a1e6ac72fd
* gnu/packages/simulation.scm: Add Sharlatan Hellseher <sharlatanus@gmail.com> to copyright header. Change-Id: I18e82c7344cfa206ff8f82dfa963b7d8b026dcf0
1435 lines
63 KiB
Scheme
1435 lines
63 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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;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
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;;; Copyright © 2022 Liliana Marie Prikler <liliana.prikler@gmail.com>
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;;; Copyright © 2023 Reza Housseini <reza@housseini.me>
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;;; Copyright © 2024 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.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 cpp)
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#:use-module (gnu packages curl)
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#:use-module (gnu packages engineering)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages fontutils)
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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 geo)
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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 image)
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#:use-module (gnu packages iso-codes)
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#:use-module (gnu packages image-processing)
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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 pdf)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages pretty-print)
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#:use-module (gnu packages protobuf)
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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 qt)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages sqlite)
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#:use-module (gnu packages ssh)
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#:use-module (gnu packages textutils)
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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 video)
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#:use-module (gnu packages xiph)
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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 gexp)
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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 pyproject)
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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 gexp)
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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 match)
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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-org
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(package
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(name "openfoam-org")
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(version "10.20230119")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://github.com/OpenFOAM/OpenFOAM-"
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(version-major version)))
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(commit (second (string-split version #\.)))))
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(sha256
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(base32
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"0icvwg7s6vnkgmdiczivia9pbrgx8nanw9a4j080fzfvdv9vxhzp"))
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(file-name (git-file-name name version))
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(modules '((guix build utils)))
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(snippet `(begin
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;; patch shell paths
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(substitute* (list "wmake/src/Makefile"
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"wmake/makefiles/general")
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(("/bin/sh")
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"sh"))
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(substitute* "etc/bashrc"
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;; only go back one folder level
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(("\\$\\(dirname \\$\\{BASH_SOURCE:-\\$0\\}\\)/../..")
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"$(dirname ${BASH_SOURCE:-$0})/..")
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;; do not use openfoam folder convention
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(("^export WM_PROJECT_DIR=.*$")
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(string-append
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"export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR\n"))
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;; do not source bash_completion (gives error)
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(("^.*bash_completion.*$" all)
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(string-append "#" all))
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;; set same version as guix package
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(("^export WM_PROJECT_VERSION=.*$")
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(string-append "export WM_PROJECT_VERSION="
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,version "\n")))
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;; add expand flag to RunFunctions
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(substitute* "bin/tools/RunFunctions"
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(("foamDictionary (.*)" all args)
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(string-append "foamDictionary -expand " args)))
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;; disable failing test
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(substitute* "test/postProcessing/channel/Allrun"
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(("^.*getApplication.*$" all)
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(string-append "#" all "\n")))))))
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(build-system gnu-build-system)
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(inputs (list boost
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cgal
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git
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gmp
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libxt
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metis
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mpfr
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ncurses
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openmpi
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openssh
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paraview
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pt-scotch32
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readline
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zlib))
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(native-inputs (list bison
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flex
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;; paraview plugin dependencies
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cli11
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cmake-minimal
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cgns
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curl
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double-conversion
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eigen
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expat
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ffmpeg
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fmt
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freetype
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gdal
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gl2ps
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glew
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gmsh
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hdf5
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jsoncpp
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libjpeg-turbo
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libogg
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libpng
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libharu
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libtheora
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libtiff
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libx11
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libxml2
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lz4
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netcdf
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nlohmann-json
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proj
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protobuf
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pugixml
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python
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python-mpi4py
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qtbase-5
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qtsvg-5
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qttools-5
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qtwebengine-5
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qtxmlpatterns
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utfcpp
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vtk
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xz))
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(propagated-inputs (list gnuplot))
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(outputs '("debug" ;~60MB
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"out"))
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(arguments
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(list
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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
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#~(list "share/OpenFOAM/platforms/linux64GccDPInt32Opt/bin"
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"share/OpenFOAM/platforms/linux64GccDPInt32Opt/lib")
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#:modules
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'((ice-9 ftw)
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(ice-9 regex)
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(ice-9 string-fun)
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(srfi srfi-1)
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(guix build gnu-build-system)
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(guix build utils))
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#:phases
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#~(modify-phases %standard-phases
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(add-before 'build 'patch-HOME-path
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(lambda _
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(setenv "HOME" "/tmp")))
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(add-before 'build 'rename-self
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(lambda _
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;; The script 'bin/foamEtcFile' derives the version name based
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;; on the current directory name (!), so make sure to follow the
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;; expected naming convention.
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(let ((here (canonicalize-path "."))
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(target #$(string-append
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"OpenFOAM-"
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(string-map (match-lambda
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(#\. #\-)
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(chr chr))
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(package-version this-package)))))
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(chdir "..")
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(format #t "renaming '~a' to '~a'~%"
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here target)
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(rename-file here target)
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(chdir target))))
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(add-before 'build 'patch-scotch
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(lambda _
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(substitute* "etc/config.sh/scotch"
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(("^export SCOTCH_VERSION=scotch_.*$")
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(string-append "export SCOTCH_VERSION=scotch_"
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#$(package-version pt-scotch32) "\n"))
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(("^export SCOTCH_ARCH_PATH=.*$")
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(string-append "export SCOTCH_ARCH_PATH="
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(assoc-ref %build-inputs "pt-scotch32")
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"\n"))) #t))
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(add-before 'build 'patch-mpi
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(lambda _
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(let* ((mpi-path (assoc-ref %build-inputs "openmpi"))
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(mpi-version #$(package-version openmpi)))
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;; specify openmpi type
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(substitute* "etc/bashrc"
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(("WM_MPLIB=SYSTEMOPENMPI")
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"WM_MPLIB=OPENMPI"))
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(substitute* "etc/config.sh/mpi"
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(("export FOAM_MPI=openmpi-.*$")
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(string-append "export FOAM_MPI=openmpi-"
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mpi-version "\n"))
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(("export MPI_ARCH_PATH=.*\\$FOAM_MPI.*$")
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(string-append "export MPI_ARCH_PATH=" mpi-path
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"\n")))) #t))
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(add-before 'build 'patch-paraview
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(lambda _
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(substitute* "etc/config.sh/paraview"
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(("^export ParaView_VERSION=.*$")
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(string-append "export ParaView_VERSION="
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#$(package-version paraview) "\n"))
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(("^export ParaView_DIR=.*$")
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(string-append "export ParaView_DIR="
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(assoc-ref %build-inputs "paraview")
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"\n"))) #t))
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(add-before 'build 'add-rpaths
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(lambda _
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(letrec* ((libraries '("boost" "cgal"
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"gmp"
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"metis"
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"mpfr"
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"pt-scotch32"
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"openmpi"
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"zlib"
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"paraview"))
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(rpaths
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(fold-right (lambda (library rpaths)
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(string-append rpaths
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"-rpath="
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(assoc-ref
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%build-inputs library)
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"/lib,")) "" libraries))
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(openfoam-lib
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(string-append #$output
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"/share/OpenFOAM/platforms/linux64GccDPInt32Opt/lib"))
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(ldflags
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(string-append "-Wl,"
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rpaths
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"-rpath="
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openfoam-lib
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","
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"-rpath="
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openfoam-lib
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"/dummy,"
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"-rpath="
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openfoam-lib
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"/paraview-"
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#$(version-major+minor (package-version
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paraview)))))
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(substitute* "wmake/rules/linux64Gcc/c++"
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(("\\$\\(LIB_HEADER_DIRS\\) -fPIC" all)
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(string-append all " " ldflags)))) #t))
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(add-before 'build 'add-vtk-include-path
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(lambda _
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(let* ((vtk-version #$(version-major+minor
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(package-version vtk)))
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(vtk-root (assoc-ref %build-inputs "vtk"))
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(vtk-inc (string-append vtk-root "/include/vtk-" vtk-version))
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(vtk-inc-flag (string-append "-I" vtk-inc)))
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(substitute* "wmake/rules/linux64Gcc/c++"
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(("\\$\\(LIB_HEADER_DIRS\\)" all)
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(string-append all " " vtk-inc-flag " "))))
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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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;; compile OpenFOAM libraries and applications
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(invoke "bash" "-c"
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(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 'cleanup
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;; Avoid unnecessary, voluminous object and dep files.
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(lambda _
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(when (file-exists? "platforms/linux64GccDPInt32Opt/src")
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(delete-file-recursively
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"platforms/linux64GccDPInt32Opt/src"))
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(when (file-exists?
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"platforms/linux64GccDPInt32OptOPENMPI")
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(delete-file-recursively
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"platforms/linux64GccDPInt32OptOPENMPI"))
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(for-each delete-file
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(find-files "." "\\.o$")) #t))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(when (file-exists? "test")
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(with-directory-excursion "test"
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(invoke "bash" "-c"
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(format #f
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"source ../etc/bashrc && ./Allrun -j~a"
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(parallel-job-count)))))
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;; too many tutorials are failing
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;; (with-directory-excursion "tutorials"
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;; (invoke "bash" "-c" "source ../etc/bashrc && ./Alltest"))
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) #t))
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(replace 'install
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(lambda _
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(let ((install-dir (string-append #$output
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"/share/OpenFOAM")))
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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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(let* ((bin (string-append #$output "/bin"))
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(lib (string-append #$output "/lib"))
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(openfoam (string-append #$output
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"/share/OpenFOAM"))
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(build-bin (string-append openfoam
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"/platforms/linux64GccDPInt32Opt/bin"))
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(build-lib (string-append openfoam
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"/platforms/linux64GccDPInt32Opt/lib"))
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(foam-bin (string-append openfoam "/bin")))
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;; add symbolic links in standard 'bin' directory
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(mkdir-p bin)
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(for-each (lambda (file)
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(unless (member file
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'("." ".."))
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(symlink (string-append build-bin "/"
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file)
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(string-append bin "/" file))))
|
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(scandir build-bin))
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(for-each (lambda (file)
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(unless (member file
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'("." ".."))
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(symlink (string-append foam-bin "/"
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file)
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(string-append bin "/" file))))
|
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(scandir foam-bin))
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;; add symbolic link for standard 'lib' directory
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(symlink build-lib lib)) #t)))))
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(native-search-paths
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(list (search-path-specification
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(variable "WM_PROJECT_DIR")
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(separator #f)
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(files '("share/OpenFOAM")))))
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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 $(dirname $(which blockMesh))/../../../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
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|
"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
|
|
with gas/liquid interfaces. Large problems may be split into smaller, connected
|
|
problems for efficient solution on parallel systems.")
|
|
(license license:gpl3+)
|
|
(home-page "https://openfoam.org")))
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|
|
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(define-public openfoam
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(deprecated-package "openfoam" openfoam-org))
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|
|
|
(define-public openfoam-com
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;; This is a fork of 'openfoam-org', maintained separately.
|
|
(package
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(inherit openfoam-org)
|
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(name "openfoam-com")
|
|
(version "2212")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://develop.openfoam.com"
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|
"/Development/openfoam/-/archive/OpenFOAM-v"
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|
version
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"/openfoam-OpenFOAM-v"
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|
version
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|
".tar.gz"))
|
|
(sha256
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|
(base32
|
|
"0i9039hfz9gvgymkdjhjvvn5500zha3cpdbpqrzfrfi8lbz10is2"))
|
|
(modules '((guix build utils)))
|
|
(snippet `(begin
|
|
(substitute* "etc/bashrc"
|
|
;; set same version as guix package
|
|
(("^export WM_PROJECT_VERSION=.*$")
|
|
(string-append "export WM_PROJECT_VERSION="
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,version "\n")))
|
|
;; patch shell paths
|
|
(substitute* (list "src/OSspecific/POSIX/POSIX.C"
|
|
"wmake/src/Makefile"
|
|
"wmake/makefiles/general"
|
|
"wmake/makefiles/info")
|
|
(("/bin/sh")
|
|
"sh"))))))
|
|
(synopsis "Framework for numerical simulation of fluid flow (from openfoam.com)")
|
|
(home-page "https://www.openfoam.com")))
|
|
|
|
(define-public open-simulation-interface
|
|
(package
|
|
(name "open-simulation-interface")
|
|
(version "3.5.0")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url (string-append "https://github.com/"
|
|
"OpenSimulationInterface/"
|
|
"open-simulation-interface"))
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"09vclrvsawx608kk0vnzywr71xn11qzwxzh2j508zjfn0kvhyx7q"))))
|
|
(build-system cmake-build-system)
|
|
(arguments (list #:tests? #f ; tests are for the python package
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-cmake
|
|
(lambda _
|
|
(substitute* "CMakeLists.txt"
|
|
(("-targets\\.cmake") "_targets.cmake")))))))
|
|
(native-inputs (list protobuf))
|
|
(home-page
|
|
"https://github.com/OpenSimulationInterface/open-simulation-interface")
|
|
(synopsis "Generic interface for environmental perception")
|
|
(description "The Open Simulation Interface is a generic interface based on
|
|
Google's protocol buffers for the environmental perception of automated driving
|
|
functions in virtual scenarios.")
|
|
(license license:mpl2.0)))
|
|
|
|
(define-public python-open-simulation-interface
|
|
(package/inherit open-simulation-interface
|
|
(name "python-open-simulation-interface")
|
|
(build-system python-build-system)
|
|
(arguments '())
|
|
(propagated-inputs
|
|
(list python-pyyaml
|
|
python-protobuf))))
|
|
|
|
(define-public esmini
|
|
(package
|
|
(name "esmini")
|
|
(version "2.37.11")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/esmini/esmini")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(patches (search-patches "esmini-use-pkgconfig.patch"))
|
|
(modules '((guix build utils) (ice-9 ftw)))
|
|
(snippet
|
|
#~(with-directory-excursion "externals"
|
|
(for-each
|
|
(lambda (dir) (unless (member dir '("." ".." "expr"))
|
|
(delete-file-recursively dir)))
|
|
(scandir "."))))
|
|
(sha256
|
|
(base32
|
|
"07pwa34nf0b4ihb9fn1pvfi0b39hd8r630nfa6v3a17dsy66a730"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
(list
|
|
#:configure-flags
|
|
#~(list "-DDYN_PROTOBUF=TRUE"
|
|
;; Missing implot package
|
|
"-DUSE_IMPLOT=FALSE")
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-cmake
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(substitute* "support/cmake/common/locations.cmake"
|
|
(("\\$\\{CMAKE_SOURCE_DIR\\}/bin")
|
|
(string-append (assoc-ref outputs "out") "/bin")))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(with-directory-excursion "EnvironmentSimulator/Unittest/"
|
|
(for-each invoke (find-files "_test$")))))
|
|
(add-after 'install 'move-libraries
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(mkdir-p (string-append out "/lib"))
|
|
(with-directory-excursion (string-append out "/bin")
|
|
(for-each
|
|
(lambda (f)
|
|
(rename-file f (string-append out "/lib/"
|
|
(basename f))))
|
|
(find-files "." "\\.(a|so)$")))))))))
|
|
(inputs (list mesa
|
|
openscenegraph `(,openscenegraph "pluginlib")
|
|
open-simulation-interface
|
|
protobuf pugixml sumo))
|
|
(native-inputs (list googletest pkg-config))
|
|
(home-page "https://github.com/esmini/esmini")
|
|
(synopsis "Basic OpenSCENARIO player")
|
|
(description "@command{esmini} is a tool to play OpenSCENARIO files.
|
|
It is provided as both a standalone application and a shared library and has
|
|
some support for generating and analysing traffic scenarios..")
|
|
(license license:mpl2.0)))
|
|
|
|
(define-public python-fenics-dijitso
|
|
(package
|
|
(name "python-fenics-dijitso")
|
|
(version "2019.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-dijitso" version))
|
|
(sha256
|
|
(base32
|
|
"0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
(list openmpi python-numpy))
|
|
(native-inputs
|
|
(list python-pytest-cov))
|
|
(propagated-inputs
|
|
(list python-mpi4py))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(replace 'check
|
|
(lambda _
|
|
(setenv "HOME" "/tmp")
|
|
(with-directory-excursion "test"
|
|
;; Disable parallel tests to avoid race condition. See
|
|
;; https://github.com/pytest-dev/pytest-cov/issues/237.
|
|
(substitute* "runtests.sh"
|
|
(("for p in 1 4 8 16; do")
|
|
"for p in 1; do"))
|
|
(invoke "./runtests.sh")))))))
|
|
(home-page "https://bitbucket.org/fenics-project/dijitso/")
|
|
(synopsis "Distributed just-in-time building of shared libraries")
|
|
(description
|
|
"Dijitso provides a core component of the @code{FEniCS} framework,
|
|
namely the just-in-time compilation of C++ code that is generated from
|
|
Python modules. It is called from within a C++ library, using ctypes
|
|
to import the dynamic shared library directly.
|
|
|
|
As long as the compiled code can provide a simple factory function to
|
|
a class implementing a predefined C++ interface, there is no limit to
|
|
the complexity of that interface. Parallel support depends on the
|
|
@code{mpi4py} interface.")
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public python-fenics-ufl
|
|
(package
|
|
(name "python-fenics-ufl")
|
|
(version "2019.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-ufl" version))
|
|
(sha256
|
|
(base32
|
|
"10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
(list python-numpy))
|
|
(native-inputs
|
|
(list python-pytest))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(invoke "py.test" "test"))))))
|
|
(home-page "https://bitbucket.org/fenics-project/ufl/")
|
|
(synopsis "Unified language for form-compilers")
|
|
(description "The Unified Form Language (UFL) is a domain specific
|
|
language for declaration of finite element discretizations of
|
|
variational forms. More precisely, it defines a flexible interface
|
|
for choosing finite element spaces and defining expressions for weak
|
|
forms in a notation close to mathematical notation.
|
|
|
|
UFL is part of the FEniCS Project.")
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public python-fenics-fiat
|
|
(package
|
|
(name "python-fenics-fiat")
|
|
(version "2019.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-fiat" version))
|
|
(sha256
|
|
(base32
|
|
"13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
(list python-pytest))
|
|
(propagated-inputs
|
|
(list python-numpy python-sympy))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(with-directory-excursion "test"
|
|
;; FIXME: three FIAT test modules are known to fail
|
|
;; with recent versions of pytest (>= 4). These are
|
|
;; skipped for FIAT version 2019.1.0 pending an
|
|
;; upstream pull request. For details see request #59
|
|
;; 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")))))))
|
|
(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
|
|
(list python-pytest))
|
|
(propagated-inputs
|
|
(list python-fenics-dijitso python-fenics-fiat python-fenics-ufl))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _
|
|
(setenv "HOME" (getcwd))
|
|
(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}).
|
|
|
|
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"))
|
|
(patches (search-patches "fenics-dolfin-algorithm.patch"
|
|
"fenics-dolfin-demo-init.patch"
|
|
"fenics-dolfin-boost.patch"
|
|
"fenics-dolfin-config-slepc.patch"))
|
|
(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
|
|
"$ENV{CATCH_DIR}/include" back "\n")))))))
|
|
(build-system cmake-build-system)
|
|
(inputs
|
|
(list openblas
|
|
boost
|
|
eigen
|
|
hdf5-parallel-openmpi
|
|
libxml2
|
|
openmpi
|
|
python-3
|
|
pt-scotch32
|
|
suitesparse
|
|
sundials-openmpi
|
|
zlib))
|
|
(native-inputs
|
|
(list catch-framework pkg-config))
|
|
(propagated-inputs
|
|
(list python-fenics-ffc petsc-openmpi slepc-openmpi))
|
|
(arguments
|
|
(list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
|
|
"-DDOLFIN_ENABLE_HDF5:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_MPI:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
|
|
"-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
|
|
"-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'patch-usr-bin-file 'mpi-setup
|
|
#$%openmpi-setup)
|
|
(add-after 'patch-source-shebangs 'set-paths
|
|
(lambda _
|
|
;; Define paths to store locations.
|
|
(setenv "BLAS_DIR"
|
|
#$(this-package-input "openblas"))
|
|
(setenv "CATCH_DIR"
|
|
#$(this-package-input "catch"))
|
|
(setenv "LAPACK_DIR"
|
|
#$(this-package-input "openblas"))
|
|
(setenv "PETSC_DIR"
|
|
#$(this-package-input "petsc"))
|
|
(setenv "SLEPC_DIR"
|
|
#$(this-package-input "slepc"))
|
|
(setenv "SCOTCH_DIR"
|
|
#$(this-package-input "scotch"))
|
|
(setenv "SUNDIALS_DIR"
|
|
#$(this-package-input "sundials"))
|
|
(setenv "UMFPACK_DIR"
|
|
#$(this-package-input "suitesparse"))))
|
|
(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.
|
|
;;
|
|
;; One serial test fails and is skipped.
|
|
;; i) 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 "
|
|
")\n") port)))))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(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
|
|
(modify-inputs (package-inputs fenics-dolfin)
|
|
(delete "python")
|
|
(prepend pybind11 python-matplotlib)))
|
|
(native-inputs
|
|
(modify-inputs (package-native-inputs fenics-dolfin)
|
|
(prepend cmake-minimal python-ply python-pytest python-decorator)))
|
|
(propagated-inputs
|
|
(list fenics-dolfin
|
|
python-petsc4py
|
|
python-slepc4py
|
|
|
|
;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
|
|
python-pkgconfig))
|
|
(arguments
|
|
(list #:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'relax-requirements
|
|
(lambda _
|
|
(substitute* "python/setup.py"
|
|
(("pybind11==")
|
|
"pybind11>="))))
|
|
(add-after 'unpack 'set-dolfin-pc-file-name
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
|
|
;; variable, hard-code the 'dolfin.pc' absolute file name.
|
|
(let ((pc-file (search-input-file inputs
|
|
"/lib/pkgconfig/dolfin.pc")))
|
|
(substitute* "python/dolfin/jit/jit.py"
|
|
(("pkgconfig\\.parse\\(\"dolfin\"\\)")
|
|
(string-append "pkgconfig.parse(\"" pc-file
|
|
"\")"))))))
|
|
(add-after 'patch-source-shebangs 'set-paths
|
|
(lambda _
|
|
;; Define paths to store locations.
|
|
(setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
|
|
;; Move to python sub-directory.
|
|
(chdir "python")))
|
|
(add-after 'build 'mpi-setup
|
|
#$%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))
|
|
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
|
|
(setenv "OPENBLAS_NUM_THREADS" "1")))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(with-directory-excursion "test"
|
|
(invoke "pytest"
|
|
"unit"
|
|
;; The test test_snes_set_from_options() in the file
|
|
;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
|
|
"--ignore"
|
|
"unit/nls/test_PETScSNES_solver.py"
|
|
;; Fails with a segfault.
|
|
"--ignore"
|
|
"unit/io/test_XDMF.py")))))
|
|
(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)$")))))))))
|
|
(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
|
|
(list 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 "5.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "meshio" version))
|
|
(sha256
|
|
(base32
|
|
"1w39qcg0rw5kb04j7sa45fnqd6k20fsdgrf62cmw2ygjgwnnjh72"))
|
|
(snippet
|
|
'(let ((file (open-file "setup.py" "a")))
|
|
(display "from setuptools import setup\nsetup()" file)
|
|
(close-port file)))))
|
|
(build-system python-build-system)
|
|
(inputs
|
|
(list python-h5py
|
|
python-netcdf4))
|
|
(native-inputs
|
|
(list python-pytest))
|
|
(propagated-inputs
|
|
(list python-importlib-metadata
|
|
python-numpy
|
|
python-rich))
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "python" "-m" "pytest" "-v" "tests")))))))
|
|
(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 "7.1.17")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/nschloe/pygmsh")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"11flp2c4ynk1fhanf4mqyzrpd0gjbnv6afrwwc7xi3mb6ms69lr0"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'workaround-gmsh-detection-failure
|
|
(lambda _
|
|
;; Due to lack of metadata, the gmsh Python package is not
|
|
;; detected although importable.
|
|
(substitute* "pyproject.toml"
|
|
(("\"gmsh\",") "")))))))
|
|
(native-inputs (list python-flit-core python-pytest))
|
|
(propagated-inputs (list gmsh python-meshio python-numpy))
|
|
(home-page "https://github.com/nschloe/pygmsh")
|
|
(synopsis "Python frontend for Gmsh")
|
|
(description "The goal of @code{pygmsh} is to combine the power of
|
|
Gmsh with the versatility of Python. The package generalises many of
|
|
the methods and functions that comprise the Gmsh Python API. In this
|
|
way the meshing of complex geometries using high-level abstractions is
|
|
made possible. The package provides a Python library together with a
|
|
command-line utility for mesh optimisation.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python-dolfin-adjoint
|
|
(package
|
|
(name "python-dolfin-adjoint")
|
|
(version "2019.1.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/dolfin-adjoint/pyadjoint")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; One of the migration tests attempts to call openmpi
|
|
;; recursively and fails. See
|
|
;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the
|
|
;; test sequentially instead.
|
|
(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
|
|
"tests/migration/viscoelasticity/test-results")))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
#~(list
|
|
;; Ignore tests which require missing packages and/or failed during
|
|
;; tests collection.
|
|
"--ignore=tests/firedrake_adjoint/test_assignment.py"
|
|
"--ignore=tests/firedrake_adjoint/test_burgers_newton.py"
|
|
"--ignore=tests/firedrake_adjoint/test_dynamic_meshes.py"
|
|
"--ignore=tests/firedrake_adjoint/test_hessian.py"
|
|
"--ignore=tests/firedrake_adjoint/test_reduced_functional.py"
|
|
"--ignore=tests/firedrake_adjoint/test_shape_derivatives.py"
|
|
"--ignore=tests/firedrake_adjoint/test_solving.py"
|
|
"--ignore=tests/firedrake_adjoint/test_tlm.py"
|
|
"--ignore=tests/migration/burgers_newton/test_burgers_newton.py"
|
|
"--ignore=tests/migration/linear_solver/test_linear_solver.py"
|
|
"--ignore=tests/migration/optimization_scipy/test_optimization_scipy.py"
|
|
"--ignore=tests/migration/projection/test_projection.py"
|
|
"--ignore=tests/migration/reduced_functional/test_reduced_functional.py"
|
|
"--ignore=tests/migration/split/test_split.py"
|
|
"-k" (string-append "not test_read_checkpoint"
|
|
" and not test_krylov_solver_preconditioner_function_ctrl"))
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup #$%openmpi-setup)
|
|
(add-before 'check 'set-environment-variables
|
|
(lambda _
|
|
(setenv "HOME" (getcwd))))
|
|
(add-after 'install 'install-doc
|
|
(lambda _
|
|
(let* ((doc (string-append #$output "/share/doc/" #$name "-" #$version))
|
|
(examples (string-append doc "/examples")))
|
|
(mkdir-p examples)
|
|
(copy-recursively "examples" examples))))
|
|
;; Remove 'sanity-check, because it tries to import
|
|
;; firedrake_adjoint after importing fenics_adjoint.
|
|
;; Both load a module named 'backend' and firedrake_adjoint
|
|
;; fails with an ImportError if it sees that the backend module
|
|
;; has already been loaded.
|
|
(delete 'sanity-check))))
|
|
(inputs
|
|
(list fenics openmpi pybind11))
|
|
(native-inputs
|
|
(list pkg-config
|
|
python-coverage
|
|
python-decorator
|
|
python-flake8
|
|
python-pkgconfig
|
|
python-pytest))
|
|
(propagated-inputs
|
|
(list python-scipy))
|
|
(home-page "https://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)))
|
|
|
|
(define %commonroad-dont-install-license-at-root
|
|
#~(substitute* "setup.py"
|
|
(("data_files=\\[\\('.', \\['LICENSE.txt'\\]\\)\\],")
|
|
"")))
|
|
|
|
(define-public python-commonroad-vehicle-models
|
|
(package
|
|
(name "python-commonroad-vehicle-models")
|
|
(version "3.0.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "commonroad-vehicle-models" version))
|
|
(sha256
|
|
(base32
|
|
"13jg0cys7y4n7rg548w6mxk9g10gd5qxmj4ynrlriczpffqy6kc7"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list #:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(propagated-inputs (list python-numpy python-omegaconf))
|
|
(home-page "https://commonroad.in.tum.de/")
|
|
(synopsis "CommonRoad vehicle models")
|
|
(description "This package provides vehicle models used in CommonRoad
|
|
benchmarks. Varying abstraction levels are used ranging from kinematic single
|
|
track models to multi-body models.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-commonroad-io
|
|
(package
|
|
(name "python-commonroad-io")
|
|
(version "2022.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "commonroad-io" version))
|
|
(sha256
|
|
(base32
|
|
"1cj9zj567mca8xb8sx9h3nnl2cccv6vh8h73imgpq61cimk9mvas"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list #:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("protobuf==3.20.1") "protobuf >= 3.20.1"))
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(propagated-inputs (list python-commonroad-vehicle-models
|
|
python-iso3166
|
|
python-lxml
|
|
python-matplotlib
|
|
python-networkx
|
|
python-numpy
|
|
python-omegaconf
|
|
python-pillow
|
|
python-protobuf
|
|
python-rtree
|
|
python-scipy
|
|
python-shapely
|
|
python-tqdm))
|
|
(native-inputs (list python-lxml python-pytest))
|
|
(home-page "https://commonroad.in.tum.de/")
|
|
(synopsis "Read, write, and visualize CommonRoad scenarios.")
|
|
(description "This package provides methods to read, write, and visualize
|
|
CommonRoad scenarios and planning problems. It can be used as a framework for
|
|
implementing motion planning algorithms to solve CommonRoad Benchmarks
|
|
and is the basis for other tools of the CommonRoad Framework.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-commonroad-route-planner
|
|
(package
|
|
(name "python-commonroad-route-planner")
|
|
(version "2022.3")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://gitlab.lrz.de/tum-cps/commonroad-route-planner")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0xn0l7bzmj56d4mlqacvbl8mdvsffkg2fn2lzfmis5jl4vp99ipf"))))
|
|
(arguments
|
|
(list #:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs (list python-commonroad-io
|
|
python-matplotlib
|
|
python-networkx
|
|
python-numpy
|
|
python-setuptools
|
|
python-shapely))
|
|
(home-page "https://gitlab.lrz.de/tum-cps/commonroad-route-planner")
|
|
(synopsis "Route planner for CommonRoad scenarios")
|
|
(description "This package provides functions for route planning, that is
|
|
finding sequences that lead from a given start lanelet to some goal
|
|
lanelet(s).")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public sumo
|
|
(package
|
|
(name "sumo")
|
|
(version "1.14.1")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/eclipse/sumo")
|
|
(commit (string-append "v"
|
|
(string-replace-substring version
|
|
"." "_")))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1965vrsff0k14z3y3b1c460zdwp9nx6q6plrdyxn496vg6846k1y"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'disable-problematic-tests
|
|
(lambda _
|
|
(substitute* "CMakeLists.txt"
|
|
;; docs/example appears to be missing
|
|
(("add_test\\(exampletest .*") ""))
|
|
(substitute* "src/traci_testclient/CMakeLists.txt"
|
|
;; requires network connection (at least to localhost)
|
|
(("add_test\\(NAME libtracitest .*") "")))))))
|
|
(inputs (list eigen
|
|
freetype
|
|
fontconfig
|
|
ffmpeg
|
|
fox
|
|
gdal
|
|
glu
|
|
gperftools ; tcmalloc
|
|
libjpeg-turbo
|
|
libtiff
|
|
libx11
|
|
libxcursor
|
|
libxft
|
|
libxi
|
|
libxrandr
|
|
libxrender
|
|
openscenegraph
|
|
proj
|
|
python
|
|
xerces-c
|
|
zlib))
|
|
(native-inputs (list googletest python))
|
|
(home-page "https://eclipse.org/sumo")
|
|
(synopsis "Traffic simulator")
|
|
(description "@acronym{SUMO, Simulation of Urban MObility} is a traffic
|
|
simulation package designed to handle large road networks and different modes
|
|
of transportation -- including road vehicles, public transport and pedestrians.
|
|
Included with SUMO is a wealth of supporting tools which automate core tasks
|
|
for the creation, the execution and evaluation of traffic simulations,
|
|
such as network import, route calculations, visualization and emission
|
|
calculation. SUMO can be enhanced with custom models and provides various
|
|
APIs to remotely control the simulation.")
|
|
(license (list license:epl2.0 license:gpl2+))))
|