
|
|
|
|
;; Once installed, should uninstall with Guix
|
2016-07-08 17:31:34 +02:00
|
|
|
|
"uninstall.py"))
|
|
|
|
|
#t))))))
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(home-page "http://www.mcs.anl.gov/petsc")
|
2014-05-17 08:44:42 +02:00
|
|
|
|
(synopsis "Library to solve PDEs")
|
2014-04-30 21:01:43 +02:00
|
|
|
|
(description "PETSc, pronounced PET-see (the S is silent), is a suite of
|
|
|
|
|
data structures and routines for the scalable (parallel) solution of
|
|
|
|
|
scientific applications modeled by partial differential equations.")
|
gnu: Update packages to use 'non-copyleft' instead of 'bsd-style'.
* gnu/packages/avr.scm, gnu/packages/compression.scm,
gnu/packages/curl.scm, gnu/packages/cyrus-sasl.scm,
gnu/packages/databases.scm, gnu/packages/firmware.scm,
gnu/packages/flex.scm, gnu/packages/fontutils.scm,
gnu/packages/gd.scm, gnu/packages/ghostscript.scm,
gnu/packages/gnunet.scm, gnu/packages/graphics.scm,
gnu/packages/hugs.scm, gnu/packages/image.scm,
gnu/packages/linux.scm, gnu/packages/mail.scm,
gnu/packages/maths.scm, gnu/packages/mit-krb5.scm,
gnu/packages/python.scm, gnu/packages/rdf.scm,
gnu/packages/ssh.scm, gnu/packages/tcl.scm,
gnu/packages/xdisorg.scm, gnu/packages/xiph.scm,
gnu/packages/yasm.scm, gnu/packages/zip.scm: Use 'non-copyleft'
instead of 'bsd-style'.
2015-03-14 19:26:34 +01:00
|
|
|
|
(license (license:non-copyleft
|
2014-04-30 21:01:43 +02:00
|
|
|
|
"http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
|
|
|
|
|
|
|
|
|
|
(define-public petsc-complex
|
|
|
|
|
(package (inherit petsc)
|
|
|
|
|
(name "petsc-complex")
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments petsc)
|
|
|
|
|
((#:configure-flags cf)
|
|
|
|
|
`(cons "--with-scalar-type=complex" ,cf))))
|
2014-05-17 08:44:42 +02:00
|
|
|
|
(synopsis "Library to solve PDEs (with complex scalars)")))
|
2014-05-02 17:44:50 +02:00
|
|
|
|
|
2014-05-08 19:33:47 +02:00
|
|
|
|
(define-public petsc-openmpi
|
|
|
|
|
(package (inherit petsc)
|
|
|
|
|
(name "petsc-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("openmpi" ,openmpi)
|
|
|
|
|
,@(package-inputs petsc)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments petsc)
|
|
|
|
|
((#:configure-flags cf)
|
|
|
|
|
``("--with-mpiexec=mpirun"
|
|
|
|
|
,(string-append "--with-mpi-dir="
|
|
|
|
|
(assoc-ref %build-inputs "openmpi"))
|
|
|
|
|
,@(delete "--with-mpi=0" ,cf)))))
|
2014-05-17 08:44:42 +02:00
|
|
|
|
(synopsis "Library to solve PDEs (with MPI support)")))
|
2014-05-08 19:33:47 +02:00
|
|
|
|
|
|
|
|
|
(define-public petsc-complex-openmpi
|
|
|
|
|
(package (inherit petsc-complex)
|
|
|
|
|
(name "petsc-complex-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("openmpi" ,openmpi)
|
|
|
|
|
,@(package-inputs petsc-complex)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments petsc-complex)
|
|
|
|
|
((#:configure-flags cf)
|
|
|
|
|
``("--with-mpiexec=mpirun"
|
|
|
|
|
,(string-append "--with-mpi-dir="
|
|
|
|
|
(assoc-ref %build-inputs "openmpi"))
|
|
|
|
|
,@(delete "--with-mpi=0" ,cf)))))
|
2014-05-17 08:44:42 +02:00
|
|
|
|
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
|
2014-05-08 19:33:47 +02:00
|
|
|
|
|
2018-05-02 18:22:33 +02:00
|
|
|
|
|
|
|
|
|
(define-public python-kiwisolver
|
|
|
|
|
(package
|
|
|
|
|
(name "python-kiwisolver")
|
|
|
|
|
(version "1.0.1")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (pypi-uri "kiwisolver" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
|
|
|
|
|
(build-system python-build-system)
|
|
|
|
|
(home-page "https://github.com/nucleic/kiwi")
|
|
|
|
|
(synopsis "Fast implementation of the Cassowary constraint solver")
|
|
|
|
|
(description
|
|
|
|
|
"Kiwi is an efficient C++ implementation of the Cassowary constraint
|
|
|
|
|
solving algorithm. Kiwi has been designed from the ground up to be
|
|
|
|
|
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
|
|
|
|
|
Cassowary solver with typical use cases gaining a 40x improvement. Memory
|
|
|
|
|
savings are consistently > 5x.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
|
|
|
|
(define-public python2-kiwisolver
|
|
|
|
|
(package-with-python2 python-kiwisolver))
|
|
|
|
|
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(define-public slepc
|
|
|
|
|
(package
|
|
|
|
|
(name "slepc")
|
2018-01-26 22:51:23 +01:00
|
|
|
|
(version "3.8.2")
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2017-08-08 07:19:51 +02:00
|
|
|
|
(uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
|
|
|
|
|
version ".tar.gz"))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-01-26 22:51:23 +01:00
|
|
|
|
"04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python" ,python-2)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("arpack" ,arpack-ng)
|
|
|
|
|
("gfortran" ,gfortran)))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("petsc" ,petsc)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:parallel-build? #f ;build is parallel by default
|
|
|
|
|
#:configure-flags
|
|
|
|
|
`(,(string-append "--with-arpack-dir="
|
2015-11-20 01:08:03 +01:00
|
|
|
|
(assoc-ref %build-inputs "arpack") "/lib"))
|
2017-08-08 07:21:20 +02:00
|
|
|
|
#:make-flags ;honor (parallel-job-count)
|
|
|
|
|
`(,(format #f "MAKE_NP=~a" (parallel-job-count)))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
2016-07-08 19:15:01 +02:00
|
|
|
|
(replace 'configure
|
2015-06-17 14:19:11 +02:00
|
|
|
|
;; configure is a python script, so we can't run it with bash.
|
|
|
|
|
(lambda* (#:key inputs outputs (configure-flags '())
|
|
|
|
|
#:allow-other-keys)
|
|
|
|
|
(let* ((prefix (assoc-ref outputs "out"))
|
|
|
|
|
(flags `(,(string-append "--prefix=" prefix)
|
|
|
|
|
,@configure-flags)))
|
|
|
|
|
(format #t "build directory: ~s~%" (getcwd))
|
|
|
|
|
(format #t "configure flags: ~s~%" flags)
|
|
|
|
|
(setenv "SLEPC_DIR" (getcwd))
|
2015-11-20 01:08:03 +01:00
|
|
|
|
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
|
2018-02-02 15:20:02 +01:00
|
|
|
|
(apply invoke "./configure" flags))))
|
2016-07-08 19:15:01 +02:00
|
|
|
|
(add-after 'install 'delete-doc
|
2015-06-17 14:19:11 +02:00
|
|
|
|
;; TODO: SLEPc installs HTML documentation alongside headers in
|
|
|
|
|
;; $out/include. We'd like to move them to share/doc, but delete
|
|
|
|
|
;; them for now, as they are incomplete and installing the complete
|
|
|
|
|
;; documentation is difficult.
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out")))
|
2018-06-30 03:38:25 +02:00
|
|
|
|
(for-each delete-file (find-files out "\\.html$"))
|
|
|
|
|
#t)))
|
2016-07-08 19:15:01 +02:00
|
|
|
|
(add-after 'install 'clean-install
|
2015-06-17 14:19:11 +02:00
|
|
|
|
;; Clean up unnecessary build logs from installation.
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(let ((f (string-append out "/lib/slepc/conf/" file)))
|
|
|
|
|
(when (file-exists? f)
|
|
|
|
|
(delete-file f))))
|
|
|
|
|
'("configure.log" "make.log" "gmake.log"
|
|
|
|
|
"test.log" "error.log" "RDict.db"
|
2018-06-30 03:38:25 +02:00
|
|
|
|
"uninstall.py"))
|
|
|
|
|
#t))))))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(home-page "http://slepc.upv.es")
|
|
|
|
|
(synopsis "Scalable library for eigenproblems")
|
|
|
|
|
(description "SLEPc is a software library for the solution of large sparse
|
|
|
|
|
eigenproblems on parallel computers. It can be used for the solution of
|
|
|
|
|
linear eigenvalue problems formulated in either standard or generalized form,
|
|
|
|
|
as well as other related problems such as the singular value decomposition.
|
|
|
|
|
The emphasis of the software is on methods and techniques appropriate for
|
|
|
|
|
problems in which the associated matrices are sparse, for example, those
|
|
|
|
|
arising after the discretization of partial differential equations.")
|
2018-01-28 23:22:08 +01:00
|
|
|
|
(license license:bsd-2)))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
|
|
|
|
|
(define-public slepc-complex
|
|
|
|
|
(package (inherit slepc)
|
|
|
|
|
(name "slepc-complex")
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("petsc" ,petsc-complex)
|
|
|
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
|
|
|
|
(synopsis "Scalable library for eigenproblems (with complex scalars)")))
|
|
|
|
|
|
|
|
|
|
(define-public slepc-openmpi
|
|
|
|
|
(package (inherit slepc)
|
|
|
|
|
(name "slepc-openmpi")
|
2018-05-12 17:53:54 +02:00
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments slepc)
|
|
|
|
|
((#:phases phases '%standard-phases)
|
|
|
|
|
`(modify-phases ,phases
|
|
|
|
|
(add-before 'check 'set-test-environment
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default, running the test suite would fail because 'ssh'
|
|
|
|
|
;; could not be found in $PATH. Define this variable to
|
|
|
|
|
;; placate Open MPI without adding a dependency on OpenSSH (the
|
|
|
|
|
;; agent isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
#t))))))
|
2015-06-17 14:19:11 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
("arpack" ,arpack-ng-openmpi)
|
|
|
|
|
,@(alist-delete "arpack" (package-inputs slepc))))
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("petsc" ,petsc-openmpi)
|
|
|
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
|
|
|
|
(synopsis "Scalable library for eigenproblems (with MPI support)")))
|
|
|
|
|
|
|
|
|
|
(define-public slepc-complex-openmpi
|
|
|
|
|
(package (inherit slepc-openmpi)
|
|
|
|
|
(name "slepc-complex-openmpi")
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("petsc" ,petsc-complex-openmpi)
|
|
|
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
|
|
|
|
|
(synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
|
|
|
|
|
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(define-public mumps
|
|
|
|
|
(package
|
|
|
|
|
(name "mumps")
|
2018-02-26 18:29:38 +01:00
|
|
|
|
(version "5.1.2")
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-02-26 18:29:38 +01:00
|
|
|
|
"1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
|
2016-04-08 14:18:13 +02:00
|
|
|
|
(patches (search-patches "mumps-build-parallelism.patch"))))
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("fortran" ,gfortran)
|
|
|
|
|
;; These are required for linking against mumps, but we let the user
|
|
|
|
|
;; declare the dependency.
|
|
|
|
|
("blas" ,openblas)
|
|
|
|
|
("metis" ,metis)
|
|
|
|
|
("scotch" ,scotch)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:modules ((ice-9 match)
|
|
|
|
|
(ice-9 popen)
|
|
|
|
|
(srfi srfi-1)
|
|
|
|
|
,@%gnu-build-system-modules)
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
2016-10-28 22:42:11 +02:00
|
|
|
|
(replace 'configure
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(call-with-output-file "Makefile.inc"
|
|
|
|
|
(lambda (port)
|
|
|
|
|
(format port "
|
|
|
|
|
PLAT =
|
|
|
|
|
LIBEXT = .a
|
|
|
|
|
OUTC = -o
|
|
|
|
|
OUTF = -o
|
|
|
|
|
RM = rm -f~:[
|
|
|
|
|
CC = gcc
|
|
|
|
|
FC = gfortran
|
|
|
|
|
FL = gfortran
|
|
|
|
|
INCSEQ = -I$(topdir)/libseq
|
|
|
|
|
LIBSEQ = -L$(topdir)/libseq -lmpiseq
|
|
|
|
|
LIBSEQNEEDED = libseqneeded~;
|
|
|
|
|
CC = mpicc
|
|
|
|
|
FC = mpifort
|
|
|
|
|
FL = mpifort~]
|
|
|
|
|
AR = ar vr # rules require trailing space, ugh...
|
|
|
|
|
RANLIB = ranlib
|
|
|
|
|
LIBBLAS = -L~a -lopenblas~@[
|
|
|
|
|
SCALAP = -L~a -lscalapack~]
|
|
|
|
|
LIBOTHERS = -pthread
|
|
|
|
|
CDEFS = -DAdd_
|
|
|
|
|
PIC = -fPIC
|
|
|
|
|
OPTF = -O2 -DALLOW_NON_INIT $(PIC)
|
|
|
|
|
OPTL = -O2 $(PIC)
|
|
|
|
|
OPTC = -O2 $(PIC)
|
|
|
|
|
INCS = $(INCSEQ)
|
|
|
|
|
LIBS = $(SCALAP) $(LIBSEQ)
|
|
|
|
|
LPORDDIR = $(topdir)/PORD/lib
|
|
|
|
|
IPORD = -I$(topdir)/PORD/include
|
|
|
|
|
LPORD = -L$(LPORDDIR) -lpord
|
|
|
|
|
ORDERINGSF = -Dpord~@[
|
|
|
|
|
METISDIR = ~a
|
|
|
|
|
IMETIS = -I$(METISDIR)/include
|
|
|
|
|
LMETIS = -L$(METISDIR)/lib -lmetis
|
|
|
|
|
ORDERINGSF += -Dmetis~]~@[~:{
|
|
|
|
|
SCOTCHDIR = ~a
|
|
|
|
|
ISCOTCH = -I$(SCOTCHDIR)/include
|
|
|
|
|
LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
|
|
|
|
|
ORDERINGSF += ~a~}~]
|
|
|
|
|
ORDERINGSC = $(ORDERINGSF)
|
|
|
|
|
LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
|
|
|
|
|
IORDERINGSF = $(ISCOTCH)
|
|
|
|
|
IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
|
|
|
|
|
(assoc-ref inputs "mpi")
|
|
|
|
|
(assoc-ref inputs "blas")
|
|
|
|
|
(assoc-ref inputs "scalapack")
|
|
|
|
|
(assoc-ref inputs "metis")
|
|
|
|
|
(match (list (assoc-ref inputs "pt-scotch")
|
|
|
|
|
(assoc-ref inputs "scotch"))
|
|
|
|
|
((#f #f)
|
|
|
|
|
#f)
|
|
|
|
|
((#f scotch)
|
|
|
|
|
`((,scotch "" "-Dscotch")))
|
|
|
|
|
((ptscotch _)
|
|
|
|
|
`((,ptscotch
|
|
|
|
|
"-lptesmumps -lptscotch -lptscotcherr "
|
|
|
|
|
"-Dptscotch")))))))))
|
2016-10-28 22:42:11 +02:00
|
|
|
|
(replace 'build
|
2015-06-16 14:10:51 +02:00
|
|
|
|
;; By default only the d-precision library is built. Make with "all"
|
|
|
|
|
;; target so that all precision libraries and examples are built.
|
|
|
|
|
(lambda _
|
2018-06-30 02:28:14 +02:00
|
|
|
|
(invoke "make" "all"
|
|
|
|
|
(format #f "-j~a" (parallel-job-count)))))
|
2016-10-28 22:42:11 +02:00
|
|
|
|
(replace 'check
|
2015-06-16 14:10:51 +02:00
|
|
|
|
;; Run the simple test drivers, which read test input from stdin:
|
|
|
|
|
;; from the "real" input for the single- and double-precision
|
|
|
|
|
;; testers, and from the "cmplx" input for complex-precision
|
|
|
|
|
;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
|
|
|
|
|
;; package to prefix execution with "mpirun".
|
|
|
|
|
(lambda* (#:key (exec-prefix '()) #:allow-other-keys)
|
|
|
|
|
(with-directory-excursion "examples"
|
|
|
|
|
(every
|
|
|
|
|
(lambda (prec type)
|
|
|
|
|
(let ((tester (apply open-pipe*
|
|
|
|
|
`(,OPEN_WRITE
|
|
|
|
|
,@exec-prefix
|
|
|
|
|
,(string-append "./" prec
|
|
|
|
|
"simpletest"))))
|
|
|
|
|
(input (open-input-file
|
|
|
|
|
(string-append "input_simpletest_" type))))
|
|
|
|
|
(begin
|
|
|
|
|
(dump-port input tester)
|
|
|
|
|
(close-port input)
|
|
|
|
|
(zero? (close-pipe tester)))))
|
|
|
|
|
'("s" "d" "c" "z")
|
|
|
|
|
'("real" "real" "cmplx" "cmplx")))))
|
2016-10-28 22:42:11 +02:00
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(libdir (string-append out "/lib")))
|
|
|
|
|
(copy-recursively "lib" libdir)
|
|
|
|
|
(copy-recursively "include" (string-append out "/include"))
|
|
|
|
|
(when (file-exists? "libseq/libmpiseq.a")
|
|
|
|
|
(install-file "libseq/libmpiseq.a" libdir))
|
|
|
|
|
#t))))))
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(home-page "http://mumps.enseeiht.fr")
|
|
|
|
|
(synopsis "Multifrontal sparse direct solver")
|
|
|
|
|
(description
|
|
|
|
|
"MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
|
|
|
|
|
sparse system of linear equations A x = b using Guassian elimination.")
|
|
|
|
|
(license license:cecill-c)))
|
|
|
|
|
|
|
|
|
|
(define-public mumps-metis
|
|
|
|
|
(package (inherit mumps)
|
|
|
|
|
(name "mumps-metis")
|
|
|
|
|
(inputs
|
|
|
|
|
(alist-delete "scotch" (package-inputs mumps)))))
|
|
|
|
|
|
|
|
|
|
(define-public mumps-openmpi
|
|
|
|
|
(package (inherit mumps)
|
|
|
|
|
(name "mumps-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
("scalapack" ,scalapack)
|
|
|
|
|
("pt-scotch" ,pt-scotch)
|
|
|
|
|
,@(alist-delete "scotch" (package-inputs mumps))))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments mumps)
|
|
|
|
|
((#:phases phases)
|
|
|
|
|
`(modify-phases ,phases
|
2018-05-12 17:53:54 +02:00
|
|
|
|
(add-before 'check 'set-test-environment
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default, running the test suite would fail because 'ssh'
|
|
|
|
|
;; could not be found in $PATH. Define this variable to
|
|
|
|
|
;; placate Open MPI without adding a dependency on OpenSSH (the
|
|
|
|
|
;; agent isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
((assoc-ref ,phases 'check)
|
|
|
|
|
#:exec-prefix '("mpirun" "-n" "2"))))))))
|
2015-06-16 14:10:51 +02:00
|
|
|
|
(synopsis "Multifrontal sparse direct solver (with MPI)")))
|
|
|
|
|
|
|
|
|
|
(define-public mumps-metis-openmpi
|
|
|
|
|
(package (inherit mumps-openmpi)
|
|
|
|
|
(name "mumps-metis-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
|
|
|
|
|
|
2016-09-12 16:17:06 +02:00
|
|
|
|
(define-public r-quadprog
|
|
|
|
|
(package
|
|
|
|
|
(name "r-quadprog")
|
|
|
|
|
(version "1.5-5")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "quadprog" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
gnu, doc: Use HTTPS for cran.r-project.org home pages.
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-24 01:01:21 +01:00
|
|
|
|
(home-page "https://cran.r-project.org/web/packages/quadprog")
|
2016-09-12 16:17:06 +02:00
|
|
|
|
(synopsis "Functions to solve quadratic programming problems")
|
|
|
|
|
(description
|
|
|
|
|
"This package contains routines and documentation for solving quadratic
|
|
|
|
|
programming problems.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2016-04-08 10:48:58 +02:00
|
|
|
|
(define-public r-pracma
|
|
|
|
|
(package
|
|
|
|
|
(name "r-pracma")
|
2018-02-13 15:21:59 +01:00
|
|
|
|
(version "2.1.4")
|
2016-04-08 10:48:58 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "pracma" version))
|
|
|
|
|
(sha256
|
2018-02-13 15:21:59 +01:00
|
|
|
|
(base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
|
2016-04-08 10:48:58 +02:00
|
|
|
|
(build-system r-build-system)
|
2016-09-12 15:02:48 +02:00
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("r-quadprog" ,r-quadprog)))
|
gnu, doc: Use HTTPS for cran.r-project.org home pages.
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-24 01:01:21 +01:00
|
|
|
|
(home-page "https://cran.r-project.org/web/packages/pracma")
|
2016-04-08 10:48:58 +02:00
|
|
|
|
(synopsis "Practical numerical math functions")
|
|
|
|
|
(description "This package provides functions for numerical analysis and
|
|
|
|
|
linear algebra, numerical optimization, differential equations, plus some
|
|
|
|
|
special functions. It uses Matlab function names where appropriate to simplify
|
|
|
|
|
porting.")
|
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2015-12-31 13:46:49 +01:00
|
|
|
|
(define-public ruby-asciimath
|
|
|
|
|
(package
|
|
|
|
|
(name "ruby-asciimath")
|
|
|
|
|
(version "1.0.4")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (rubygems-uri "asciimath" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
|
|
|
|
|
(build-system ruby-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
;; Apply this patch
|
|
|
|
|
;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
|
|
|
|
|
(add-after 'unpack 'patch-remove-spurious-backslashes
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "spec/parser_spec.rb"
|
|
|
|
|
(("\\\\\"")
|
|
|
|
|
"\"")))))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("bundler" ,bundler)
|
|
|
|
|
("ruby-rspec" ,ruby-rspec)))
|
|
|
|
|
(synopsis "AsciiMath parsing and conversion library")
|
|
|
|
|
(description
|
|
|
|
|
"A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
|
|
|
|
|
easy-to-write markup language for mathematics.")
|
|
|
|
|
(home-page "https://github.com/asciidoctor/asciimath")
|
|
|
|
|
(license license:expat)))
|
|
|
|
|
|
2014-05-02 17:44:50 +02:00
|
|
|
|
(define-public superlu
|
|
|
|
|
(package
|
|
|
|
|
(name "superlu")
|
2016-07-07 23:59:53 +02:00
|
|
|
|
(version "5.2.1")
|
2014-05-02 17:44:50 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
|
|
|
|
"superlu_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
2016-07-07 23:59:53 +02:00
|
|
|
|
(base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Replace the non-free implementation of MC64 with a stub adapted
|
|
|
|
|
;; from Debian
|
|
|
|
|
'(begin
|
|
|
|
|
(use-modules (ice-9 regex)
|
|
|
|
|
(ice-9 rdelim))
|
|
|
|
|
(call-with-output-file "SRC/mc64ad.c"
|
|
|
|
|
(lambda (port)
|
|
|
|
|
(display "
|
|
|
|
|
#include <stdio.h>
|
|
|
|
|
#include <stdlib.h>
|
|
|
|
|
void mc64id_(int *a) {
|
|
|
|
|
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
|
|
|
|
abort ();
|
|
|
|
|
}
|
|
|
|
|
void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
|
|
|
|
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
|
|
|
|
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
|
|
|
|
abort ();
|
|
|
|
|
}\n" port)))
|
|
|
|
|
;; Remove the corresponding license verbiage. MC64 license follows
|
|
|
|
|
;; a "------" line separator.
|
|
|
|
|
(with-atomic-file-replacement "License.txt"
|
|
|
|
|
(let ((rx (make-regexp "-{8}")))
|
|
|
|
|
(lambda (in out)
|
|
|
|
|
(let loop ()
|
|
|
|
|
(let ((line (read-line in 'concat)))
|
|
|
|
|
(unless (regexp-exec rx line)
|
|
|
|
|
(display line out)
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
(loop))))
|
|
|
|
|
#t)))))))
|
2016-07-07 23:59:53 +02:00
|
|
|
|
(build-system cmake-build-system)
|
2014-05-02 17:44:50 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("tcsh" ,tcsh)))
|
|
|
|
|
(inputs
|
2016-07-07 23:59:53 +02:00
|
|
|
|
`(("blas" ,openblas)
|
2015-06-25 17:56:07 +02:00
|
|
|
|
("gfortran" ,gfortran)))
|
2014-05-02 17:44:50 +02:00
|
|
|
|
(arguments
|
2016-07-07 23:59:53 +02:00
|
|
|
|
`(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
|
|
|
|
|
"-DTPL_BLAS_LIBRARIES=openblas"
|
2017-12-19 15:25:12 +01:00
|
|
|
|
"-DBUILD_SHARED_LIBS:BOOL=YES")))
|
2014-05-02 17:44:50 +02:00
|
|
|
|
(home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
|
|
|
|
|
(synopsis "Supernodal direct solver for sparse linear systems")
|
|
|
|
|
(description
|
|
|
|
|
"SuperLU is a general purpose library for the direct solution of large,
|
|
|
|
|
sparse, nonsymmetric systems of linear equations on high performance machines.
|
|
|
|
|
The library is written in C and is callable from either C or Fortran. The
|
|
|
|
|
library routines perform an LU decomposition with partial pivoting and
|
|
|
|
|
triangular system solves through forward and back substitution. The library
|
|
|
|
|
also provides threshold-based ILU factorization preconditioners.")
|
2016-07-07 23:59:53 +02:00
|
|
|
|
(license (list license:bsd-3
|
|
|
|
|
license:gpl2+ ;EXAMPLE/*fgmr.c
|
|
|
|
|
(license:fsf-free "file://SRC/colamd.h")))))
|
2014-05-19 07:08:30 +02:00
|
|
|
|
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(define-public superlu-dist
|
|
|
|
|
(package
|
|
|
|
|
(name "superlu-dist")
|
2018-05-12 17:52:42 +02:00
|
|
|
|
(version "5.3.0")
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
|
|
|
|
"superlu_dist_" version ".tar.gz"))
|
|
|
|
|
(sha256
|
2018-05-12 17:52:42 +02:00
|
|
|
|
(base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
|
|
|
|
|
(modules '((guix build utils)))
|
2016-07-09 00:44:30 +02:00
|
|
|
|
(snippet
|
|
|
|
|
;; Replace the non-free implementation of MC64 with a stub
|
|
|
|
|
'(begin
|
|
|
|
|
(use-modules (ice-9 regex)
|
|
|
|
|
(ice-9 rdelim))
|
2018-05-12 17:52:42 +02:00
|
|
|
|
(call-with-output-file "SRC/mc64ad_dist.c"
|
2016-07-09 00:44:30 +02:00
|
|
|
|
(lambda (port)
|
|
|
|
|
(display "
|
|
|
|
|
#include <stdio.h>
|
|
|
|
|
#include <stdlib.h>
|
2018-05-12 17:52:42 +02:00
|
|
|
|
void mc64id_dist(int *a) {
|
2016-07-09 00:44:30 +02:00
|
|
|
|
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
|
|
|
|
abort ();
|
|
|
|
|
}
|
2018-05-12 17:52:42 +02:00
|
|
|
|
void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
2016-07-09 00:44:30 +02:00
|
|
|
|
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
|
|
|
|
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
|
|
|
|
abort ();
|
|
|
|
|
}\n" port)))
|
|
|
|
|
(substitute* "SRC/util.c" ;adjust default algorithm
|
|
|
|
|
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
"RowPerm = NOROWPERM"))
|
|
|
|
|
#t))
|
2016-04-08 14:18:13 +02:00
|
|
|
|
(patches (search-patches "superlu-dist-scotchmetis.patch"))))
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("tcsh" ,tcsh)))
|
|
|
|
|
(inputs
|
2015-06-25 17:56:07 +02:00
|
|
|
|
`(("gfortran" ,gfortran)))
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("openmpi" ,openmpi) ;headers include MPI heades
|
|
|
|
|
("lapack" ,lapack) ;required to link with output library
|
|
|
|
|
("pt-scotch" ,pt-scotch))) ;same
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:parallel-build? #f ;race conditions using ar
|
|
|
|
|
#:phases
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(call-with-output-file "make.inc"
|
|
|
|
|
(lambda (port)
|
|
|
|
|
(format port "
|
2014-05-19 07:12:46 +02:00
|
|
|
|
PLAT =
|
|
|
|
|
DSuperLUroot = ~a
|
|
|
|
|
DSUPERLULIB = ~a/lib/libsuperlu_dist.a
|
|
|
|
|
BLASDEF = -DUSE_VENDOR_BLAS
|
|
|
|
|
BLASLIB = -L~a/lib -lblas
|
|
|
|
|
PARMETISLIB = -L~a/lib \
|
|
|
|
|
-lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
|
|
|
|
|
-lscotch -lscotcherr -lscotcherrexit
|
|
|
|
|
METISLIB = -L~:*~a/lib \
|
|
|
|
|
-lscotchmetis -lscotch -lscotcherr -lscotcherrexit
|
|
|
|
|
LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
|
|
|
|
|
ARCH = ar
|
|
|
|
|
ARCHFLAGS = cr
|
|
|
|
|
RANLIB = ranlib
|
|
|
|
|
CC = mpicc
|
|
|
|
|
PIC = -fPIC
|
|
|
|
|
CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
|
|
|
|
|
NOOPTS = -O0 -g $(PIC)
|
|
|
|
|
FORTRAN = mpifort
|
|
|
|
|
FFLAGS = -O2 -g $(PIC)
|
|
|
|
|
LOADER = $(CC)
|
|
|
|
|
CDEFS = -DAdd_"
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(getcwd)
|
|
|
|
|
(assoc-ref outputs "out")
|
|
|
|
|
(assoc-ref inputs "lapack")
|
|
|
|
|
(assoc-ref inputs "pt-scotch"))))
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'unpack 'remove-broken-symlinks
|
|
|
|
|
(lambda _
|
|
|
|
|
(for-each delete-file
|
|
|
|
|
(find-files "MAKE_INC" "\\.#make\\..*"))
|
|
|
|
|
#t))
|
|
|
|
|
(add-before 'build 'create-install-directories
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(for-each
|
|
|
|
|
(lambda (dir)
|
|
|
|
|
(mkdir-p (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/" dir)))
|
|
|
|
|
'("lib" "include"))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'check
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(lambda _
|
2018-05-12 17:53:54 +02:00
|
|
|
|
;; By default, running the test suite would fail because 'ssh'
|
|
|
|
|
;; could not be found in $PATH. Define this variable to placate
|
|
|
|
|
;; Open MPI without adding a dependency on OpenSSH (the agent
|
|
|
|
|
;; isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(with-directory-excursion "EXAMPLE"
|
2018-06-30 02:29:43 +02:00
|
|
|
|
(invoke "mpirun" "-n" "2"
|
|
|
|
|
"./pddrive" "-r" "1" "-c" "2" "g20.rua")
|
|
|
|
|
(invoke "mpirun" "-n" "2"
|
|
|
|
|
"./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
|
|
|
|
|
#t))
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; Library is placed in lib during the build phase. Copy over
|
|
|
|
|
;; headers to include.
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(incdir (string-append out "/include")))
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(let ((base (basename file)))
|
|
|
|
|
(format #t "installing `~a' to `~a'~%"
|
|
|
|
|
base incdir)
|
|
|
|
|
(copy-file file
|
|
|
|
|
(string-append incdir "/" base))))
|
|
|
|
|
(find-files "SRC" ".*\\.h$")))
|
|
|
|
|
#t)))))
|
2014-05-19 07:12:46 +02:00
|
|
|
|
(home-page (package-home-page superlu))
|
|
|
|
|
(synopsis "Parallel supernodal direct solver")
|
|
|
|
|
(description
|
|
|
|
|
"SuperLU_DIST is a parallel extension to the serial SuperLU library.
|
|
|
|
|
It is targeted for distributed memory parallel machines. SuperLU_DIST is
|
|
|
|
|
implemented in ANSI C, and MPI for communications.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
2014-05-19 07:08:30 +02:00
|
|
|
|
(define-public scotch
|
|
|
|
|
(package
|
|
|
|
|
(name "scotch")
|
2018-03-02 21:05:34 +01:00
|
|
|
|
(version "6.0.5a")
|
2014-05-19 07:08:30 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2018-03-25 18:25:53 +02:00
|
|
|
|
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
|
|
|
|
|
"latestfile/298/scotch_" version ".tar.gz"))
|
2014-05-19 07:08:30 +02:00
|
|
|
|
(sha256
|
2018-03-02 21:05:34 +01:00
|
|
|
|
(base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
|
2016-04-08 14:18:13 +02:00
|
|
|
|
(patches (search-patches "scotch-test-threading.patch"
|
2018-03-02 21:05:34 +01:00
|
|
|
|
"scotch-build-parallelism.patch"
|
|
|
|
|
"scotch-graph-induce-type-64.patch"
|
|
|
|
|
"scotch-graph-diam-64.patch"))))
|
2014-05-19 07:08:30 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
2017-05-15 22:51:01 +02:00
|
|
|
|
("flex" ,flex)
|
2014-05-19 07:08:30 +02:00
|
|
|
|
("bison" ,bison)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
2015-06-15 12:09:55 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after
|
|
|
|
|
'unpack 'chdir-to-src
|
2018-06-30 02:32:11 +02:00
|
|
|
|
(lambda _ (chdir "src") #t))
|
2015-06-15 12:09:55 +02:00
|
|
|
|
(replace
|
|
|
|
|
'configure
|
|
|
|
|
(lambda _
|
|
|
|
|
(call-with-output-file "Makefile.inc"
|
|
|
|
|
(lambda (port)
|
|
|
|
|
(format port "
|
2014-05-19 07:08:30 +02:00
|
|
|
|
EXE =
|
|
|
|
|
LIB = .a
|
|
|
|
|
OBJ = .o
|
|
|
|
|
MAKE = make
|
|
|
|
|
AR = ar
|
|
|
|
|
ARFLAGS = -ruv
|
2015-06-15 13:00:01 +02:00
|
|
|
|
CAT = cat
|
2014-05-19 07:08:30 +02:00
|
|
|
|
CCS = gcc
|
|
|
|
|
CCP = mpicc
|
|
|
|
|
CCD = gcc
|
|
|
|
|
CPPFLAGS =~{ -D~a~}
|
2015-01-10 08:02:46 +01:00
|
|
|
|
CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
|
2014-05-19 07:08:30 +02:00
|
|
|
|
LDFLAGS = -lz -lm -lrt -lpthread
|
|
|
|
|
CP = cp
|
|
|
|
|
LEX = flex -Pscotchyy -olex.yy.c
|
|
|
|
|
LN = ln
|
|
|
|
|
MKDIR = mkdir
|
|
|
|
|
MV = mv
|
|
|
|
|
RANLIB = ranlib
|
|
|
|
|
YACC = bison -pscotchyy -y -b y
|
|
|
|
|
"
|
2015-06-15 12:09:55 +02:00
|
|
|
|
'("COMMON_FILE_COMPRESS_GZ"
|
|
|
|
|
"COMMON_PTHREAD"
|
|
|
|
|
"COMMON_RANDOM_FIXED_SEED"
|
2017-06-26 17:00:36 +02:00
|
|
|
|
"INTSIZE64" ;use 'long' instead of 'int'
|
2015-06-15 13:00:01 +02:00
|
|
|
|
;; Prevents symbolc clashes with libesmumps
|
|
|
|
|
"SCOTCH_RENAME"
|
2015-06-15 12:09:55 +02:00
|
|
|
|
;; XXX: Causes invalid frees in superlu-dist tests
|
|
|
|
|
;; "SCOTCH_PTHREAD"
|
|
|
|
|
;; "SCOTCH_PTHREAD_NUMBER=2"
|
2018-06-30 02:32:11 +02:00
|
|
|
|
"restrict=__restrict"))))
|
|
|
|
|
#t))
|
2015-06-15 13:00:01 +02:00
|
|
|
|
(add-after
|
|
|
|
|
'build 'build-esmumps
|
|
|
|
|
(lambda _
|
2018-05-12 17:53:54 +02:00
|
|
|
|
;; By default, running the test suite would fail because 'ssh'
|
|
|
|
|
;; could not be found in $PATH. Define this variable to placate
|
|
|
|
|
;; Open MPI without adding a dependency on OpenSSH (the agent
|
|
|
|
|
;; isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
|
2018-06-30 02:32:11 +02:00
|
|
|
|
(invoke "make"
|
|
|
|
|
(format #f "-j~a" (parallel-job-count))
|
|
|
|
|
"esmumps")))
|
2015-06-15 12:09:55 +02:00
|
|
|
|
(replace
|
2014-05-19 07:08:30 +02:00
|
|
|
|
'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(mkdir out)
|
2018-06-30 02:32:11 +02:00
|
|
|
|
(invoke "make"
|
|
|
|
|
(string-append "prefix=" out)
|
|
|
|
|
"install")
|
2015-06-15 13:00:01 +02:00
|
|
|
|
;; esmumps files are not installed with the above
|
|
|
|
|
(for-each (lambda (f)
|
|
|
|
|
(copy-file f (string-append out "/include/" f)))
|
|
|
|
|
(find-files "../include" ".*esmumps.h$"))
|
|
|
|
|
(for-each (lambda (f)
|
|
|
|
|
(copy-file f (string-append out "/lib/" f)))
|
2018-06-30 02:32:11 +02:00
|
|
|
|
(find-files "../lib" "^lib.*esmumps.*"))
|
|
|
|
|
#t))))))
|
2014-05-19 07:08:30 +02:00
|
|
|
|
(home-page "http://www.labri.fr/perso/pelegrin/scotch/")
|
|
|
|
|
(synopsis "Programs and libraries for graph algorithms")
|
|
|
|
|
(description "SCOTCH is a set of programs and libraries which implement
|
|
|
|
|
the static mapping and sparse matrix reordering algorithms developed within
|
|
|
|
|
the SCOTCH project. Its purpose is to apply graph theory, with a divide and
|
|
|
|
|
conquer approach, to scientific computing problems such as graph and mesh
|
|
|
|
|
partitioning, static mapping, and sparse matrix ordering, in application
|
|
|
|
|
domains ranging from structural mechanics to operating systems or
|
|
|
|
|
bio-chemistry.")
|
|
|
|
|
;; See LICENSE_en.txt
|
|
|
|
|
(license license:cecill-c)))
|
2014-05-19 07:09:15 +02:00
|
|
|
|
|
2017-08-24 16:56:44 +02:00
|
|
|
|
(define-public scotch32
|
|
|
|
|
;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
|
|
|
|
|
;; some applications.
|
|
|
|
|
(package (inherit scotch)
|
|
|
|
|
(name "scotch32")
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments scotch)
|
|
|
|
|
((#:phases scotch-phases)
|
|
|
|
|
`(modify-phases ,scotch-phases
|
|
|
|
|
(replace
|
|
|
|
|
'configure
|
|
|
|
|
(lambda _
|
|
|
|
|
(call-with-output-file "Makefile.inc"
|
|
|
|
|
(lambda (port)
|
|
|
|
|
(format port "
|
|
|
|
|
EXE =
|
|
|
|
|
LIB = .a
|
|
|
|
|
OBJ = .o
|
|
|
|
|
MAKE = make
|
|
|
|
|
AR = ar
|
|
|
|
|
ARFLAGS = -ruv
|
|
|
|
|
CAT = cat
|
|
|
|
|
CCS = gcc
|
|
|
|
|
CCP = mpicc
|
|
|
|
|
CCD = gcc
|
|
|
|
|
CPPFLAGS =~{ -D~a~}
|
|
|
|
|
CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
|
|
|
|
|
LDFLAGS = -lz -lm -lrt -lpthread
|
|
|
|
|
CP = cp
|
|
|
|
|
LEX = flex -Pscotchyy -olex.yy.c
|
|
|
|
|
LN = ln
|
|
|
|
|
MKDIR = mkdir
|
|
|
|
|
MV = mv
|
|
|
|
|
RANLIB = ranlib
|
|
|
|
|
YACC = bison -pscotchyy -y -b y
|
|
|
|
|
"
|
|
|
|
|
'("COMMON_FILE_COMPRESS_GZ"
|
|
|
|
|
"COMMON_PTHREAD"
|
|
|
|
|
"COMMON_RANDOM_FIXED_SEED"
|
|
|
|
|
"INTSIZE32" ;use 32-bit integers. See INSTALL.txt
|
|
|
|
|
;; Prevents symbolc clashes with libesmumps
|
|
|
|
|
"SCOTCH_RENAME"
|
|
|
|
|
;; XXX: Causes invalid frees in superlu-dist tests
|
|
|
|
|
;; "SCOTCH_PTHREAD"
|
|
|
|
|
;; "SCOTCH_PTHREAD_NUMBER=2"
|
|
|
|
|
"restrict=__restrict"))))))))))
|
|
|
|
|
(synopsis
|
|
|
|
|
"Programs and libraries for graph algorithms (32-bit integers)")))
|
|
|
|
|
|
2014-05-19 07:09:15 +02:00
|
|
|
|
(define-public pt-scotch
|
|
|
|
|
(package (inherit scotch)
|
|
|
|
|
(name "pt-scotch")
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("openmpi" ,openmpi))) ;Headers include MPI headers
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments scotch)
|
|
|
|
|
((#:phases scotch-phases)
|
2015-06-15 12:09:55 +02:00
|
|
|
|
`(modify-phases ,scotch-phases
|
|
|
|
|
(replace
|
|
|
|
|
'build
|
|
|
|
|
(lambda _
|
|
|
|
|
(and
|
2015-06-15 13:00:01 +02:00
|
|
|
|
(zero? (system* "make"
|
|
|
|
|
(format #f "-j~a" (parallel-job-count))
|
|
|
|
|
"ptscotch" "ptesmumps"))
|
2015-06-15 12:09:55 +02:00
|
|
|
|
;; Install the serial metis compatibility library
|
|
|
|
|
(zero? (system* "make" "-C" "libscotchmetis" "install")))))
|
|
|
|
|
(replace
|
|
|
|
|
'check
|
|
|
|
|
(lambda _ (zero? (system* "make" "ptcheck"))))))))
|
2014-05-19 07:09:15 +02:00
|
|
|
|
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
|
gnu: Add gsegrafix and dependent libraries.
* gnu/packages/math.scm (gsegrafix): New variable.
* gnu/packages/gtk.scm (pangox-compat): New variable.
* gnu/packages/gnome.scm (libidl, orbit2, libbonobo, gconf, gnome-mime-data,
gnome-vfs, libgnome, libart-lgpl, libgnomecanvas, libgnomeui, libglade,
libgnomeprint, libgnomeprintui, libbonoboui): New variables.
2014-05-25 07:29:30 +02:00
|
|
|
|
|
2017-08-24 16:56:45 +02:00
|
|
|
|
(define-public pt-scotch32
|
|
|
|
|
(package (inherit scotch32)
|
|
|
|
|
(name "pt-scotch32")
|
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("openmpi" ,openmpi))) ;headers include MPI headers
|
|
|
|
|
(arguments
|
2017-09-01 18:19:48 +02:00
|
|
|
|
(substitute-keyword-arguments (package-arguments scotch32)
|
|
|
|
|
((#:phases scotch32-phases)
|
|
|
|
|
`(modify-phases ,scotch32-phases
|
2017-08-24 16:56:45 +02:00
|
|
|
|
(replace 'build
|
|
|
|
|
(lambda _
|
|
|
|
|
(and
|
|
|
|
|
(zero? (system* "make"
|
|
|
|
|
(format #f "-j~a" (parallel-job-count))
|
|
|
|
|
"ptscotch" "ptesmumps"))
|
|
|
|
|
;; Install the serial metis compatibility library
|
|
|
|
|
(zero? (system* "make" "-C" "libscotchmetis" "install")))))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
(zero? (system* "make" "ptcheck"))))))))
|
|
|
|
|
(synopsis
|
|
|
|
|
"Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
|
|
|
|
|
|
2015-06-25 22:53:12 +02:00
|
|
|
|
(define-public metis
|
|
|
|
|
(package
|
|
|
|
|
(name "metis")
|
|
|
|
|
(version "5.1.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
|
|
|
|
|
"metis-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("blas" ,openblas)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ;no tests
|
|
|
|
|
#:configure-flags `("-DSHARED=ON"
|
|
|
|
|
,(string-append "-DGKLIB_PATH=" (getcwd)
|
|
|
|
|
"/metis-" ,version "/GKlib"))))
|
|
|
|
|
(home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
|
|
|
|
|
(synopsis "Graph partitioning and fill-reducing matrix ordering library")
|
|
|
|
|
(description
|
|
|
|
|
"METIS is a set of serial programs for partitioning graphs, partitioning
|
|
|
|
|
finite element meshes, and producing fill-reducing orderings for sparse
|
|
|
|
|
matrices. The algorithms implemented in METIS are based on the multilevel
|
|
|
|
|
recursive-bisection, multilevel k-way, and multi-constraint partitioning
|
|
|
|
|
schemes.")
|
|
|
|
|
(license license:asl2.0))) ;As of version 5.0.3
|
|
|
|
|
|
2015-06-16 12:38:42 +02:00
|
|
|
|
(define-public p4est
|
|
|
|
|
(package
|
|
|
|
|
(name "p4est")
|
2017-10-25 02:19:13 +02:00
|
|
|
|
(version "2.0")
|
2015-06-16 12:38:42 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://p4est.github.io/release/p4est-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-10-25 02:19:13 +02:00
|
|
|
|
"16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
|
2015-06-16 12:38:42 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("fortran" ,gfortran)
|
|
|
|
|
("blas" ,openblas)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
|
|
|
|
|
(assoc-ref %build-inputs "blas")
|
|
|
|
|
" -lopenblas")
|
|
|
|
|
,(string-append "LAPACK_LIBS=-L"
|
|
|
|
|
(assoc-ref %build-inputs "lapack")
|
2018-05-12 17:53:54 +02:00
|
|
|
|
" -llapack"))
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'set-test-environment
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default, running the test suite would fail because
|
|
|
|
|
;; 'ssh' could not be found in $PATH. Define this
|
|
|
|
|
;; variable to placate Open MPI without adding a
|
|
|
|
|
;; dependency on OpenSSH (the agent isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
#t)))))
|
2015-06-16 12:38:42 +02:00
|
|
|
|
(home-page "http://www.p4est.org")
|
|
|
|
|
(synopsis "Adaptive mesh refinement on forests of octrees")
|
|
|
|
|
(description
|
|
|
|
|
"The p4est software library enables the dynamic management of a
|
|
|
|
|
collection of adaptive octrees, conveniently called a forest of octrees.
|
|
|
|
|
p4est is designed to work in parallel and scales to hundreds of thousands of
|
|
|
|
|
processor cores.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
|
|
|
|
(define-public p4est-openmpi
|
|
|
|
|
(package (inherit p4est)
|
|
|
|
|
(name "p4est-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
,@(package-inputs p4est)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments p4est)
|
|
|
|
|
((#:configure-flags cf)
|
|
|
|
|
``("--enable-mpi" ,@,cf))))
|
|
|
|
|
(synopsis "Parallel adaptive mesh refinement on forests of octrees")))
|
|
|
|
|
|
gnu: Add gsegrafix and dependent libraries.
* gnu/packages/math.scm (gsegrafix): New variable.
* gnu/packages/gtk.scm (pangox-compat): New variable.
* gnu/packages/gnome.scm (libidl, orbit2, libbonobo, gconf, gnome-mime-data,
gnome-vfs, libgnome, libart-lgpl, libgnomecanvas, libgnomeui, libglade,
libgnomeprint, libgnomeprintui, libbonoboui): New variables.
2014-05-25 07:29:30 +02:00
|
|
|
|
(define-public gsegrafix
|
|
|
|
|
(package
|
|
|
|
|
(name "gsegrafix")
|
|
|
|
|
(version "1.0.6")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://gnu/" name "/" name "-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags '("LDFLAGS=-lm")))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("libgnomecanvas" ,libgnomecanvas)
|
|
|
|
|
("libbonoboui" ,libbonoboui)
|
|
|
|
|
("libgnomeui" ,libgnomeui)
|
|
|
|
|
("libgnomeprintui" ,libgnomeprintui)
|
|
|
|
|
("popt" ,popt)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("pkg-config" ,pkg-config)))
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/gsegrafix/")
|
gnu: Add gsegrafix and dependent libraries.
* gnu/packages/math.scm (gsegrafix): New variable.
* gnu/packages/gtk.scm (pangox-compat): New variable.
* gnu/packages/gnome.scm (libidl, orbit2, libbonobo, gconf, gnome-mime-data,
gnome-vfs, libgnome, libart-lgpl, libgnomecanvas, libgnomeui, libglade,
libgnomeprint, libgnomeprintui, libbonoboui): New variables.
2014-05-25 07:29:30 +02:00
|
|
|
|
(synopsis "GNOME application to create scientific and engineering plots")
|
|
|
|
|
(description "GSEGrafix is an application which produces high-quality graphical
|
|
|
|
|
plots for science and engineering. Plots are specified via simple ASCII
|
|
|
|
|
parameter files and data files and are presented in an anti-aliased GNOME
|
|
|
|
|
canvas. The program supports rectangular two-dimensional plots, histograms,
|
|
|
|
|
polar-axis plots and three-dimensional plots. Plots can be printed or saved
|
|
|
|
|
to BMP, JPEG or PNG image formats.")
|
|
|
|
|
(license license:gpl3+)))
|
2014-07-05 14:31:49 +02:00
|
|
|
|
|
|
|
|
|
(define-public maxima
|
|
|
|
|
(package
|
|
|
|
|
(name "maxima")
|
2017-10-14 18:53:54 +02:00
|
|
|
|
(version "5.41.0")
|
2014-07-05 14:31:49 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
|
|
|
|
|
version "-source/" name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-10-14 18:53:54 +02:00
|
|
|
|
"0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
|
2016-04-08 14:18:13 +02:00
|
|
|
|
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
|
2014-07-05 14:31:49 +02:00
|
|
|
|
(build-system gnu-build-system)
|
2014-09-23 16:20:02 +02:00
|
|
|
|
(inputs
|
2017-07-09 00:50:48 +02:00
|
|
|
|
`(("gcl" ,gcl)
|
2014-09-23 16:20:02 +02:00
|
|
|
|
("gnuplot" ,gnuplot) ;for plots
|
2014-09-25 17:04:13 +02:00
|
|
|
|
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
|
2014-09-23 16:20:02 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("texinfo" ,texinfo)
|
2016-11-03 21:14:05 +01:00
|
|
|
|
("perl" ,perl)
|
|
|
|
|
("python" ,python)))
|
2014-07-05 14:31:49 +02:00
|
|
|
|
(arguments
|
2014-09-23 16:20:02 +02:00
|
|
|
|
`(#:configure-flags
|
|
|
|
|
(list "--enable-gcl"
|
|
|
|
|
(string-append "--with-posix-shell="
|
|
|
|
|
(assoc-ref %build-inputs "bash")
|
|
|
|
|
"/bin/sh")
|
|
|
|
|
(string-append "--with-wish="
|
|
|
|
|
(assoc-ref %build-inputs "tk")
|
|
|
|
|
"/bin/wish"
|
|
|
|
|
(let ((v ,(package-version tk)))
|
|
|
|
|
(string-take v (string-index-right v #\.)))))
|
|
|
|
|
;; By default Maxima attempts to write temporary files to
|
2015-05-26 04:03:39 +02:00
|
|
|
|
;; '/tmp/nix-build-maxima-*', which won't exist at run time.
|
|
|
|
|
;; Work around that.
|
2014-09-23 16:20:02 +02:00
|
|
|
|
#:make-flags (list "TMPDIR=/tmp")
|
2017-07-09 00:57:15 +02:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'pre-check
|
|
|
|
|
(lambda _
|
|
|
|
|
(chmod "src/maxima" #o555)
|
|
|
|
|
#t))
|
|
|
|
|
;; Make sure the doc and emacs files are found in the
|
|
|
|
|
;; standard location. Also configure maxima to find gnuplot
|
|
|
|
|
;; without having it on the PATH.
|
|
|
|
|
(add-after 'install 'post-install
|
|
|
|
|
(lambda* (#:key outputs inputs #:allow-other-keys)
|
|
|
|
|
(let* ((gnuplot (assoc-ref inputs "gnuplot"))
|
|
|
|
|
(out (assoc-ref outputs "out"))
|
|
|
|
|
(datadir (string-append out "/share/maxima/" ,version))
|
|
|
|
|
(binutils (string-append (assoc-ref inputs "binutils")
|
|
|
|
|
"/bin")))
|
|
|
|
|
(with-directory-excursion out
|
|
|
|
|
(mkdir-p "share/emacs")
|
|
|
|
|
(mkdir-p "share/doc")
|
|
|
|
|
(symlink
|
|
|
|
|
(string-append datadir "/emacs/")
|
|
|
|
|
(string-append out "/share/emacs/site-lisp"))
|
|
|
|
|
(symlink
|
|
|
|
|
(string-append datadir "/doc/")
|
|
|
|
|
(string-append out "/share/doc/maxima"))
|
|
|
|
|
(with-atomic-file-replacement
|
|
|
|
|
(string-append datadir "/share/maxima-init.lisp")
|
|
|
|
|
(lambda (in out)
|
|
|
|
|
(format out "~a ~s~a~%"
|
|
|
|
|
"(setf $gnuplot_command "
|
|
|
|
|
(string-append gnuplot "/bin/gnuplot") ")")
|
|
|
|
|
(dump-port in out))))
|
|
|
|
|
;; Ensure that Maxima will have access to the GNU binutils
|
|
|
|
|
;; components at runtime.
|
|
|
|
|
(wrap-program (string-append out "/bin/maxima")
|
|
|
|
|
`("PATH" prefix (,binutils))))
|
|
|
|
|
#t)))))
|
2014-07-05 14:31:49 +02:00
|
|
|
|
(home-page "http://maxima.sourceforge.net")
|
|
|
|
|
(synopsis "Numeric and symbolic expression manipulation")
|
|
|
|
|
(description "Maxima is a system for the manipulation of symbolic and
|
|
|
|
|
numerical expressions. It yields high precision numeric results by using
|
|
|
|
|
exact fractions, arbitrary precision integers, and variable precision floating
|
gnu packages: Clean up synopses and descriptions.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm, gnu/packages/bittorrent.scm,
gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/databases.scm, gnu/packages/enchant.scm,
gnu/packages/firmware.scm, gnu/packages/fonts.scm,
gnu/packages/freedesktop.scm, gnu/packages/games.scm, gnu/packages/gd.scm,
gnu/packages/gl.scm, gnu/packages/gnome.scm, gnu/packages/gsasl.scm,
gnu/packages/gstreamer.scm, gnu/packages/gtk.scm, gnu/packages/guile.scm,
gnu/packages/haskell.scm, gnu/packages/language.scm,
gnu/packages/lesstif.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/llvm.scm, gnu/packages/maths.scm,
gnu/packages/mcrypt.scm, gnu/packages/mit-krb5.scm, gnu/packages/mp3.scm,
gnu/packages/ncdu.scm, gnu/packages/networking.scm, gnu/packages/ntp.scm,
gnu/packages/ocaml.scm, gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/pretty-print.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python.scm,
gnu/packages/rdesktop.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm,
gnu/packages/slang.scm, gnu/packages/slim.scm, gnu/packages/telephony.scm,
gnu/packages/tls.scm, gnu/packages/tmux.scm, gnu/packages/tre.scm,
gnu/packages/unrtf.scm, gnu/packages/version-control.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wget.scm,
gnu/packages/xdisorg.scm, gnu/packages/xfce.scm, gnu/packages/xiph.scm:
Fix typos. Trim long lines. Add missing periods in the end of sentences.
Use double spaces between sentences. Remove trailing whitespaces.
2015-07-17 14:16:07 +02:00
|
|
|
|
point numbers.")
|
2014-07-05 14:31:49 +02:00
|
|
|
|
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
|
|
|
|
|
;; Others simply say "GNU General Public License" without stating a
|
|
|
|
|
;; version (which implicitly means gpl1+).
|
|
|
|
|
;; At least one file (src/maxima.asd) says "version 2."
|
|
|
|
|
;; GPLv2 only is therefore the smallest subset.
|
2014-09-25 17:04:13 +02:00
|
|
|
|
(license license:gpl2)))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(define-public wxmaxima
|
|
|
|
|
(package
|
|
|
|
|
(name "wxmaxima")
|
2018-02-24 06:01:21 +01:00
|
|
|
|
(version "18.02.0")
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2017-07-08 04:58:27 +02:00
|
|
|
|
(uri (string-append "https://github.com/andrejv/" name "/archive"
|
|
|
|
|
"/Version-" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-02-24 06:01:21 +01:00
|
|
|
|
"03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
|
|
|
|
|
(patches
|
|
|
|
|
(search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
|
|
|
|
|
(build-system cmake-build-system)
|
2017-07-08 04:58:27 +02:00
|
|
|
|
(native-inputs
|
2018-02-24 06:01:21 +01:00
|
|
|
|
`(("gettext" ,gettext-minimal)))
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("wxwidgets" ,wxwidgets)
|
2016-05-15 09:26:46 +02:00
|
|
|
|
("maxima" ,maxima)
|
|
|
|
|
;; Runtime support.
|
|
|
|
|
("adwaita-icon-theme" ,adwaita-icon-theme)
|
|
|
|
|
("gtk+" ,gtk+)
|
|
|
|
|
("shared-mime-info" ,shared-mime-info)))
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(arguments
|
2018-02-24 06:01:21 +01:00
|
|
|
|
`(#:tests? #f ; no check target
|
|
|
|
|
#:phases
|
2017-08-13 22:24:39 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'install 'wrap-program
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(wrap-program (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/bin/wxmaxima")
|
|
|
|
|
`("PATH" ":" prefix
|
|
|
|
|
(,(string-append (assoc-ref inputs "maxima")
|
|
|
|
|
"/bin")))
|
|
|
|
|
;; For GtkFileChooserDialog.
|
|
|
|
|
`("GSETTINGS_SCHEMA_DIR" =
|
|
|
|
|
(,(string-append (assoc-ref inputs "gtk+")
|
|
|
|
|
"/share/glib-2.0/schemas")))
|
|
|
|
|
`("XDG_DATA_DIRS" ":" prefix
|
|
|
|
|
(;; Needed by gdk-pixbuf to know supported icon formats.
|
|
|
|
|
,(string-append
|
|
|
|
|
(assoc-ref inputs "shared-mime-info") "/share")
|
|
|
|
|
;; The default icon theme of GTK+.
|
|
|
|
|
,(string-append
|
|
|
|
|
(assoc-ref inputs "adwaita-icon-theme") "/share"))))
|
|
|
|
|
#t)))))
|
2015-05-26 05:29:53 +02:00
|
|
|
|
(home-page "https://andrejv.github.io/wxmaxima/")
|
|
|
|
|
(synopsis "Graphical user interface for the Maxima computer algebra system")
|
|
|
|
|
(description
|
|
|
|
|
"wxMaxima is a graphical user interface for the Maxima computer algebra
|
|
|
|
|
system. It eases the use of Maxima by making most of its commands available
|
|
|
|
|
through a menu system and by providing input dialogs for commands that require
|
|
|
|
|
more than one argument. It also implements its own display engine that
|
|
|
|
|
outputs mathematical symbols directly instead of depicting them with ASCII
|
|
|
|
|
characters.
|
|
|
|
|
|
|
|
|
|
wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
|
|
|
|
|
text and mathematical calculations to create documents, exporting of input and
|
|
|
|
|
output to TeX, and a browser for Maxima's manual including command index and
|
|
|
|
|
full text searching.")
|
|
|
|
|
(license license:gpl2+)))
|
|
|
|
|
|
2015-12-21 12:37:23 +01:00
|
|
|
|
(define-public armadillo
|
|
|
|
|
(package
|
|
|
|
|
(name "armadillo")
|
2017-04-06 14:25:14 +02:00
|
|
|
|
(version "7.800.2")
|
2015-12-21 12:37:23 +01:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/arma/armadillo-"
|
2016-10-26 15:41:28 +02:00
|
|
|
|
version ".tar.xz"))
|
2015-12-21 12:37:23 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-04-06 14:25:14 +02:00
|
|
|
|
"1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
|
2015-12-21 12:37:23 +01:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments `(#:tests? #f)) ;no test target
|
|
|
|
|
(inputs
|
|
|
|
|
`(("openblas" ,openblas)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("arpack" ,arpack-ng)))
|
|
|
|
|
(home-page "http://arma.sourceforge.net/")
|
|
|
|
|
(synopsis "C++ linear algebra library")
|
|
|
|
|
(description
|
|
|
|
|
"Armadillo is a C++ linear algebra library, aiming towards a good balance
|
|
|
|
|
between speed and ease of use. It is useful for algorithm development
|
|
|
|
|
directly in C++, or quick conversion of research code into production
|
|
|
|
|
environments. It can be used for machine learning, pattern recognition,
|
|
|
|
|
signal processing, bioinformatics, statistics, econometrics, etc. The library
|
|
|
|
|
provides efficient classes for vectors, matrices and cubes, as well as 150+
|
|
|
|
|
associated functions (eg. contiguous and non-contiguous submatrix views).")
|
2017-04-06 15:41:14 +02:00
|
|
|
|
(license license:asl2.0)))
|
2015-12-21 12:37:23 +01:00
|
|
|
|
|
2015-03-04 09:16:57 +01:00
|
|
|
|
(define-public muparser
|
2016-07-20 08:17:30 +02:00
|
|
|
|
;; When switching download sites, muparser re-issued a 2.2.5 release with a
|
|
|
|
|
;; different hash. In order to make `guix package --upgrade` work correctly,
|
|
|
|
|
;; we set a Guix packaging revision.
|
|
|
|
|
;; When the next version of muparser is released, we can remove
|
|
|
|
|
;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
|
|
|
|
|
(let ((upstream-version "2.2.5")
|
|
|
|
|
(revision "2"))
|
|
|
|
|
(package
|
|
|
|
|
(name "muparser")
|
|
|
|
|
(version (string-append upstream-version "-" revision))
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/beltoforion/muparser/archive/v"
|
|
|
|
|
upstream-version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags '("--enable-samples=no")
|
|
|
|
|
#:tests? #f)) ;no "check" target
|
|
|
|
|
(home-page "http://muparser.beltoforion.de/")
|
|
|
|
|
(synopsis "Fast parser library for mathematical expressions")
|
|
|
|
|
(description
|
|
|
|
|
"muParser is an extensible high performance math parser library. It is
|
|
|
|
|
based on transforming an expression into a bytecode and precalculating constant
|
|
|
|
|
parts of it.")
|
|
|
|
|
(license license:expat))))
|
2015-03-04 09:16:57 +01:00
|
|
|
|
|
2015-03-17 12:24:45 +01:00
|
|
|
|
(define-public openblas
|
|
|
|
|
(package
|
|
|
|
|
(name "openblas")
|
2018-07-30 15:32:10 +02:00
|
|
|
|
(version "0.3.2")
|
2015-03-17 12:24:45 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
|
|
|
|
|
version))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-07-30 15:32:10 +02:00
|
|
|
|
"0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
|
2015-03-17 12:24:45 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2017-08-31 18:49:49 +02:00
|
|
|
|
`(#:test-target "test"
|
2015-10-29 15:43:21 +01:00
|
|
|
|
;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
|
|
|
|
|
;; TARGET is specified, OpenBLAS will tune itself to the build host, so
|
|
|
|
|
;; we need to disable substitutions.
|
2015-10-01 10:32:29 +02:00
|
|
|
|
#:substitutable?
|
|
|
|
|
,(let ((system (or (%current-target-system) (%current-system))))
|
|
|
|
|
(or (string-prefix? "x86_64" system)
|
2015-10-29 15:43:21 +01:00
|
|
|
|
(string-prefix? "i686" system)
|
2017-03-21 21:02:43 +01:00
|
|
|
|
(string-prefix? "mips" system)
|
|
|
|
|
(string-prefix? "aarch64" system)))
|
2015-03-17 12:24:45 +01:00
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
|
|
|
|
|
"SHELL=bash"
|
2015-03-25 19:20:11 +01:00
|
|
|
|
;; Build the library for all supported CPUs. This allows
|
|
|
|
|
;; switching CPU targets at runtime with the environment variable
|
|
|
|
|
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
|
2015-10-01 10:32:29 +02:00
|
|
|
|
;; Unfortunately, this is not supported on non-x86 architectures,
|
|
|
|
|
;; where it leads to failed builds.
|
|
|
|
|
,@(let ((system (or (%current-target-system) (%current-system))))
|
2015-07-20 15:05:55 +02:00
|
|
|
|
(cond
|
|
|
|
|
((or (string-prefix? "x86_64" system)
|
2015-10-01 10:32:29 +02:00
|
|
|
|
(string-prefix? "i686" system))
|
2015-07-20 15:05:55 +02:00
|
|
|
|
'("DYNAMIC_ARCH=1"))
|
|
|
|
|
;; On MIPS we force the "SICORTEX" TARGET, as for the other
|
|
|
|
|
;; two available MIPS targets special extended instructions
|
|
|
|
|
;; for Loongson cores are used.
|
|
|
|
|
((string-prefix? "mips" system)
|
|
|
|
|
'("TARGET=SICORTEX"))
|
2017-03-21 21:02:43 +01:00
|
|
|
|
;; On aarch64 force the generic 'armv8-a' target
|
|
|
|
|
((string-prefix? "aarch64" system)
|
|
|
|
|
'("TARGET=ARMV8"))
|
2015-07-20 15:05:55 +02:00
|
|
|
|
(else '()))))
|
2015-03-17 12:24:45 +01:00
|
|
|
|
;; no configure script
|
2017-12-23 20:36:12 +01:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)
|
|
|
|
|
(add-before 'build 'set-extralib
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
;; Get libgfortran found when building in utest.
|
|
|
|
|
(setenv "FEXTRALIB"
|
|
|
|
|
(string-append "-L" (assoc-ref inputs "fortran-lib")
|
|
|
|
|
"/lib"))
|
|
|
|
|
#t)))))
|
2015-03-17 12:24:45 +01:00
|
|
|
|
(inputs
|
2017-12-23 20:36:12 +01:00
|
|
|
|
`(("fortran-lib" ,gfortran "lib")))
|
2015-03-17 12:24:45 +01:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("cunit" ,cunit)
|
2017-12-23 20:36:12 +01:00
|
|
|
|
("fortran" ,gfortran)
|
2015-03-17 12:24:45 +01:00
|
|
|
|
("perl" ,perl)))
|
|
|
|
|
(home-page "http://www.openblas.net/")
|
|
|
|
|
(synopsis "Optimized BLAS library based on GotoBLAS")
|
|
|
|
|
(description
|
|
|
|
|
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
2017-09-07 15:38:56 +02:00
|
|
|
|
(define* (make-blis implementation #:optional substitutable?)
|
|
|
|
|
"Return a BLIS package with the given IMPLEMENTATION (see config/ in the
|
|
|
|
|
source tree for a list of implementations.)
|
|
|
|
|
|
|
|
|
|
SUBSTITUTABLE? determines whether the package is made available as a
|
|
|
|
|
substitute.
|
|
|
|
|
|
|
|
|
|
Currently the specialization must be selected at configure-time, but work is
|
|
|
|
|
underway to allow BLIS to select the right optimized kernels at run time:
|
|
|
|
|
<https://github.com/flame/blis/issues/129>."
|
|
|
|
|
(package
|
|
|
|
|
(name (if (string=? implementation "reference")
|
|
|
|
|
"blis"
|
|
|
|
|
(string-append "blis-" implementation)))
|
|
|
|
|
(version "0.2.2")
|
|
|
|
|
(home-page "https://github.com/flame/blis")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference (url home-page) (commit version)))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
|
|
|
|
|
(file-name (git-file-name "blis" version))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:test-target "test"
|
|
|
|
|
|
|
|
|
|
#:substitutable? ,substitutable?
|
|
|
|
|
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; This is a home-made 'configure' script.
|
|
|
|
|
(let ((out (assoc-ref outputs "out")))
|
|
|
|
|
(zero? (system* "./configure" "-p" out
|
|
|
|
|
"-d" "opt"
|
|
|
|
|
"--disable-static"
|
|
|
|
|
"--enable-shared"
|
|
|
|
|
"--enable-threading=openmp"
|
|
|
|
|
|
|
|
|
|
,implementation)))))
|
|
|
|
|
(add-before 'check 'show-test-output
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default "make check" is silent. Make it verbose.
|
|
|
|
|
(system "tail -F output.testsuite &")
|
|
|
|
|
#t)))))
|
|
|
|
|
(synopsis "High-performance basic linear algebra (BLAS) routines")
|
|
|
|
|
(description
|
|
|
|
|
"BLIS is a portable software framework for instantiating high-performance
|
|
|
|
|
BLAS-like dense linear algebra libraries. The framework was designed to
|
|
|
|
|
isolate essential kernels of computation that, when optimized, immediately
|
|
|
|
|
enable optimized implementations of most of its commonly used and
|
|
|
|
|
computationally intensive operations. While BLIS exports a new BLAS-like API,
|
|
|
|
|
it also includes a BLAS compatibility layer which gives application developers
|
|
|
|
|
access to BLIS implementations via traditional BLAS routine calls.")
|
|
|
|
|
(license license:bsd-3)))
|
|
|
|
|
|
|
|
|
|
(define-public blis
|
|
|
|
|
;; This is the "reference" implementation, which is the non-optimized but
|
|
|
|
|
;; portable variant (no assembly).
|
|
|
|
|
(make-blis "reference" #t))
|
|
|
|
|
|
|
|
|
|
(define ignorance blis)
|
|
|
|
|
|
|
|
|
|
(define-syntax-rule (blis/x86_64 processor)
|
|
|
|
|
"Expand to a package specialized for PROCESSOR."
|
|
|
|
|
(package
|
|
|
|
|
(inherit (make-blis processor))
|
|
|
|
|
(supported-systems '("x86_64-linux"))))
|
|
|
|
|
|
|
|
|
|
(define-public blis-sandybridge
|
|
|
|
|
;; BLIS specialized for Sandy Bridge processors (launched 2011):
|
|
|
|
|
;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
|
|
|
|
|
(blis/x86_64 "sandybridge"))
|
|
|
|
|
|
|
|
|
|
(define-public blis-haswell
|
|
|
|
|
;; BLIS specialized for Haswell processors (launched 2013):
|
|
|
|
|
;; <http://ark.intel.com/products/codename/42174/Haswell>.
|
|
|
|
|
(blis/x86_64 "haswell"))
|
|
|
|
|
|
|
|
|
|
(define-public blis-knl
|
|
|
|
|
;; BLIS specialized for Knights Landing processor (launched 2016):
|
|
|
|
|
;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
|
|
|
|
|
(blis/x86_64 "knl"))
|
|
|
|
|
|
|
|
|
|
|
2015-03-09 11:07:13 +01:00
|
|
|
|
(define-public openlibm
|
|
|
|
|
(package
|
|
|
|
|
(name "openlibm")
|
2018-07-28 18:12:13 +02:00
|
|
|
|
(version "0.6.0")
|
2015-03-09 11:07:13 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-07-28 18:12:13 +02:00
|
|
|
|
"0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
|
2015-03-09 11:07:13 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:make-flags
|
|
|
|
|
(list (string-append "prefix=" (assoc-ref %outputs "out")))
|
|
|
|
|
#:phases
|
|
|
|
|
;; no configure script
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(modify-phases %standard-phases (delete 'configure))
|
2015-03-09 11:07:13 +01:00
|
|
|
|
#:tests? #f)) ;the tests are part of the default target
|
|
|
|
|
(home-page "http://openlibm.org/")
|
|
|
|
|
(synopsis "Portable C mathematical library (libm)")
|
|
|
|
|
(description
|
|
|
|
|
"OpenLibm is an effort to have a high quality, portable, standalone C
|
|
|
|
|
mathematical library (libm). It can be used standalone in applications and
|
|
|
|
|
programming language implementations. The project was born out of a need to
|
gnu packages: Clean up synopses and descriptions.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm, gnu/packages/bittorrent.scm,
gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/databases.scm, gnu/packages/enchant.scm,
gnu/packages/firmware.scm, gnu/packages/fonts.scm,
gnu/packages/freedesktop.scm, gnu/packages/games.scm, gnu/packages/gd.scm,
gnu/packages/gl.scm, gnu/packages/gnome.scm, gnu/packages/gsasl.scm,
gnu/packages/gstreamer.scm, gnu/packages/gtk.scm, gnu/packages/guile.scm,
gnu/packages/haskell.scm, gnu/packages/language.scm,
gnu/packages/lesstif.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/llvm.scm, gnu/packages/maths.scm,
gnu/packages/mcrypt.scm, gnu/packages/mit-krb5.scm, gnu/packages/mp3.scm,
gnu/packages/ncdu.scm, gnu/packages/networking.scm, gnu/packages/ntp.scm,
gnu/packages/ocaml.scm, gnu/packages/openbox.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/pretty-print.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python.scm,
gnu/packages/rdesktop.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm,
gnu/packages/slang.scm, gnu/packages/slim.scm, gnu/packages/telephony.scm,
gnu/packages/tls.scm, gnu/packages/tmux.scm, gnu/packages/tre.scm,
gnu/packages/unrtf.scm, gnu/packages/version-control.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wget.scm,
gnu/packages/xdisorg.scm, gnu/packages/xfce.scm, gnu/packages/xiph.scm:
Fix typos. Trim long lines. Add missing periods in the end of sentences.
Use double spaces between sentences. Remove trailing whitespaces.
2015-07-17 14:16:07 +02:00
|
|
|
|
have a good libm for the Julia programming language that worked consistently
|
2015-03-09 11:07:13 +01:00
|
|
|
|
across compilers and operating systems, and in 32-bit and 64-bit
|
|
|
|
|
environments.")
|
2016-09-21 21:32:53 +02:00
|
|
|
|
;; Each architecture has its own make target, and there is none for mips.
|
|
|
|
|
(supported-systems (delete "mips64el-linux" %supported-systems))
|
2015-03-09 11:07:13 +01:00
|
|
|
|
;; See LICENSE.md for details.
|
|
|
|
|
(license (list license:expat
|
|
|
|
|
license:isc
|
|
|
|
|
license:bsd-2
|
|
|
|
|
license:public-domain
|
|
|
|
|
license:lgpl2.1+))))
|
|
|
|
|
|
2015-03-09 11:27:52 +01:00
|
|
|
|
(define-public openspecfun
|
|
|
|
|
(package
|
|
|
|
|
(name "openspecfun")
|
2018-01-26 22:43:06 +01:00
|
|
|
|
(version "0.5.3")
|
2015-03-09 11:27:52 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-01-26 22:43:06 +01:00
|
|
|
|
"1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
|
2015-03-09 11:27:52 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2018-01-26 22:43:06 +01:00
|
|
|
|
'(#:tests? #f ; no "check" target
|
2015-03-09 11:27:52 +01:00
|
|
|
|
#:make-flags
|
|
|
|
|
(list (string-append "prefix=" (assoc-ref %outputs "out")))
|
2018-01-26 22:43:06 +01:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure)))) ; no configure script
|
2015-03-09 11:27:52 +01:00
|
|
|
|
(inputs
|
2015-06-25 17:56:07 +02:00
|
|
|
|
`(("fortran" ,gfortran)))
|
2015-03-09 11:27:52 +01:00
|
|
|
|
(home-page "https://github.com/JuliaLang/openspecfun")
|
|
|
|
|
(synopsis "Collection of special mathematical functions")
|
|
|
|
|
(description
|
|
|
|
|
"Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
|
|
|
|
|
portable package for Bessel Functions of a Complex Argument and Nonnegative
|
|
|
|
|
Order; it contains subroutines for computing Bessel functions and Airy
|
|
|
|
|
functions. Faddeeva allows computing the various error functions of arbitrary
|
|
|
|
|
complex arguments (Faddeeva function, error function, complementary error
|
|
|
|
|
function, scaled complementary error function, imaginary error function, and
|
|
|
|
|
Dawson function); given these, one can also easily compute Voigt functions,
|
|
|
|
|
Fresnel integrals, and similar related functions as well.")
|
|
|
|
|
;; Faddeeva is released under the Expat license; AMOS is included as
|
|
|
|
|
;; public domain software.
|
|
|
|
|
(license (list license:expat license:public-domain))))
|
|
|
|
|
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(define-public suitesparse
|
|
|
|
|
(package
|
|
|
|
|
(name "suitesparse")
|
2017-08-09 04:43:15 +02:00
|
|
|
|
(version "4.5.5")
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-08-09 04:43:15 +02:00
|
|
|
|
"1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Remove bundled metis source
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(delete-file-recursively "metis-5.1.0")
|
|
|
|
|
#t))))
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2017-08-09 04:43:15 +02:00
|
|
|
|
'(#:tests? #f ;no "check" target
|
2015-03-10 11:32:48 +01:00
|
|
|
|
#:make-flags
|
|
|
|
|
(list "CC=gcc"
|
|
|
|
|
"BLAS=-lblas"
|
|
|
|
|
"TBB=-ltbb"
|
2017-08-09 04:43:15 +02:00
|
|
|
|
"MY_METIS_LIB=-lmetis"
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(string-append "INSTALL_LIB="
|
|
|
|
|
(assoc-ref %outputs "out") "/lib")
|
|
|
|
|
(string-append "INSTALL_INCLUDE="
|
2017-08-09 04:43:15 +02:00
|
|
|
|
(assoc-ref %outputs "out") "/include")
|
|
|
|
|
"library")
|
2015-03-10 11:32:48 +01:00
|
|
|
|
#:phases
|
2017-08-09 03:00:09 +02:00
|
|
|
|
(modify-phases %standard-phases
|
2017-08-09 04:43:15 +02:00
|
|
|
|
(delete 'configure)))) ;no configure script
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(inputs
|
|
|
|
|
`(("tbb" ,tbb)
|
2017-08-09 04:43:15 +02:00
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("metis" ,metis)))
|
2015-03-10 11:32:48 +01:00
|
|
|
|
(home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
|
|
|
|
|
(synopsis "Suite of sparse matrix software")
|
|
|
|
|
(description
|
|
|
|
|
"SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
|
|
|
|
|
multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
|
|
|
|
|
multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
|
|
|
|
|
simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
|
|
|
|
|
CXSparse, a concise sparse Cholesky factorization package; and many other
|
|
|
|
|
packages.")
|
|
|
|
|
;; LGPLv2.1+:
|
|
|
|
|
;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
|
|
|
|
|
;; GPLv2+:
|
|
|
|
|
;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
|
|
|
|
|
(license (list license:gpl2+ license:lgpl2.1+))))
|
|
|
|
|
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(define-public atlas
|
|
|
|
|
(package
|
|
|
|
|
(name "atlas")
|
2016-08-22 09:56:03 +02:00
|
|
|
|
(version "3.10.3")
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-07-21 08:35:30 +02:00
|
|
|
|
(uri (string-append "mirror://sourceforge/math-atlas/Stable/"
|
|
|
|
|
version "/atlas" version ".tar.bz2"))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2016-08-22 09:56:03 +02:00
|
|
|
|
"1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(home-page "http://math-atlas.sourceforge.net/")
|
2015-06-25 17:56:07 +02:00
|
|
|
|
(inputs `(("gfortran" ,gfortran)
|
2014-10-26 11:03:02 +01:00
|
|
|
|
("lapack-tar" ,(package-source lapack))))
|
|
|
|
|
(outputs '("out" "doc"))
|
2014-12-08 09:30:40 +01:00
|
|
|
|
;; For the moment we drop support for MIPS at it fails to compile. See
|
|
|
|
|
;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
|
|
|
|
|
(supported-systems (delete "mips64el-linux" %supported-systems))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(arguments
|
|
|
|
|
`(#:parallel-build? #f
|
|
|
|
|
#:parallel-tests? #f
|
2014-10-28 10:17:55 +01:00
|
|
|
|
|
|
|
|
|
;; ATLAS tunes itself for the machine it is built on, as explained at
|
|
|
|
|
;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
|
|
|
|
|
;; For this reason, we want users to build it locally instead of using
|
|
|
|
|
;; substitutes.
|
|
|
|
|
#:substitutable? #f
|
|
|
|
|
|
2014-10-26 11:03:02 +01:00
|
|
|
|
#:modules ((srfi srfi-26)
|
|
|
|
|
(srfi srfi-1)
|
|
|
|
|
(guix build gnu-build-system)
|
|
|
|
|
(guix build utils))
|
2015-03-12 22:16:12 +01:00
|
|
|
|
#:configure-flags
|
2014-10-26 11:03:02 +01:00
|
|
|
|
`(;; Generate position independent code suitable for dynamic libraries
|
|
|
|
|
;; and use WALL timer to get more accurate timing.
|
|
|
|
|
"-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
|
|
|
|
|
;; Set word width.
|
|
|
|
|
"-b"
|
|
|
|
|
,,(if (string-match "64" (%current-system))
|
|
|
|
|
"64"
|
|
|
|
|
"32")
|
|
|
|
|
;; Disable parallel build as it gives errors: atlas_pthread.h is
|
|
|
|
|
;; needed to compile C files before it is generated.
|
|
|
|
|
"-Ss" "pmake" "make -j 1"
|
2014-11-22 16:42:41 +01:00
|
|
|
|
;; Probe is failing for MIPS. We therefore define the system
|
|
|
|
|
;; architecture explicitly by setting (-A) MACHINETYPE = 49
|
|
|
|
|
;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
|
|
|
|
|
,,@(if (string-prefix? "mips" (%current-system))
|
|
|
|
|
(list "-A" "49" "-V" "1")
|
|
|
|
|
(list))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
;; Generate shared libraries.
|
|
|
|
|
"--shared"
|
|
|
|
|
;; Build a full LAPACK library.
|
|
|
|
|
,(string-append "--with-netlib-lapack-tarfile="
|
|
|
|
|
(assoc-ref %build-inputs "lapack-tar")))
|
|
|
|
|
#:phases
|
2016-08-19 15:16:06 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'install 'install-doc
|
|
|
|
|
(lambda* (#:key outputs inputs #:allow-other-keys)
|
|
|
|
|
(let ((doc (string-append (assoc-ref outputs "doc")
|
|
|
|
|
"/share/doc/atlas")))
|
|
|
|
|
(mkdir-p doc)
|
|
|
|
|
(fold (lambda (file previous)
|
|
|
|
|
(and previous (zero? (system* "cp" file doc))))
|
|
|
|
|
#t (find-files "../ATLAS/doc" ".*")))))
|
|
|
|
|
(add-after 'check 'check-pt
|
|
|
|
|
(lambda _ (zero? (system* "make" "ptcheck"))))
|
|
|
|
|
;; Fix files required to run configure.
|
|
|
|
|
(add-before 'configure 'fix-/bin/sh
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(lambda _
|
|
|
|
|
;; Use `sh', not `/bin/sh'.
|
|
|
|
|
(substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
|
|
|
|
|
(("/bin/sh")
|
2016-08-19 15:16:06 +02:00
|
|
|
|
"sh"))))
|
|
|
|
|
;; Fix /bin/sh in generated make files.
|
|
|
|
|
(add-after 'configure 'fix-/bin/sh-in-generated-files
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* (find-files "." "^[Mm]ake\\.inc.*")
|
|
|
|
|
(("/bin/sh")
|
|
|
|
|
"sh"))))
|
|
|
|
|
;; ATLAS configure program does not accepts the default flags
|
|
|
|
|
;; passed by the 'gnu-build-system'.
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda* (#:key native-inputs inputs outputs
|
|
|
|
|
(configure-flags '())
|
|
|
|
|
#:allow-other-keys #:rest args)
|
|
|
|
|
(let* ((prefix (assoc-ref outputs "out"))
|
|
|
|
|
(bash (or (and=> (assoc-ref
|
|
|
|
|
(or native-inputs inputs) "bash")
|
|
|
|
|
(cut string-append <> "/bin/bash"))
|
|
|
|
|
"/bin/sh"))
|
|
|
|
|
(flags `(,(string-append "--prefix=" prefix)
|
|
|
|
|
,@configure-flags))
|
|
|
|
|
(abs-srcdir (getcwd))
|
|
|
|
|
(srcdir (string-append "../" (basename abs-srcdir))))
|
|
|
|
|
(format #t "source directory: ~s (relative from build: ~s)~%"
|
|
|
|
|
abs-srcdir srcdir)
|
|
|
|
|
(mkdir "../build")
|
|
|
|
|
(chdir "../build")
|
|
|
|
|
(format #t "build directory: ~s~%" (getcwd))
|
|
|
|
|
(format #t "configure flags: ~s~%" flags)
|
|
|
|
|
(zero? (apply system* bash
|
|
|
|
|
(string-append srcdir "/configure")
|
|
|
|
|
flags))))))))
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(synopsis "Automatically Tuned Linear Algebra Software")
|
|
|
|
|
(description
|
|
|
|
|
"ATLAS is an automatically tuned linear algebra software library
|
|
|
|
|
providing C and Fortran77 interfaces to a portably efficient BLAS
|
|
|
|
|
implementation, as well as a few routines from LAPACK.
|
|
|
|
|
|
2014-10-28 10:17:55 +01:00
|
|
|
|
Optimization occurs at build time. For this reason, the library is built on
|
|
|
|
|
the machine where it is installed, without resorting to pre-built substitutes.
|
2014-10-26 11:03:02 +01:00
|
|
|
|
|
2014-10-28 10:17:55 +01:00
|
|
|
|
Before building the library, CPU throttling should be disabled. This can be
|
2016-07-19 04:45:20 +02:00
|
|
|
|
done in the BIOS, or, on GNU/Linux, with the following command:
|
2014-10-26 11:03:02 +01:00
|
|
|
|
|
2016-07-19 23:03:09 +02:00
|
|
|
|
@example
|
2016-07-19 04:45:20 +02:00
|
|
|
|
# cpupower --governor performance
|
2016-07-19 23:03:09 +02:00
|
|
|
|
@end example
|
2014-10-26 11:03:02 +01:00
|
|
|
|
|
2016-07-19 04:45:20 +02:00
|
|
|
|
Failure to do so will result in a library with poor performance.")
|
2014-10-26 11:03:02 +01:00
|
|
|
|
(license license:bsd-3)))
|
2015-03-14 17:36:07 +01:00
|
|
|
|
|
|
|
|
|
(define-public glm
|
|
|
|
|
(package
|
|
|
|
|
(name "glm")
|
2018-07-28 17:55:04 +02:00
|
|
|
|
(version "0.9.9.0")
|
2015-03-14 17:36:07 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2018-07-28 17:55:04 +02:00
|
|
|
|
(uri (string-append "https://github.com/g-truc/glm/releases/download/"
|
|
|
|
|
version "/glm-" version ".zip"))
|
2015-03-14 17:36:07 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-07-28 17:55:04 +02:00
|
|
|
|
"0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1"))))
|
2015-03-14 17:36:07 +01:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("unzip" ,unzip)))
|
2018-07-28 17:56:59 +02:00
|
|
|
|
(home-page "https://glm.g-truc.net/")
|
2015-03-14 17:36:07 +01:00
|
|
|
|
(synopsis "OpenGL Mathematics library")
|
|
|
|
|
(description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
|
|
|
|
|
library for graphics software based on the OpenGL Shading Language (GLSL)
|
|
|
|
|
specifications.")
|
|
|
|
|
(license license:expat)))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
|
|
|
|
|
(define-public lpsolve
|
|
|
|
|
(package
|
|
|
|
|
(name "lpsolve")
|
2018-02-21 06:50:30 +01:00
|
|
|
|
(version "5.5.2.5")
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
|
|
|
|
|
"/lp_solve_" version "_source.tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-02-21 06:50:30 +01:00
|
|
|
|
"12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
|
|
|
|
|
(("^c=cc") "c=gcc")
|
|
|
|
|
;; Pretend to be on a 64 bit platform to obtain a common directory
|
|
|
|
|
;; name for the build results on all architectures; nothing else
|
|
|
|
|
;; seems to depend on it.
|
|
|
|
|
(("^PLATFORM=.*$") "PLATFORM=ux64\n")
|
|
|
|
|
|
|
|
|
|
;; The check for 'isnan' as it is written fails with
|
|
|
|
|
;; "non-floating-point argument in call to function
|
|
|
|
|
;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
|
|
|
|
|
;; definition, which in turn leads to bad things. Fix the feature
|
|
|
|
|
;; test.
|
|
|
|
|
(("isnan\\(0\\)") "isnan(0.)"))
|
|
|
|
|
#t))))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2018-02-21 05:15:55 +01:00
|
|
|
|
`(#:tests? #f ; no check target
|
2015-05-16 21:07:53 +02:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
2018-02-21 05:15:55 +01:00
|
|
|
|
(delete 'configure) ; no configure script
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(replace 'build
|
|
|
|
|
(lambda _
|
2018-02-21 05:15:55 +01:00
|
|
|
|
(with-directory-excursion "lpsolve55"
|
|
|
|
|
(invoke "bash" "ccc"))
|
|
|
|
|
(with-directory-excursion "lp_solve"
|
|
|
|
|
(invoke "bash" "ccc"))
|
|
|
|
|
#t))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(replace 'install
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin"))
|
|
|
|
|
(lib (string-append out "/lib"))
|
|
|
|
|
;; This is where LibreOffice expects to find the header
|
|
|
|
|
;; files, and where they are installed by Debian.
|
|
|
|
|
(include (string-append out "/include/lpsolve")))
|
2018-02-21 05:15:55 +01:00
|
|
|
|
(install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
|
|
|
|
|
(install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 22:22:22 +02:00
|
|
|
|
(install-file "lp_solve/bin/ux64/lp_solve" bin)
|
|
|
|
|
|
2015-05-16 21:07:53 +02:00
|
|
|
|
;; Install a subset of the header files as on Debian
|
|
|
|
|
;; (plus lp_bit.h, which matches the regular expression).
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 22:22:22 +02:00
|
|
|
|
(for-each (lambda (name)
|
|
|
|
|
(install-file name include))
|
|
|
|
|
(find-files "." "lp_[HMSa-z].*\\.h$"))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
(with-directory-excursion "shared"
|
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-28 22:22:22 +02:00
|
|
|
|
(for-each (lambda (name)
|
|
|
|
|
(install-file name include))
|
|
|
|
|
(find-files "." "\\.h$")))
|
2015-05-16 21:07:53 +02:00
|
|
|
|
#t))))))
|
|
|
|
|
(home-page "http://lpsolve.sourceforge.net/")
|
|
|
|
|
(synopsis "Mixed integer linear programming (MILP) solver")
|
|
|
|
|
(description
|
|
|
|
|
"lp_solve is a mixed integer linear programming solver based on the
|
|
|
|
|
revised simplex and the branch-and-bound methods.")
|
|
|
|
|
(license license:lgpl2.1+)))
|
2015-06-23 11:05:11 +02:00
|
|
|
|
|
|
|
|
|
(define-public dealii
|
|
|
|
|
(package
|
|
|
|
|
(name "dealii")
|
2017-10-25 02:19:55 +02:00
|
|
|
|
(version "8.5.1")
|
2015-06-23 11:05:11 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/dealii/dealii/releases/"
|
|
|
|
|
"download/v" version "/dealii-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-10-25 02:19:55 +02:00
|
|
|
|
"1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
|
2015-06-23 11:05:11 +02:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
'(begin
|
|
|
|
|
(delete-file-recursively "bundled")
|
|
|
|
|
#t))))
|
2015-06-23 11:05:11 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("tbb" ,tbb)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("boost" ,boost)
|
|
|
|
|
("p4est" ,p4est)
|
|
|
|
|
("blas" ,openblas)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("arpack" ,arpack-ng)
|
|
|
|
|
("muparser" ,muparser)
|
|
|
|
|
("gfortran" ,gfortran)
|
|
|
|
|
("suitesparse" ,suitesparse))) ;for UMFPACK
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
|
2017-08-09 08:08:10 +02:00
|
|
|
|
#:configure-flags
|
|
|
|
|
;; Work around a bug in libsuitesparseconfig linking
|
|
|
|
|
;; see https://github.com/dealii/dealii/issues/4745
|
|
|
|
|
'("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
|
2015-06-23 11:05:11 +02:00
|
|
|
|
(home-page "https://www.dealii.org")
|
|
|
|
|
(synopsis "Finite element library")
|
|
|
|
|
(description
|
|
|
|
|
"Deal.II is a C++ program library targeted at the computational solution
|
|
|
|
|
of partial differential equations using adaptive finite elements. The main
|
|
|
|
|
aim of deal.II is to enable rapid development of modern finite element codes,
|
|
|
|
|
using among other aspects adaptive meshes and a wide array of tools often used
|
|
|
|
|
in finite element programs.")
|
|
|
|
|
(license license:lgpl2.1+)))
|
|
|
|
|
|
|
|
|
|
(define-public dealii-openmpi
|
|
|
|
|
(package (inherit dealii)
|
|
|
|
|
(name "dealii-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
;;Supported only with MPI:
|
|
|
|
|
("p4est" ,p4est-openmpi)
|
|
|
|
|
("petsc" ,petsc-openmpi)
|
|
|
|
|
("slepc" ,slepc-openmpi)
|
|
|
|
|
("metis" ,metis) ;for MUMPS
|
|
|
|
|
("scalapack" ,scalapack) ;for MUMPS
|
|
|
|
|
("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
|
|
|
|
|
("arpack" ,arpack-ng-openmpi)
|
|
|
|
|
,@(fold alist-delete (package-inputs dealii)
|
|
|
|
|
'("p4est" "arpack"))))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments dealii)
|
|
|
|
|
((#:configure-flags cf)
|
|
|
|
|
``("-DMPI_C_COMPILER=mpicc"
|
|
|
|
|
"-DMPI_CXX_COMPILER=mpicxx"
|
|
|
|
|
"-DMPI_Fortran_COMPILER=mpifort"
|
|
|
|
|
,@,cf))))
|
|
|
|
|
(synopsis "Finite element library (with MPI support)")))
|
2015-09-06 19:34:09 +02:00
|
|
|
|
|
|
|
|
|
(define-public flann
|
|
|
|
|
(package
|
|
|
|
|
(name "flann")
|
|
|
|
|
(version "1.8.4")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri
|
|
|
|
|
(string-append
|
|
|
|
|
"http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
|
|
|
|
|
version "-src.zip"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-06-12 09:26:40 +02:00
|
|
|
|
"022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
|
|
|
|
|
(patches (search-patches "flann-cmake-3.11.patch"))))
|
2015-09-06 19:34:09 +02:00
|
|
|
|
(build-system cmake-build-system)
|
2017-04-06 18:13:30 +02:00
|
|
|
|
(outputs '("out"
|
|
|
|
|
"octave")) ;46 MiB .mex file that pulls Octave
|
2015-09-06 19:34:09 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("unzip" ,unzip)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("hdf5" ,hdf5)
|
|
|
|
|
("octave" ,octave)
|
|
|
|
|
("python" ,python-2) ; print syntax
|
|
|
|
|
;; ("python2-numpy" ,python2-numpy) ; only required for the tests
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(arguments
|
2016-05-19 11:47:27 +02:00
|
|
|
|
`(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
|
|
|
|
|
;; taken 46 MiB unstripped, and 6 MiB stripped.
|
|
|
|
|
#:strip-directories '("lib" "lib64" "libexec"
|
|
|
|
|
"bin" "sbin" "share/flann/octave")
|
|
|
|
|
|
2016-05-19 14:50:22 +02:00
|
|
|
|
;; Save 12 MiB by not installing .a files. Passing
|
|
|
|
|
;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
2017-04-06 18:13:30 +02:00
|
|
|
|
(add-before 'configure 'set-octave-directory
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; Install the .mex file in the "octave" output.
|
|
|
|
|
(let ((out (assoc-ref outputs "octave")))
|
|
|
|
|
(substitute* "src/matlab/CMakeLists.txt"
|
|
|
|
|
(("share/flann/octave")
|
|
|
|
|
(string-append out "/share/flann/octave")))
|
|
|
|
|
#t)))
|
2016-05-19 14:50:22 +02:00
|
|
|
|
(add-after 'install 'remove-static-libraries
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(lib (string-append out "/lib")))
|
|
|
|
|
(for-each delete-file
|
|
|
|
|
(find-files lib "\\.a$"))
|
|
|
|
|
#t))))
|
|
|
|
|
|
2016-05-19 11:47:27 +02:00
|
|
|
|
#:tests? #f)) ; The test data are downloaded from the Internet.
|
2015-09-06 19:34:09 +02:00
|
|
|
|
(home-page "http://www.cs.ubc.ca/research/flann/")
|
|
|
|
|
(synopsis "Library for approximate nearest neighbors computation")
|
|
|
|
|
(description "FLANN is a library for performing fast approximate
|
|
|
|
|
nearest neighbor searches in high dimensional spaces. It implements a
|
|
|
|
|
collection of algorithms and a system for automatically choosing the best
|
|
|
|
|
algorithm and optimum parameters depending on the dataset.
|
|
|
|
|
|
|
|
|
|
FLANN is written in C++ and contains bindings for C, Octave and Python.")
|
|
|
|
|
(license (license:non-copyleft "file://COPYING"
|
|
|
|
|
"See COPYING in the distribution."))))
|
2015-11-06 13:43:15 +01:00
|
|
|
|
|
|
|
|
|
(define-public wcalc
|
|
|
|
|
(package
|
|
|
|
|
(name "wcalc")
|
|
|
|
|
(version "2.5")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2016-07-21 08:35:30 +02:00
|
|
|
|
(uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
|
|
|
|
|
"wcalc-" version ".tar.bz2"))
|
2015-11-06 13:43:15 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpfr" ,mpfr)
|
|
|
|
|
("readline" ,readline)))
|
|
|
|
|
(home-page "http://w-calc.sourceforge.net/index.php")
|
|
|
|
|
(synopsis "Flexible command-line scientific calculator")
|
|
|
|
|
(description "Wcalc is a very capable calculator. It has standard functions
|
|
|
|
|
(sin, asin, and sinh for example, in either radians or degrees), many
|
|
|
|
|
pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
|
|
|
|
|
variables, a command history, hex/octal/binary input and output, unit
|
|
|
|
|
conversions, embedded comments, and an expandable expression entry field. It
|
|
|
|
|
evaluates expressions using the standard order of operations.")
|
|
|
|
|
(license license:gpl2+)))
|
2015-12-15 21:00:38 +01:00
|
|
|
|
|
|
|
|
|
(define-public xaos
|
|
|
|
|
(package
|
|
|
|
|
(name "xaos")
|
|
|
|
|
(version "3.6")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
2016-07-21 08:35:30 +02:00
|
|
|
|
(uri (string-append "mirror://sourceforge/xaos/XaoS/" version
|
|
|
|
|
"/xaos-" version ".tar.gz"))
|
2015-12-15 21:00:38 +01:00
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
|
|
|
|
|
(build-system gnu-build-system)
|
2016-09-25 09:33:02 +02:00
|
|
|
|
(native-inputs `(("gettext" ,gettext-minimal)))
|
2015-12-15 21:00:38 +01:00
|
|
|
|
(inputs `(("libx11" ,libx11)
|
|
|
|
|
("zlib" ,zlib)
|
|
|
|
|
("libpng" ,libpng)
|
|
|
|
|
("gsl" ,gsl)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ;no "check" target
|
|
|
|
|
#:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
|
|
|
|
|
(synopsis "Real-time fractal zoomer")
|
|
|
|
|
(description "GNU XaoS is a graphical program that generates fractal
|
|
|
|
|
patterns and allows you to zoom in and out of them infinitely in a fluid,
|
|
|
|
|
continuous manner. It also includes tutorials that help to explain how fractals
|
|
|
|
|
are built. It can generate many different fractal types such as the Mandelbrot
|
|
|
|
|
set.")
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/xaos/")
|
2015-12-15 21:00:38 +01:00
|
|
|
|
(license license:gpl2+)))
|
2016-03-17 15:15:18 +01:00
|
|
|
|
|
|
|
|
|
(define-public hypre
|
|
|
|
|
(package
|
|
|
|
|
(name "hypre")
|
|
|
|
|
(version "2.11.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/LLNL/hypre/archive/"
|
|
|
|
|
"v" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
|
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Remove use of __DATE__ and __TIME__ for reproducibility;
|
|
|
|
|
;; substitute the tarball creation time.
|
|
|
|
|
(substitute* "src/utilities/HYPRE_utilities.h"
|
|
|
|
|
(("Date Compiled: .*$")
|
|
|
|
|
"Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
|
|
|
|
|
#t))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(outputs '("out" ;6.1 MiB of headers and libraries
|
|
|
|
|
"doc")) ;4.8 MiB of documentation
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("doc++" ,doc++)
|
|
|
|
|
("netpbm" ,netpbm)
|
2018-05-12 16:32:52 +02:00
|
|
|
|
("perl" ,perl) ;needed to run 'ppmquant' during tests
|
2016-03-17 15:15:18 +01:00
|
|
|
|
("texlive" ,texlive) ;full package required for fonts
|
|
|
|
|
("ghostscript" ,ghostscript)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("blas" ,openblas)
|
|
|
|
|
("lapack" ,lapack)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:modules ((srfi srfi-1)
|
|
|
|
|
,@%gnu-build-system-modules)
|
|
|
|
|
#:configure-flags '("--enable-shared"
|
|
|
|
|
"--disable-fortran"
|
|
|
|
|
"--without-MPI"
|
|
|
|
|
"--with-openmp"
|
|
|
|
|
"--with-fei"
|
|
|
|
|
"--with-lapack"
|
|
|
|
|
"--with-blas")
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'chdir-src
|
|
|
|
|
(lambda _ (chdir "src")))
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda* (#:key build target configure-flags
|
|
|
|
|
#:allow-other-keys #:rest args)
|
|
|
|
|
(let* ((configure (assoc-ref %standard-phases 'configure)))
|
|
|
|
|
(apply configure
|
|
|
|
|
(append args
|
|
|
|
|
(list #:configure-flags
|
|
|
|
|
(cons (string-append
|
|
|
|
|
"--host=" (or target build))
|
|
|
|
|
configure-flags)))))))
|
|
|
|
|
(add-after 'build 'build-docs
|
|
|
|
|
(lambda _
|
|
|
|
|
(zero? (system* "make" "-Cdocs" "pdf" "html"))))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
|
|
|
|
|
(setenv "PATH" (string-append "." ":" (getenv "PATH")))
|
|
|
|
|
(and (system* "make" "check" "CHECKRUN=")
|
|
|
|
|
(fold (lambda (filename result)
|
|
|
|
|
(and result
|
|
|
|
|
(let ((size (stat:size (stat filename))))
|
|
|
|
|
(when (not (zero? size))
|
|
|
|
|
(format #t "~a size ~d; error indication~%"
|
|
|
|
|
filename size))
|
|
|
|
|
(zero? size))))
|
|
|
|
|
#t
|
|
|
|
|
(find-files "test" ".*\\.err$")))))
|
|
|
|
|
(add-after 'install 'install-docs
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; Custom install because docs/Makefile doesn't honor ${docdir}.
|
|
|
|
|
(let* ((doc (assoc-ref outputs "doc"))
|
|
|
|
|
(docdir (string-append doc "/share/doc/hypre-" ,version)))
|
|
|
|
|
(with-directory-excursion "docs"
|
|
|
|
|
(for-each (lambda (base)
|
|
|
|
|
(install-file (string-append base ".pdf") docdir)
|
|
|
|
|
(copy-recursively base docdir)) ;html docs
|
|
|
|
|
'("HYPRE_usr_manual"
|
|
|
|
|
"HYPRE_ref_manual")))
|
|
|
|
|
#t))))))
|
|
|
|
|
(home-page "http://www.llnl.gov/casc/hypre/")
|
|
|
|
|
(synopsis "Library of solvers and preconditioners for linear equations")
|
|
|
|
|
(description
|
|
|
|
|
"HYPRE is a software library of high performance preconditioners and
|
|
|
|
|
solvers for the solution of large, sparse linear systems of equations. It
|
|
|
|
|
features multigrid solvers for both structured and unstructured grid
|
|
|
|
|
problems.")
|
|
|
|
|
(license license:lgpl2.1)))
|
|
|
|
|
|
|
|
|
|
(define-public hypre-openmpi
|
|
|
|
|
(package (inherit hypre)
|
|
|
|
|
(name "hypre-openmpi")
|
|
|
|
|
(inputs
|
|
|
|
|
`(("mpi" ,openmpi)
|
|
|
|
|
,@(package-inputs hypre)))
|
|
|
|
|
(arguments
|
|
|
|
|
(substitute-keyword-arguments (package-arguments hypre)
|
|
|
|
|
((#:configure-flags flags)
|
|
|
|
|
``("--with-MPI"
|
2018-05-12 17:53:54 +02:00
|
|
|
|
,@(delete "--without-MPI" ,flags)))
|
|
|
|
|
((#:phases phases)
|
|
|
|
|
`(modify-phases ,phases
|
|
|
|
|
(add-before 'check 'set-test-environment
|
|
|
|
|
(lambda _
|
|
|
|
|
;; By default, running the test suite would fail because 'ssh'
|
|
|
|
|
;; could not be found in $PATH. Define this variable to
|
|
|
|
|
;; placate Open MPI without adding a dependency on OpenSSH (the
|
|
|
|
|
;; agent isn't used anyway.)
|
|
|
|
|
(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
|
|
|
|
|
#t))))))
|
2016-03-17 15:15:18 +01:00
|
|
|
|
(synopsis "Parallel solvers and preconditioners for linear equations")
|
|
|
|
|
(description
|
|
|
|
|
"HYPRE is a software library of high performance preconditioners and
|
|
|
|
|
solvers for the solution of large, sparse linear systems of equations on
|
|
|
|
|
parallel computers. It features parallel multigrid solvers for both
|
|
|
|
|
structured and unstructured grid problems.")))
|
2016-04-12 16:59:26 +02:00
|
|
|
|
|
|
|
|
|
(define-public matio
|
|
|
|
|
(package
|
|
|
|
|
(name "matio")
|
|
|
|
|
(version "1.5.6")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
2016-07-21 08:35:30 +02:00
|
|
|
|
(uri (string-append "mirror://sourceforge/matio/matio/" version "/"
|
2016-04-12 16:59:26 +02:00
|
|
|
|
"matio-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("zlib" ,zlib)
|
|
|
|
|
("hdf5" ,hdf5)))
|
|
|
|
|
(home-page "http://matio.sourceforge.net/")
|
|
|
|
|
(synopsis "Library for reading and writing MAT files")
|
|
|
|
|
(description "Matio is a library for reading and writing MAT files. It
|
|
|
|
|
supports compressed MAT files, as well as newer (version 7.3) MAT files.")
|
|
|
|
|
(license license:bsd-2)))
|
2016-07-07 21:41:41 +02:00
|
|
|
|
|
2016-09-30 19:38:20 +02:00
|
|
|
|
(define-public vc
|
|
|
|
|
(package
|
|
|
|
|
(name "vc")
|
2017-12-29 23:36:41 +01:00
|
|
|
|
(version "1.3.3")
|
2016-09-30 19:38:20 +02:00
|
|
|
|
(source
|
|
|
|
|
(origin (method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/VcDevel/Vc/releases/"
|
|
|
|
|
"download/" version "/Vc-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-12-29 23:36:41 +01:00
|
|
|
|
"1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
|
2016-09-30 19:38:20 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:configure-flags
|
2018-04-08 21:53:22 +02:00
|
|
|
|
'("-DBUILD_TESTING=ON"
|
|
|
|
|
;; By default, Vc will optimize for the CPU of the build machine.
|
|
|
|
|
;; Setting this to "none" makes it create portable binaries. See
|
|
|
|
|
;; "cmake/OptimizeForArchitecture.cmake".
|
|
|
|
|
"-DTARGET_ARCHITECTURE=none")))
|
2016-09-30 19:38:20 +02:00
|
|
|
|
(synopsis "SIMD vector classes for C++")
|
|
|
|
|
(description "Vc provides portable, zero-overhead C++ types for explicitly
|
|
|
|
|
data-parallel programming. It is a library designed to ease explicit
|
|
|
|
|
vectorization of C++ code. Its types enable explicitly stating data-parallel
|
|
|
|
|
operations on multiple values. The parallelism is therefore added via the type
|
|
|
|
|
system. Vc has an intuitive API and provides portability between different
|
|
|
|
|
compilers and compiler versions as well as portability between different vector
|
|
|
|
|
instruction sets. Thus, an application written with Vc can be compiled for:
|
|
|
|
|
@enumerate
|
|
|
|
|
@item AVX and AVX2
|
2017-04-16 18:06:57 +02:00
|
|
|
|
@item SSE2 up to SSE4.2 or SSE4a
|
2016-09-30 19:38:20 +02:00
|
|
|
|
@item Scalar
|
|
|
|
|
@item MIC
|
|
|
|
|
@item NEON (in development)
|
|
|
|
|
@item NVIDIA GPUs / CUDA (in development)
|
|
|
|
|
@end enumerate\n")
|
|
|
|
|
(home-page "https://github.com/VcDevel/Vc")
|
2017-08-03 12:34:18 +02:00
|
|
|
|
;; "No support_???.cpp file exists for this architecture."
|
|
|
|
|
(supported-systems '("x86_64-linux" "i686-linux"))
|
2016-09-30 19:38:20 +02:00
|
|
|
|
(license license:bsd-3)))
|
2017-01-30 07:27:53 +01:00
|
|
|
|
|
|
|
|
|
(define-public reducelcs
|
|
|
|
|
;; This is the last commit which is available upstream, no
|
|
|
|
|
;; release happened since 2010.
|
|
|
|
|
(let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
|
|
|
|
|
(revision "1"))
|
|
|
|
|
(package
|
|
|
|
|
(name "reducelcs")
|
|
|
|
|
(version (string-append "1.0-" revision "." (string-take commit 7)))
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method git-fetch)
|
|
|
|
|
(uri (git-reference
|
|
|
|
|
(url "https://github.com/gdv/Reduce-Expand-for-LCS")
|
|
|
|
|
(commit commit)))
|
|
|
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(inputs
|
|
|
|
|
`(("openlibm" ,openlibm)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:tests? #f ; no tests
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(delete 'configure) ; No configure script exists.
|
|
|
|
|
(replace 'install ; No install phase exists.
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
|
|
|
(bin (string-append out "/bin")))
|
|
|
|
|
(install-file "Approximation" bin)
|
|
|
|
|
(install-file "CollectResults" bin)
|
|
|
|
|
(install-file "GenerateInstances" bin)
|
|
|
|
|
#t))))))
|
|
|
|
|
(synopsis "Approximate Longest Commons Subsequence computation tool")
|
|
|
|
|
(description
|
|
|
|
|
"@code{reduceLCS} is an implementation of the Reduce-Expand
|
|
|
|
|
algorithm for LCS. It is a fast program to compute the approximate
|
|
|
|
|
Longest Commons Subsequence of a set of strings.")
|
|
|
|
|
(home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
|
2017-01-30 07:27:53 +01:00
|
|
|
|
(license license:gpl3+))))
|
2017-02-26 20:28:48 +01:00
|
|
|
|
|
|
|
|
|
(define-public jacal
|
|
|
|
|
(package
|
|
|
|
|
(name "jacal")
|
|
|
|
|
(version "1c4")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
|
|
|
|
|
version ".zip"))
|
|
|
|
|
(sha256 (base32
|
|
|
|
|
"055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
|
|
|
|
|
(patches (search-patches "jacal-fix-texinfo.patch"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'build 'pre-build
|
|
|
|
|
;; Don't use upstream's script - it really doesn't fit into
|
|
|
|
|
;; Guix's functional paradigm.
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(substitute* "Makefile"
|
|
|
|
|
(("^install: install-script") "install: "))))
|
|
|
|
|
(add-after 'install 'post-install
|
|
|
|
|
;; Instead, we provide our own simplified script.
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(let ((wrapper (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/bin/jacal")))
|
|
|
|
|
(format (open wrapper (logior O_WRONLY O_CREAT))
|
|
|
|
|
(string-append "#!~a\nexec ~a/bin/scm -ip1 "
|
|
|
|
|
"-e '(slib:load \"~a/lib/jacal/math\") "
|
|
|
|
|
"(math)' \"$@\"\n")
|
|
|
|
|
(which "bash")
|
|
|
|
|
(assoc-ref inputs "scm")
|
|
|
|
|
(assoc-ref outputs "out"))
|
|
|
|
|
(chmod wrapper #o555))))
|
|
|
|
|
(replace 'configure
|
|
|
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
|
|
|
(zero? (system* "./configure"
|
|
|
|
|
(string-append "--prefix="
|
|
|
|
|
(assoc-ref outputs "out")))))))))
|
|
|
|
|
(inputs `(("scm" ,scm)))
|
|
|
|
|
(native-inputs `(("unzip" ,unzip)
|
|
|
|
|
("texinfo" ,texinfo)))
|
|
|
|
|
(synopsis "Symbolic mathematics system")
|
|
|
|
|
(description "GNU JACAL is an interactive symbolic mathematics program based on
|
|
|
|
|
Scheme. It manipulate and simplify a range of mathematical expressions such
|
|
|
|
|
as equations, scalars, vectors, and matrices.")
|
2017-03-30 00:48:16 +02:00
|
|
|
|
(home-page "https://www.gnu.org/software/jacal/")
|
2017-02-26 20:28:48 +01:00
|
|
|
|
(license license:gpl3+)))
|
|
|
|
|
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(define-public z3
|
|
|
|
|
(package
|
|
|
|
|
(name "z3")
|
|
|
|
|
(version "4.5.0")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/Z3Prover/z3/archive/z3-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
|
2017-08-02 12:10:12 +02:00
|
|
|
|
(build-system cmake-build-system)
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(arguments
|
2017-08-02 12:10:12 +02:00
|
|
|
|
`(#:configure-flags
|
|
|
|
|
(list "-DBUILD_PYTHON_BINDINGS=true"
|
|
|
|
|
"-DINSTALL_PYTHON_BINDINGS=true"
|
|
|
|
|
(string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
|
|
|
|
|
%output
|
2017-12-19 15:25:12 +01:00
|
|
|
|
"/lib/python2.7/site-packages"))
|
2017-07-25 18:11:12 +02:00
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
2017-08-02 12:10:12 +02:00
|
|
|
|
(add-before 'configure 'bootstrap
|
|
|
|
|
(lambda _
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(zero?
|
2017-08-02 12:10:12 +02:00
|
|
|
|
(system* "python" "contrib/cmake/bootstrap.py" "create"))))
|
|
|
|
|
(add-before 'check 'make-test-z3
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(lambda _
|
2017-08-02 12:10:12 +02:00
|
|
|
|
;; Build the test suite executable.
|
|
|
|
|
(zero? (system* "make" "test-z3" "-j"
|
|
|
|
|
(number->string (parallel-job-count))))))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
;; Run all the tests that don't require arguments.
|
|
|
|
|
(zero? (system* "./test-z3" "/a")))))))
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(native-inputs
|
|
|
|
|
`(("python" ,python-2)))
|
|
|
|
|
(synopsis "Theorem prover")
|
|
|
|
|
(description "Z3 is a theorem prover and @dfn{satisfiability modulo
|
2017-08-02 12:10:12 +02:00
|
|
|
|
theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
|
2017-07-25 18:11:12 +02:00
|
|
|
|
(home-page "https://github.com/Z3Prover/z3")
|
|
|
|
|
(license license:expat)))
|
2017-07-30 10:23:08 +02:00
|
|
|
|
|
|
|
|
|
(define-public cubicle
|
|
|
|
|
(package
|
|
|
|
|
(name "cubicle")
|
|
|
|
|
(version "1.1.1")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://cubicle.lri.fr/cubicle-"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("ocaml" ,ocaml)
|
2017-08-07 01:52:31 +02:00
|
|
|
|
("which" ,(@@ (gnu packages base) which))))
|
2017-07-30 10:23:08 +02:00
|
|
|
|
(propagated-inputs
|
|
|
|
|
`(("z3" ,z3)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:configure-flags (list "--with-z3")
|
|
|
|
|
#:tests? #f
|
|
|
|
|
#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-before 'configure 'configure-for-release
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "Makefile.in"
|
|
|
|
|
(("SVNREV=") "#SVNREV="))))
|
|
|
|
|
(add-before 'configure 'fix-/bin/sh
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "configure"
|
|
|
|
|
(("/bin/sh") (which "sh")))))
|
|
|
|
|
(add-before 'configure 'fix-smt-z3wrapper.ml
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "Makefile.in"
|
|
|
|
|
(("\\\\n") "")))))))
|
|
|
|
|
(home-page "http://cubicle.lri.fr/")
|
|
|
|
|
(synopsis "Model checker for array-based systems")
|
2017-11-08 15:41:41 +01:00
|
|
|
|
(description "Cubicle is a model checker for verifying safety properties
|
|
|
|
|
of array-based systems. This is a syntactically restricted class of
|
|
|
|
|
parametrized transition systems with states represented as arrays indexed by
|
|
|
|
|
an arbitrary number of processes. Cache coherence protocols and mutual
|
|
|
|
|
exclusion algorithms are typical examples of such systems.")
|
2017-07-30 10:23:08 +02:00
|
|
|
|
(license license:asl2.0)))
|
2018-01-31 23:56:10 +01:00
|
|
|
|
|
|
|
|
|
(define-public elemental
|
|
|
|
|
(package
|
|
|
|
|
(name "elemental")
|
|
|
|
|
(version "0.87.7")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/elemental/Elemental/"
|
|
|
|
|
"archive/v" version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(home-page "http://libelemental.org")
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("blas" ,openblas)
|
|
|
|
|
("gfortran:lib" ,gfortran "lib")
|
|
|
|
|
("gmp" ,gmp)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("metis" ,metis)
|
|
|
|
|
("mpc" ,mpc)
|
|
|
|
|
("mpfr" ,mpfr)
|
|
|
|
|
("mpi" ,openmpi)
|
|
|
|
|
("qd" ,qd)))
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:build-type "Release" ;default RelWithDebInfo not supported
|
|
|
|
|
#:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
|
|
|
|
|
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
|
|
|
|
|
"-DEL_CACHE_WARNINGS:BOOL=YES"
|
|
|
|
|
"-DEL_TESTS:BOOL=YES"
|
|
|
|
|
"-DCMAKE_INSTALL_LIBDIR=lib"
|
|
|
|
|
"-DGFORTRAN_LIB=gfortran")
|
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
|
|
|
(add-before 'check 'setup-tests
|
|
|
|
|
(lambda _
|
|
|
|
|
;; Parallelism is done at the MPI layer.
|
|
|
|
|
(setenv "OMP_NUM_THREADS" "1")
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'install 'remove-tests
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
;; Tests are installed, with no easy configuration
|
|
|
|
|
;; switch to prevent this, so delete them.
|
|
|
|
|
(delete-file-recursively
|
|
|
|
|
(string-append (assoc-ref outputs "out") "/bin"))
|
|
|
|
|
#t)))))
|
|
|
|
|
(synopsis "Dense and sparse-direct linear algebra and optimization")
|
|
|
|
|
(description "Elemental is a modern C++ library for distributed-memory
|
|
|
|
|
dense and sparse-direct linear algebra, conic optimization, and lattice
|
|
|
|
|
reduction.")
|
|
|
|
|
(license license:bsd-2)))
|
2018-02-08 08:50:06 +01:00
|
|
|
|
|
|
|
|
|
(define-public mcrl2
|
|
|
|
|
(package
|
|
|
|
|
(name "mcrl2")
|
|
|
|
|
(version "201707.1.15162")
|
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
|
|
|
|
|
version
|
|
|
|
|
".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("subversion" ,subversion)))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("boost" ,boost)
|
|
|
|
|
("glu" ,glu)
|
|
|
|
|
("mesa" ,mesa)
|
2018-07-29 14:32:22 +02:00
|
|
|
|
("qtbase" ,qtbase)))
|
2018-02-08 08:50:06 +01:00
|
|
|
|
(build-system cmake-build-system)
|
2018-02-08 14:42:32 +01:00
|
|
|
|
(synopsis "Toolset for the mCRL2 formal specification language")
|
2018-02-08 08:50:06 +01:00
|
|
|
|
(description
|
2018-02-08 14:42:32 +01:00
|
|
|
|
"@dfn{mCRL2} (micro Common Representation Language 2) is a formal
|
|
|
|
|
specification language for describing concurrent discrete event systems. Its
|
|
|
|
|
toolset supports analysis and automatic verification, linearisation, simulation,
|
|
|
|
|
state-space exploration and generation, and tools to optimise and analyse
|
2018-02-08 08:50:06 +01:00
|
|
|
|
specifications. Also, state spaces can be manipulated, visualised and
|
|
|
|
|
analysed.")
|
|
|
|
|
(home-page "http://mcrl2.org")
|
|
|
|
|
(license license:boost1.0)))
|
2018-02-17 22:47:57 +01:00
|
|
|
|
|
|
|
|
|
(define-public r-subplex
|
|
|
|
|
(package
|
|
|
|
|
(name "r-subplex")
|
2018-04-21 08:33:17 +02:00
|
|
|
|
(version "1.5-4")
|
2018-02-17 22:47:57 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "subplex" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-04-21 08:33:17 +02:00
|
|
|
|
"10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
|
2018-02-17 22:47:57 +01:00
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(home-page "https://cran.r-project.org/web/packages/subplex")
|
|
|
|
|
(synopsis "Unconstrained optimization using the subplex algorithm")
|
|
|
|
|
(description "This package implements the Subplex optimization algorithm.
|
|
|
|
|
It solves unconstrained optimization problems using a simplex method on
|
|
|
|
|
subspaces. The method is well suited for optimizing objective functions that
|
|
|
|
|
are noisy or are discontinuous at the solution.")
|
|
|
|
|
(license license:gpl3+)))
|
2018-02-17 22:55:07 +01:00
|
|
|
|
|
|
|
|
|
(define-public r-desolve
|
|
|
|
|
(package
|
|
|
|
|
(name "r-desolve")
|
2018-05-16 15:44:17 +02:00
|
|
|
|
(version "1.21")
|
2018-02-17 22:55:07 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "deSolve" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-05-16 15:44:17 +02:00
|
|
|
|
"0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
|
2018-02-17 22:55:07 +01:00
|
|
|
|
(properties `((upstream-name . "deSolve")))
|
|
|
|
|
(build-system r-build-system)
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("gfortran" ,gfortran)))
|
|
|
|
|
(home-page "https://desolve.r-forge.r-project.org/")
|
|
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(synopsis "Solvers for initial value problems of differential equations")
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(description "This package provides functions that solve initial
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value problems of a system of first-order ordinary differential equations (ODE),
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of partial differential equations (PDE), of differential algebraic equations
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(DAE), and of delay differential equations. The functions provide an interface
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to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
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to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
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the Runge-Kutta family with fixed or variable time steps. The package contains
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routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
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differential equations (PDE) that have been converted to ODEs by numerical
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differencing.")
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(license license:gpl2+)))
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2018-03-28 02:42:15 +02:00
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(define-public tcalc
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(package
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(name "tcalc")
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(version "2.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
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version ".tar.gz"))
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(sha256
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(base32
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"0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
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(build-system gnu-build-system)
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(synopsis "The terminal calculator")
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(description
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"The terminal calculator is a small program to help users of the GNU/Linux
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terminal do calculations simply and quickly. The formula to be calculated can
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be fed to @command{tcalc} through the command line.")
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(home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
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(license license:gpl3+)))
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