d6c2fc3729
*gnu/packages/simulation.scm (python-pygmsh): Update to 7.1.11. [source](snippet): Re-phrase comment.
975 lines
41 KiB
Scheme
975 lines
41 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
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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 simulation)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages admin)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bash)
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#:use-module (gnu packages bison)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cmake)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages gettext)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages m4)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages version-control)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xorg)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix svn-download)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (ice-9 ftw)
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#:use-module (ice-9 regex)
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#:use-module (srfi srfi-1))
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(define-public openfoam
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(package
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(name "openfoam")
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(version "4.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"http://dl.openfoam.org/source/"
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(string-map (lambda (x) (if (eq? x #\.) #\- x)) version)))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d"))
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(patches (search-patches "openfoam-4.1-cleanup.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides
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;; 'major' and 'minor'.
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(substitute* "src/OSspecific/POSIX/fileStat.C"
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(("#include <unistd\\.h>")
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"#include <unistd.h>\n#include <sys/sysmacros.h>\n"))
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#t))))
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(build-system gnu-build-system)
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|
(inputs
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`(("boost" ,boost)
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("cgal" ,cgal)
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("flex" ,flex)
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("git" ,git)
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("gmp" ,gmp)
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("libxt" ,libxt)
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("metis" ,metis)
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("mpfr" ,mpfr)
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("ncurses" ,ncurses)
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("readline" ,readline)
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("scotch" ,pt-scotch32)
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("zlib" ,zlib)))
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(native-inputs
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`(("bison" ,bison)))
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(propagated-inputs
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`(("gzip" ,gzip)
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("gnuplot" ,gnuplot)
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("openmpi" ,openmpi)))
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(outputs '("debug" ;~60MB
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"out"))
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(arguments
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`( ;; Executable files and shared libraries are located in the 'platforms'
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;; subdirectory.
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#:strip-directories (list (string-append
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"lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/bin")
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(string-append
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"lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib"))
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#:tests? #f ; no tests to run
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#:modules ((ice-9 ftw)
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(ice-9 regex)
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(guix build gnu-build-system)
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(guix build utils))
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#:phases (modify-phases %standard-phases
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(add-after 'unpack 'rename-build-directory
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(lambda _
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(chdir "..")
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;; Use 'OpenFOAM-version' convention to match the file
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;; name expectations in the build phase.
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(let ((unpack-dir (string-append
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(getcwd) "/"
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(list-ref (scandir (getcwd) (lambda (name)
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(string-match "^OpenFOAM" name))) 0)))
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(build-dir (string-append
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(getcwd) "/OpenFOAM-" ,version)))
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(rename-file unpack-dir build-dir) ; rename build directory
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(chdir (basename build-dir))) ; move to build directory
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#t))
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(delete 'configure) ; no configure phase
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(replace 'build
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(lambda _
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(let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))
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;; set variables to define store paths
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(for-each (lambda (library)
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(setenv (string-append
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(string-upcase library) "_ROOT")
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(assoc-ref %build-inputs library))) libraries))
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;; set variables to define package versions
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(setenv "SCOTCHVERSION" ,(package-version scotch))
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(setenv "METISVERSION" ,(package-version metis))
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;; set variable to pass extra 'rpath' arguments to linker
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(setenv "LDFLAGS"
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(string-append
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"-Wl,"
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"-rpath=" %output "/lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib,"
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"-rpath=" %output "/lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib/dummy"))
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;; compile OpenFOAM libraries and applications
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(zero? (system (format #f
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"source ./etc/bashrc && ./Allwmake -j~a"
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(parallel-job-count))))))
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(add-after 'build 'update-configuration-files
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(lambda _
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;; record store paths and package versions in
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;; configuration files
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(substitute* "etc/config.sh/CGAL"
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(("$BOOST_ROOT") (getenv "BOOST_ROOT")))
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(substitute* "etc/config.sh/CGAL"
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(("$CGAL_ROOT") (getenv "CGAL_ROOT")))
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(substitute* "etc/config.sh/metis"
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(("$METIS_ROOT") (getenv "METIS_ROOT")))
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(substitute* "etc/config.sh/metis"
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(("$METISVERSION") (getenv "METISVERSION")))
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(substitute* "etc/config.sh/scotch"
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(("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT")))
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(substitute* "etc/config.sh/scotch"
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(("$SCOTCHVERSION") (getenv "SCOTCHVERSION")))
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(substitute* "etc/config.sh/settings"
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(("$GMP_ROOT") (getenv "GMP_ROOT")))
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(substitute* "etc/config.sh/settings"
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(("$MPFR_ROOT") (getenv "MPFR_ROOT")))
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;; reset lockDir variable to refer to write-enabled
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;; directory
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(substitute* "wmake/wmake"
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((" lockDir=.*$")
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" lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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(substitute* "wmake/wmakeScheduler"
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(("lockDir=.*$")
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"lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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(substitute* "wmake/wmakeSchedulerUptime"
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(("lockDir=.*$")
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"lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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#t))
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(add-after 'build 'cleanup
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;; Avoid unncessary, voluminous object and dep files.
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(lambda _
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(delete-file-recursively
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"platforms/linux64GccDPInt32Opt/src")
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(delete-file-recursively
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"platforms/linux64GccDPInt32OptSYSTEMOPENMPI")
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(for-each delete-file (find-files "." "\\.o$"))
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#t))
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(replace 'install
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(lambda _
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;; use 'OpenFOAM-version' convention
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(let ((install-dir (string-append
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%output "/lib/OpenFOAM-" ,version)))
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(mkdir-p install-dir) ; create install directory
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;; move contents of build directory to install directory
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(copy-recursively "." install-dir))))
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(add-after 'install 'add-symbolic-link
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(lambda _
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;; add symbolic link for standard 'bin' directory
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(symlink
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(string-append "./lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/bin")
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(string-append %output "/bin"))
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#t)))))
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;; Note:
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;; Tutorial files are installed read-only in /gnu/store.
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;; To allow write permissions on files copied from the store a
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;; 'chmod' step is needed before running the applications. For
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;; example, from a user's login:
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;; $ source $GUIX_PROFILE/lib/OpenFOAM-4.1/etc/bashrc
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;; $ mkdir -p $FOAM_RUN
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;; $ cd $FOAM_RUN
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;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
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;; $ cd pitzDaily
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;; $ chmod -R u+w .
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;; $ blockMesh
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(synopsis "Framework for numerical simulation of fluid flow")
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(description "OpenFOAM provides a set of solvers and methods for tackling
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problems in the field of Computational Fluid Dynamics (CFD). It is written in
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C++. Governing equations such as the Navier-Stokes equations can be solved in
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integral form. Physical processes such as phase change, droplet transport and
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chemical reaction can be modelled. Numerical methods are included to deal with
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sharp gradients, such as those encountered in flows with shock waves and flows
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with gas/liquid interfaces. Large problems may be split into smaller, connected
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problems for efficient solution on parallel systems.")
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(license license:gpl3+)
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(home-page "https://openfoam.org")))
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(define-public python-fenics-dijitso
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(package
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(name "python-fenics-dijitso")
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(version "2019.1.0")
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(source
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|
(origin
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(method url-fetch)
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(uri (pypi-uri "fenics-dijitso" version))
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(sha256
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(base32
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"0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
|
|
(build-system python-build-system)
|
|
(inputs
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`(("openmpi" ,openmpi)
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("python-numpy" ,python-numpy)))
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(native-inputs
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`(("python-pytest-cov" ,python-pytest-cov)))
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|
(propagated-inputs
|
|
`(("python-mpi4py" ,python-mpi4py)))
|
|
(arguments
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`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup
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,%openmpi-setup)
|
|
(replace 'check
|
|
(lambda _
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|
(setenv "HOME" "/tmp")
|
|
(setenv "PYTHONPATH"
|
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
|
|
(with-directory-excursion "test"
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;; Disable parallel tests to avoid race condition. See
|
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;; https://github.com/pytest-dev/pytest-cov/issues/237.
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|
(substitute* "runtests.sh"
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|
(("for p in 1 4 8 16; do")
|
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"for p in 1; do"))
|
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(invoke "./runtests.sh"))
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#t)))))
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|
(home-page "https://bitbucket.org/fenics-project/dijitso/")
|
|
(synopsis "Distributed just-in-time building of shared libraries")
|
|
(description
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|
"Dijitso provides a core component of the @code{FEniCS} framework,
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namely the just-in-time compilation of C++ code that is generated from
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Python modules. It is called from within a C++ library, using ctypes
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to import the dynamic shared library directly.
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As long as the compiled code can provide a simple factory function to
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a class implementing a predefined C++ interface, there is no limit to
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the complexity of that interface. Parallel support depends on the
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@code{mpi4py} interface.")
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(license license:lgpl3+)))
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|
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(define-public python-fenics-ufl
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(package
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(name "python-fenics-ufl")
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(version "2019.1.0")
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(source
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|
(origin
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(method url-fetch)
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|
(uri (pypi-uri "fenics-ufl" version))
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|
(sha256
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|
(base32
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|
"10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
`(("python-numpy" ,python-numpy)))
|
|
(native-inputs
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`(("python-pytest" ,python-pytest)))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
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|
(setenv "PYTHONPATH"
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
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|
(with-directory-excursion "test"
|
|
(invoke "py.test"))
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#t)))))
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|
(home-page "https://bitbucket.org/fenics-project/ufl/")
|
|
(synopsis "Unified language for form-compilers")
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|
(description "The Unified Form Language (UFL) is a domain specific
|
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language for declaration of finite element discretizations of
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variational forms. More precisely, it defines a flexible interface
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for choosing finite element spaces and defining expressions for weak
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forms in a notation close to mathematical notation.
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UFL is part of the FEniCS Project.")
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(license license:lgpl3+)))
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|
|
(define-public python-fenics-fiat
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|
(package
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|
(name "python-fenics-fiat")
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|
(version "2019.1.0")
|
|
(source
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|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-fiat" version))
|
|
(sha256
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|
(base32
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|
"13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
`(("python-pytest" ,python-pytest)))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-sympy" ,python-sympy)))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(setenv "PYTHONPATH"
|
|
(string-append (getcwd) ":" (getenv "PYTHONPATH")))
|
|
(with-directory-excursion "test"
|
|
;; FIXME: three FIAT test modules are known to fail
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|
;; with recent versions of pytest (>= 4). These are
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|
;; skipped for FIAT version 2019.1.0 pending an
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;; upstream pull request. For details see request #59
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|
;; at https://bitbucket.org/fenics-project/fiat/.
|
|
(invoke "py.test" "unit/"
|
|
"--ignore=unit/test_fiat.py"
|
|
"--ignore=unit/test_quadrature.py"
|
|
"--ignore=unit/test_reference_element.py"))
|
|
#t)))))
|
|
(home-page "https://bitbucket.org/fenics-project/fiat/")
|
|
(synopsis "Tabulation of finite element function spaces")
|
|
(description
|
|
"The FInite element Automatic Tabulator (FIAT) supports
|
|
generation of arbitrary order instances of the Lagrange elements on
|
|
lines, triangles, and tetrahedra. It is also capable of generating
|
|
arbitrary order instances of Jacobi-type quadrature rules on the same
|
|
element shapes. Further, H(div) and H(curl) conforming finite element
|
|
spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini
|
|
and Nedelec are supported on triangles and tetrahedra. Upcoming
|
|
versions will also support Hermite and nonconforming elements.
|
|
|
|
FIAT is part of the FEniCS Project.")
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public python-fenics-ffc
|
|
(package
|
|
(name "python-fenics-ffc")
|
|
(version "2019.1.0.post0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-ffc" version))
|
|
(sha256
|
|
(base32
|
|
"1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
`(("python-pytest" ,python-pytest)))
|
|
(propagated-inputs
|
|
`(("python-fenics-dijitso" ,python-fenics-dijitso)
|
|
("python-fenics-fiat" ,python-fenics-fiat)
|
|
("python-fenics-ufl" ,python-fenics-ufl)))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(setenv "HOME" (getcwd))
|
|
(setenv "PYTHONPATH"
|
|
(string-append (getcwd) ":" (getenv "PYTHONPATH")))
|
|
(with-directory-excursion "test"
|
|
;; FIXME: the tests in subdirectory
|
|
;; 'unit/ufc/finite_element' require the ffc_factory
|
|
;; extension module. This module, located in the 'libs'
|
|
;; subdirectory, needs to be built and made accessible
|
|
;; prior to running the tests.
|
|
(invoke "py.test" "unit/" "--ignore=unit/ufc/")
|
|
(with-directory-excursion "uflacs"
|
|
(invoke "py.test" "unit/")))
|
|
#t)))))
|
|
(home-page "https://bitbucket.org/fenics-project/ffc/")
|
|
(synopsis "Compiler for finite element variational forms")
|
|
(description "The FEniCS Form Compiler (FFC) is a compiler for
|
|
finite element variational forms. From a high-level description of
|
|
the form, it generates efficient low-level C++ code that can be used
|
|
to assemble the corresponding discrete operator (tensor). In
|
|
particular, a bilinear form may be assembled into a matrix and a
|
|
linear form may be assembled into a vector. FFC may be used either
|
|
from the command line (by invoking the @code{ffc} command) or as a
|
|
Python module (@code{import ffc}).
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|
|
|
FFC is part of the FEniCS Project.")
|
|
;; There are two files released with a public domain licence;
|
|
;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
|
|
(license (list license:public-domain license:lgpl3+))))
|
|
|
|
(define-public fenics-dolfin
|
|
(package
|
|
(name "fenics-dolfin")
|
|
(version "2019.1.0.post0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://bitbucket.org/fenics-project/dolfin/get/"
|
|
version ".tar.gz"))
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Make sure we don't use the bundled test framework.
|
|
(delete-file-recursively "test/unit/cpp/catch")
|
|
(substitute* "test/unit/cpp/main.cpp"
|
|
;; Use standard search paths for 'catch' header file.
|
|
(("#include.*")
|
|
"#include <catch.hpp>\n"))
|
|
(substitute* "test/unit/cpp/CMakeLists.txt"
|
|
;; Specify directory to find the header file.
|
|
(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
|
|
(string-append front
|
|
"$ENV{CATCH_DIR}/include" back "\n")))
|
|
#t))))
|
|
(build-system cmake-build-system)
|
|
(inputs
|
|
`(("blas" ,openblas)
|
|
("boost" ,boost)
|
|
("eigen" ,eigen)
|
|
("hdf5" ,hdf5-parallel-openmpi)
|
|
("lapack" ,lapack)
|
|
("libxml2" ,libxml2)
|
|
("openmpi" ,openmpi)
|
|
("python" ,python-3)
|
|
("scotch" ,pt-scotch32)
|
|
("suitesparse" ,suitesparse)
|
|
("sundials" ,sundials-openmpi)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("catch" ,catch-framework2-1)
|
|
("pkg-config" ,pkg-config)))
|
|
(propagated-inputs
|
|
`(("ffc" ,python-fenics-ffc)
|
|
("petsc" ,petsc-openmpi)
|
|
("slepc" ,slepc-openmpi)))
|
|
(arguments
|
|
`(#:configure-flags
|
|
`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
|
|
"-DDOLFIN_ENABLE_HDF5:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_MPI:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
|
|
"-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'patch-usr-bin-file 'mpi-setup
|
|
,%openmpi-setup)
|
|
(add-after 'patch-source-shebangs 'set-paths
|
|
(lambda _
|
|
;; Define paths to store locations.
|
|
(setenv "BLAS_DIR" (assoc-ref %build-inputs "blas"))
|
|
(setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
|
|
(setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
|
|
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
|
|
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
|
|
(setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
|
|
(setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
|
|
(setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
|
|
#t))
|
|
(add-before 'check 'pre-check
|
|
(lambda _
|
|
;; The Dolfin repository uses git-lfs, whereby web links are
|
|
;; substituted for large files. Guix does not currently support
|
|
;; git-lfs, so only the links are downloaded. The tests that
|
|
;; require the absent meshes cannot run and are skipped.
|
|
;;
|
|
;; Two other serial tests fail and are skipped.
|
|
;; i) demo_stokes-iterative_serial,
|
|
;; The MPI_Comm_rank() function was called before MPI_INIT was
|
|
;; invoked
|
|
;; ii) demo_multimesh-stokes_serial:
|
|
;; Warning: Found no facets matching domain for boundary
|
|
;; condition.
|
|
;;
|
|
;; One mpi test fails and is skipped.
|
|
;; i) demo_stokes-iterative_mpi:
|
|
;; The MPI_Comm_rank() function was called before MPI_INIT was
|
|
;; invoked
|
|
(call-with-output-file "CTestCustom.cmake"
|
|
(lambda (port)
|
|
(display
|
|
(string-append
|
|
"set(CTEST_CUSTOM_TESTS_IGNORE "
|
|
"demo_bcs_serial "
|
|
"demo_bcs_mpi "
|
|
"demo_eigenvalue_serial "
|
|
"demo_eigenvalue_mpi "
|
|
"demo_navier-stokes_serial "
|
|
"demo_navier-stokes_mpi "
|
|
"demo_stokes-taylor-hood_serial "
|
|
"demo_stokes-taylor-hood_mpi "
|
|
"demo_subdomains_serial "
|
|
"demo_advection-diffusion_serial "
|
|
"demo_advection-diffusion_mpi "
|
|
"demo_auto-adaptive-navier-stokes_serial "
|
|
"demo_contact-vi-snes_serial "
|
|
"demo_contact-vi-snes_mpi "
|
|
"demo_contact-vi-tao_serial "
|
|
"demo_contact-vi-tao_mpi "
|
|
"demo_curl-curl_serial "
|
|
"demo_curl-curl_mpi "
|
|
"demo_dg-advection-diffusion_serial "
|
|
"demo_dg-advection-diffusion_mpi "
|
|
"demo_elasticity_serial "
|
|
"demo_elasticity_mpi "
|
|
"demo_elastodynamics_serial "
|
|
"demo_elastodynamics_mpi "
|
|
"demo_lift-drag_serial "
|
|
"demo_lift-drag_mpi "
|
|
"demo_mesh-quality_serial "
|
|
"demo_mesh-quality_mpi "
|
|
"demo_multimesh-stokes_serial "
|
|
"demo_stokes-iterative_serial "
|
|
"demo_stokes-iterative_mpi "
|
|
")\n") port)))
|
|
#t))
|
|
(replace 'check
|
|
(lambda _
|
|
(and (invoke "make" "unittests")
|
|
(invoke "make" "demos")
|
|
(invoke "ctest" "-R" "unittests")
|
|
(invoke "ctest" "-R" "demo" "-R" "serial")
|
|
(invoke "ctest" "-R" "demo" "-R" "mpi")))))))
|
|
(home-page "https://bitbucket.org/fenics-project/dolfin/")
|
|
(synopsis "Problem solving environment for differential equations")
|
|
(description
|
|
"DOLFIN is a computational framework for finding numerical
|
|
solutions to problems described by differential equations. Numerical
|
|
models in DOLFIN are constructed using general families of finite
|
|
elements. Data structures are provided for discretizing the governing
|
|
system on a computational mesh. A compact syntax, similar to
|
|
mathematical notation, is made available for defining function spaces
|
|
and expressing variational forms. Interfaces to specialized matrix
|
|
solvers are provided for solving the resultant linear systems.
|
|
|
|
@code{fenics-dolfin} is part of the FEniCS project. It is the C++
|
|
user interface to the FEniCS core components and external libraries.")
|
|
;; The source code for the DOLFIN C++ library is licensed under the
|
|
;; GNU Lesser General Public License, version 3 or later, with the
|
|
;; following exceptions:
|
|
;;
|
|
;; public-domain: dolfin/geometry/predicates.cpp
|
|
;; dolfin/geometry/predicates.h
|
|
;;
|
|
;; zlib: dolfin/io/base64.cpp
|
|
;; dolfin/io/base64.h
|
|
;;
|
|
;; expat: dolfin/io/pugiconfig.hpp
|
|
;; dolfin/io/pugixml.cpp
|
|
;; dolfin/io/pugixml.hpp
|
|
(license (list license:public-domain
|
|
license:zlib
|
|
license:expat
|
|
license:lgpl3+))))
|
|
|
|
(define-public fenics
|
|
(package/inherit fenics-dolfin
|
|
(name "fenics")
|
|
(build-system python-build-system)
|
|
(inputs
|
|
`(("pybind11" ,pybind11)
|
|
("python-matplotlib" ,python-matplotlib)
|
|
,@(alist-delete "python" (package-inputs fenics-dolfin))))
|
|
(native-inputs
|
|
`(("cmake" ,cmake-minimal)
|
|
("ply" ,python-ply)
|
|
("pytest" ,python-pytest)
|
|
("python-decorator" ,python-decorator)
|
|
("python-pkgconfig" ,python-pkgconfig)
|
|
,@(package-native-inputs fenics-dolfin)))
|
|
(propagated-inputs
|
|
`(("dolfin" ,fenics-dolfin)
|
|
("petsc4py" ,python-petsc4py)
|
|
("slepc4py" ,python-slepc4py)))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'patch-source-shebangs 'set-paths
|
|
(lambda _
|
|
;; Define paths to store locations.
|
|
(setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
|
|
;; Move to python sub-directory.
|
|
(chdir "python")
|
|
#t))
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(add-before 'check 'pre-check
|
|
(lambda _
|
|
;; Exclude three tests that generate
|
|
;; 'NotImplementedError' in matplotlib version 3.1.2.
|
|
;; See
|
|
;; <https://github.com/matplotlib/matplotlib/issues/15382>.
|
|
;; Also exclude tests that require meshes supplied by
|
|
;; git-lfs.
|
|
(substitute* "demo/test.py"
|
|
(("(.*stem !.*)" line)
|
|
(string-append
|
|
line "\n"
|
|
"excludeList = [\n"
|
|
"'built-in-meshes', \n"
|
|
"'hyperelasticity', \n"
|
|
"'elasticity', \n"
|
|
"'multimesh-quadrature', \n"
|
|
"'multimesh-marking', \n"
|
|
"'mixed-poisson-sphere', \n"
|
|
"'mesh-quality', \n"
|
|
"'lift-drag', \n"
|
|
"'elastodynamics', \n"
|
|
"'dg-advection-diffusion', \n"
|
|
"'curl-curl', \n"
|
|
"'contact-vi-tao', \n"
|
|
"'contact-vi-snes', \n"
|
|
"'collision-detection', \n"
|
|
"'buckling-tao', \n"
|
|
"'auto-adaptive-navier-stokes', \n"
|
|
"'advection-diffusion', \n"
|
|
"'subdomains', \n"
|
|
"'stokes-taylor-hood', \n"
|
|
"'stokes-mini', \n"
|
|
"'navier-stokes', \n"
|
|
"'eigenvalue']\n"
|
|
"demos = ["
|
|
"d for d in demos if d[0].stem not in "
|
|
"excludeList]\n")))
|
|
(setenv "HOME" (getcwd))
|
|
(setenv "PYTHONPATH"
|
|
(string-append
|
|
(getcwd) "/build/lib.linux-x86_64-"
|
|
,(version-major+minor (package-version python)) ":"
|
|
(getenv "PYTHONPATH")))
|
|
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
|
|
(setenv "OPENBLAS_NUM_THREADS" "1")
|
|
#t))
|
|
(replace 'check
|
|
(lambda _
|
|
(with-directory-excursion "test"
|
|
;; Note: The test test_snes_set_from_options() in the file
|
|
;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
|
|
;; Limit the number of jobs to 3 as 500 MiB of memory is used
|
|
;; per process.
|
|
(invoke "mpirun" "-np" (number->string
|
|
(min 3 (parallel-job-count)))
|
|
"python" "-B" "-m"
|
|
"pytest" "unit" "--ignore"
|
|
"unit/nls/test_PETScSNES_solver.py"))
|
|
#t))
|
|
(add-after 'install 'install-demo-files
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((demos (string-append
|
|
(assoc-ref outputs "out")
|
|
"/share/python-dolfin/demo")))
|
|
(mkdir-p demos)
|
|
(with-directory-excursion "demo"
|
|
(for-each (lambda (file)
|
|
(let* ((dir (dirname file))
|
|
(tgt-dir (string-append demos "/" dir)))
|
|
(unless (equal? "." dir)
|
|
(mkdir-p tgt-dir)
|
|
(install-file file tgt-dir))))
|
|
(find-files "." ".*\\.(py|gz|xdmf)$"))))
|
|
#t)))))
|
|
(home-page "https://fenicsproject.org/")
|
|
(synopsis "High-level environment for solving differential equations")
|
|
(description
|
|
"@code{fenics} is a computing platform for solving general classes of
|
|
problems that involve differential equations. @code{fenics} facilitates
|
|
access to efficient methods for dealing with ordinary differential
|
|
equations (ODEs) and partial differential equations (PDEs). Systems of
|
|
equations such as these are commonly encountered in areas of engineering,
|
|
mathematics and the physical sciences. It is particularly well-suited to
|
|
problems that can be solved using the Finite Element Method (FEM).
|
|
|
|
@code{fenics} is the top level of the set of packages that are developed
|
|
within the FEniCS project. It provides the python user interface to the
|
|
FEniCS core components and external libraries.")
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public fullswof-2d
|
|
(let ((revision 505)
|
|
(release "1.09.01"))
|
|
(package
|
|
(name "fullswof-2d")
|
|
(version release)
|
|
(source (origin
|
|
(method svn-fetch)
|
|
(uri (svn-reference
|
|
(url (string-append "https://subversion.renater.fr/"
|
|
"anonscm/svn/fullswof-2d/tags/"
|
|
"release-" version))
|
|
(revision revision)))
|
|
(file-name (string-append "fullswof-2d-" version "-checkout"))
|
|
(sha256
|
|
(base32
|
|
"16v08dx7h7n4wyddzbwimazwyj74ynis12mpjfkay4243npy44b8"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("inetutils" ,inetutils))) ; for 'hostname', used in the check phase
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure) ; no configure script
|
|
(add-after 'build 'build-tools
|
|
(lambda _
|
|
(with-directory-excursion "Tools/ConvertFormat"
|
|
(invoke "make" "../../bin/asc2xyz")
|
|
(invoke "make" "../../bin/xyz2asc"))
|
|
(with-directory-excursion "Tools/ExtractWindow"
|
|
(invoke "make" "../../bin/cropxyz"))
|
|
#t))
|
|
(replace 'check ; no check target
|
|
(lambda _
|
|
(invoke "make" "benchref")))
|
|
(replace 'install ; no install target
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin"))
|
|
(doc (string-append
|
|
out "/share/doc/" ,name "-" ,version))
|
|
(examples (string-append doc "/Examples")))
|
|
(with-directory-excursion "bin"
|
|
(for-each (lambda (binary) (install-file binary bin))
|
|
(list "asc2xyz" "xyz2asc" "cropxyz"
|
|
"FullSWOF_2D")))
|
|
(with-directory-excursion "doc"
|
|
(for-each (lambda (pdf) (install-file pdf doc))
|
|
(list "Documentation.pdf" "refman.pdf")))
|
|
(with-directory-excursion "Tools"
|
|
(for-each (lambda (dir)
|
|
(copy-file
|
|
(string-append dir "/README.txt")
|
|
(string-append doc "/README_" dir ".txt")))
|
|
(list "ConvertFormat" "ExtractWindow")))
|
|
(copy-recursively "Examples" examples)
|
|
#t))))))
|
|
(home-page "https://www.idpoisson.fr/fullswof/")
|
|
(synopsis "Two dimensional flow solver for flood modelling")
|
|
(description "@code{FullSWOF_2d} is a numerical tool for solving
|
|
the shallow water equations on structured grids. The name FullSWOF
|
|
refers to the Full form of the Shallow Water equations for Overland
|
|
Flow. The discretized system of equations is solved using the finite
|
|
volume method. A choice of shock-capturing methods is available to
|
|
locate the transition boundaries between the wet areas and the dry
|
|
areas in the model. A semi-implicit method is used to advance the
|
|
solution in time. The tool is typically applied to the modelling of
|
|
river flooding.")
|
|
(license license:cecill))))
|
|
|
|
(define-public python-meshio
|
|
(package
|
|
(name "python-meshio")
|
|
(version "4.4.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "meshio" version))
|
|
(sha256
|
|
(base32
|
|
"0kv832s2vyff30zz8yqypw5jifwdanvh5x56d2bzkvy94h4jlddy"))
|
|
(snippet
|
|
'(begin
|
|
(let ((file (open-file "setup.py" "a")))
|
|
(display "from setuptools import setup\nsetup()" file)
|
|
(close-port file))
|
|
#t))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
`(("h5py" ,python-h5py)
|
|
("netcdf4" ,python-netcdf4)))
|
|
(native-inputs
|
|
`(("pytest" ,python-pytest)))
|
|
(propagated-inputs
|
|
`(("importlib-metadata" ,python-importlib-metadata)
|
|
("numpy" ,python-numpy)))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key outputs inputs #:allow-other-keys)
|
|
(add-installed-pythonpath inputs outputs)
|
|
(invoke "python" "-m" "pytest" "-v" "tests")
|
|
#t)))))
|
|
(home-page "https://github.com/nschloe/meshio")
|
|
(synopsis "I/O for mesh files")
|
|
(description "There are various file formats available for
|
|
representing unstructured meshes and mesh data. The @code{meshio}
|
|
package is able to read and write mesh files in many formats and to
|
|
convert files from one format to another. Formats such as cgns, h5m,
|
|
gmsh, xdmf and vtk are supported. The package provides command-line
|
|
tools and a collection of Python modules for programmatic use.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-pygmsh
|
|
(package
|
|
(name "python-pygmsh")
|
|
(version "7.1.11")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/nschloe/pygmsh")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0g4yllmxks7yb50vild5xi1cma0yl16vsq6rfvdwmqaj4hwxcabk"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
(let ((file (open-file "setup.py" "a")))
|
|
(display "from setuptools import setup\nsetup()" file)
|
|
(close-port file))
|
|
;; A reference to setuptools in the configuration file
|
|
;; triggers an attempt to download the package from pypi.
|
|
;; The reference is not needed since the package is
|
|
;; provided by the build system.
|
|
(substitute* "setup.cfg"
|
|
(("^[[:blank:]]+setuptools>=42\n") ""))
|
|
#t))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
`(("pytest" ,python-pytest)
|
|
("wheel" ,python-wheel)))
|
|
(propagated-inputs
|
|
`(("importlib-metadata" ,python-importlib-metadata)
|
|
("gmsh" ,gmsh)
|
|
("meshio" ,python-meshio)
|
|
("numpy" ,python-numpy)))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
|
(when tests?
|
|
(add-installed-pythonpath inputs outputs)
|
|
(invoke "python" "-m" "pytest" "-v" "tests"))
|
|
#t)))))
|
|
(home-page "https://github.com/nschloe/pygmsh")
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(synopsis "Python frontend for Gmsh")
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(description "The goal of @code{pygmsh} is to combine the power of
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Gmsh with the versatility of Python. The package generalises many of
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the methods and functions that comprise the Gmsh Python API. In this
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way the meshing of complex geometries using high-level abstractions is
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made possible. The package provides a Python library together with a
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command-line utility for mesh optimisation.")
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(license license:lgpl3)))
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(define-public python-dolfin-adjoint
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(package
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(name "python-dolfin-adjoint")
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(version "2019.1.0")
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(source
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|
(origin
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|
(method git-fetch)
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|
(uri (git-reference
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|
(url "https://github.com/dolfin-adjoint/pyadjoint")
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|
(commit version)))
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|
(file-name (git-file-name name version))
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|
(sha256
|
|
(base32
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|
"0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
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|
(modules '((guix build utils)))
|
|
(snippet
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|
'(begin
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|
;; One of the migration tests attempts to call openmpi
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|
;; recursively and fails. See
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|
;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the
|
|
;; test sequentially instead.
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|
(with-directory-excursion "tests/migration/optimal_control_mms"
|
|
(substitute* "test_optimal_control_mms.py"
|
|
(("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") "")))
|
|
;; Result files are regenerated in the check phase.
|
|
(delete-file-recursively
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|
"tests/migration/viscoelasticity/test-results")
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|
#t))))
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|
(build-system python-build-system)
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|
(inputs
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|
`(("fenics" ,fenics)
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|
("openmpi" ,openmpi)
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|
("pybind11" ,pybind11)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)
|
|
("python-coverage" ,python-coverage)
|
|
("python-decorator" ,python-decorator)
|
|
("python-flake8" ,python-flake8)
|
|
("python-pkgconfig" ,python-pkgconfig)
|
|
("python-pytest" ,python-pytest)))
|
|
(propagated-inputs
|
|
`(("scipy" ,python-scipy)))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(add-after 'install 'install-doc
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((doc (string-append (assoc-ref outputs "out")
|
|
"/share/doc/" ,name "-"
|
|
,version))
|
|
(examples (string-append doc "/examples")))
|
|
(mkdir-p examples)
|
|
(copy-recursively "examples" examples))
|
|
#t))
|
|
(replace 'check
|
|
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
|
|
(when tests?
|
|
(add-installed-pythonpath inputs outputs)
|
|
(setenv "HOME" (getcwd))
|
|
(and (invoke "py.test" "-v" "tests/fenics_adjoint")
|
|
(invoke "py.test" "-v" "tests/migration")
|
|
(invoke "py.test" "-v" "tests/pyadjoint")))
|
|
#t)))))
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|
(home-page "http://www.dolfin-adjoint.org")
|
|
(synopsis "Automatic differentiation library")
|
|
(description "@code{python-dolfin-adjoint} is a solver of
|
|
differential equations associated with a governing system and a
|
|
functional of interest. Working from the forward model the solver
|
|
automatically derives the discrete adjoint and tangent linear models.
|
|
These additional models are key ingredients in many algorithms such as
|
|
data assimilation, optimal control, sensitivity analysis, design
|
|
optimisation and error estimation. The dolfin-adjoint project
|
|
provides the necessary tools and data structures for cases where the
|
|
forward model is implemented in @code{fenics} or
|
|
@url{https://firedrakeproject.org,firedrake}.")
|
|
(license license:lgpl3)))
|