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* gnu/packages/simulation.scm (python-simpy): New variable. Change-Id: Ic95e6b0656dc2e2deffb543491c64ad5ae14632c Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
1675 lines
74 KiB
Scheme
1675 lines
74 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@guixotic.coop>
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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 © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
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;;; Copyright © 2025 Francisco-Galindo <yo@franciscogalindo.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 "13")
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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/OpenFOAM/OpenFOAM-dev")
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(commit (string-append "version-" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "10s1x82znfnwspq5iif928j1ks4v0slmmycg6py8xw1vvhjp7arh"))))
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(build-system gnu-build-system)
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(native-inputs (list bison flex git))
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(inputs (list bash-completion
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boost
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cgal
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cgns
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cli11
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cmake-minimal
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coreutils
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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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findutils
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fmt-11
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freetype
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gdal
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gl2ps
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glew
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gmp
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gmsh
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gnuplot
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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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libxslt
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libxt
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lz4
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metis
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mpfr
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ncurses
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netcdf
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nlohmann-json
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openmpi
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paraview
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proj
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protobuf
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pt-scotch32
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pugixml
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python
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python-mpi4py
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qt5compat
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qtbase
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qtsvg
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qttools
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qtwebengine
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readline
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trilinos-zoltan
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utfcpp
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vtk
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xz
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zlib))
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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 (string-append "OpenFOAM-"
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#$(package-version this-package)
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"/platforms/linux64GccDPInt32Opt/bin")
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(string-append "OpenFOAM-"
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#$(package-version this-package)
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"/platforms/linux64GccDPInt32Opt/lib"))
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#:modules '((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-after 'unpack 'rename-self
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(lambda _
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(let* ((old-build-path (getcwd))
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(root-path (canonicalize-path (string-append
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old-build-path "/..")))
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(new-build-path (string-append root-path "/OpenFOAM-"
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#$(package-version
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this-package))))
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(chdir root-path)
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(rename-file old-build-path new-build-path)
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(chdir new-build-path))))
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(add-before 'configure 'patch-version
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(lambda _
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(substitute* "etc/bashrc"
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(("export WM_PROJECT_VERSION=.*$")
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(string-append "export WM_PROJECT_VERSION="
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#$(package-version this-package) "\n")))))
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(add-before 'configure 'patch-foamcleanpath
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(lambda _
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(substitute* "bin/foamCleanPath"
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(("getconf")
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(which "getconf")))))
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(add-before 'configure 'patch-shell-path
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(lambda _
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(substitute* "wmake/makefiles/general"
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(("/bin/sh")
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(which "sh")))))
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;; needed for tests
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(add-before 'configure 'patch-HOME-path
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(lambda _
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(setenv "HOME" "/tmp")))
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(add-before 'configure 'patch-bash-completion
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(lambda _
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(substitute* "etc/bashrc"
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;; do not source bash_completion (gives error)
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(("^.*bash_completion.*$" all)
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(string-append "#" all)))))
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(add-before 'configure 'patch-rpaths
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(lambda _
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(letrec* ((libraries '(#$(this-package-input "boost")
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#$(this-package-input "cgal")
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#$(this-package-input "gmp")
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#$(this-package-input "metis")
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#$(this-package-input "mpfr")
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#$(this-package-input "pt-scotch32")
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#$(this-package-input "openmpi")
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#$(this-package-input "zlib")
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#$(this-package-input "paraview")))
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(rpaths (fold-right (lambda (lib rpaths)
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(string-append rpaths "-rpath="
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lib "/lib,")) ""
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libraries))
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(openfoam-lib (string-append #$output
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"/share/OpenFOAM-"
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#$(package-version this-package)
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"/platforms/linux64GccDPInt32Opt/lib"))
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(ldflags (string-append "-Wl,"
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rpaths
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"-rpath="
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openfoam-lib
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","
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"-rpath="
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openfoam-lib
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"/dummy,"
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"-rpath="
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openfoam-lib
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"/paraview-"
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#$(version-major+minor (package-version
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(this-package-input
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"paraview"))))))
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(substitute* "wmake/rules/linux64Gcc/c++"
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(("-fPIC" all)
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(string-append all " " ldflags))))))
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(add-before 'configure 'patch-paraview
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(lambda _
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(substitute* "etc/config.sh/paraview"
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(("ldd")
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(which "ldd")))
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(substitute* "bin/paraFoam"
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(("paraview \"\\$@\"")
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(string-append #$paraview "/bin/paraview \"$@\"")))))
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(add-before 'configure 'patch-mpi
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(lambda _
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(substitute* "etc/config.sh/mpi"
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(("mpicc")
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(string-append #$(this-package-input "openmpi") "/bin/mpicc")))))
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(add-before 'configure 'patch-paraview
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(lambda _
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(substitute* "etc/config.sh/paraview"
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(("\\$paraviewBinDir/paraview")
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"$paraviewBinDir/.paraview-real")
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(("libpqCore-pv")
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"libpqCore"))))
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(add-before 'configure 'patch-vtk-include-path
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(lambda _
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(let* ((vtk-version #$(version-major+minor (package-version (this-package-input
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"vtk"))))
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(vtk-inc (string-append #$(this-package-input "vtk")
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"/include/vtk-" vtk-version))
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(vtk-inc-flag (string-append "-I" vtk-inc)))
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(substitute* "wmake/makefiles/general"
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(("SYS_INC =" all)
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(string-append all " " vtk-inc-flag))))))
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(replace 'configure
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(lambda _
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(substitute* "etc/bashrc"
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(("export ParaView_TYPE=.*$")
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"export ParaView_TYPE=system\n")
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(("export SCOTCH_TYPE=.*$")
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"export SCOTCH_TYPE=system\n")
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(("export METIS_TYPE=.*$")
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"export METIS_TYPE=system\n")
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(("export ZOLTAN_TYPE=.*$")
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"export ZOLTAN_TYPE=system\n"))
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(substitute* "etc/config.sh/scotch"
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(("export SCOTCH_ARCH_PATH=.*$")
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(string-append "export SCOTCH_ARCH_PATH="
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#$(this-package-input "pt-scotch32") "\n")))
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(substitute* "etc/config.sh/metis"
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(("export METIS_ARCH_PATH=.*$")
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(string-append "export METIS_ARCH_PATH="
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#$(this-package-input "metis") "\n")))
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(substitute* "etc/config.sh/zoltan"
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(("export ZOLTAN_ARCH_PATH=.*$")
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(string-append "export ZOLTAN_ARCH_PATH="
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#$(this-package-input "trilinos-zoltan") "\n")))))
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(replace 'build
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(lambda _
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;; compile OpenFOAM libraries and applications
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(invoke "bash" "-c"
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(format #f "source ./etc/bashrc && ./Allwmake -j~a"
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(parallel-job-count)))))
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(add-after 'build 'cleanup
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;; Avoid unnecessary, voluminous object and dep files.
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(lambda _
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(when (file-exists? "platforms/linux64GccDPInt32Opt/src")
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(delete-file-recursively "platforms/linux64GccDPInt32Opt/src"))
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(when (file-exists?
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"platforms/linux64GccDPInt32OptSYSTEMOPENMPI")
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(delete-file-recursively
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"platforms/linux64GccDPInt32OptSYSTEMOPENMPI"))
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(for-each delete-file
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(find-files "." "\\.o$"))
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(for-each delete-file
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(find-files "." "\\.dep$"))
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;; Remove spurious files in src tree
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;; (invoke "bash" "-c" "source ./etc/bashrc && wclean all")
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))
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(add-before 'check 'disable-failing-tests
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(lambda _
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;; disable failing test
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(substitute* "test/postProcessing/channel/Allrun"
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(("^.*foam.*$" all)
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(string-append "#" all "\n")))
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(substitute* "test/Lagrangian/boundaries/system/decomposeParDict"
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(("numberOfSubdomains 6")
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"numberOfSubdomains 4")
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(("n \\(3 2 1\\)")
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"n (2 2 1)"))
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(substitute* "test/Lagrangian/parabolic/system/decomposeParDict"
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(("numberOfSubdomains 6")
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"numberOfSubdomains 4")
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(("n \\(3 2 1\\)")
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"n (2 2 1)"))))
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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 "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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)))
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(replace 'install
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(lambda _
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(let ((install-path (string-append #$output "/share/OpenFOAM-"
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#$(package-version
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this-package))))
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(mkdir-p install-path) ;create install directory
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;; move contents of build directory to install directory
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(copy-recursively "." install-path))))
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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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(etc (string-append #$output "/etc"))
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(openfoam (string-append #$output "/share/OpenFOAM-"
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#$(package-version this-package)))
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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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(symlink file
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(string-append bin "/"
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(basename file))))
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(find-files build-bin))
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(for-each (lambda (file)
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(symlink file
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(string-append bin "/"
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(basename file))))
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(find-files foam-bin))
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;; add symbolic link for standard 'lib' directory
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(symlink build-lib lib)
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;; add symbolic link for bashrc file
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(mkdir-p etc)
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(symlink (string-append openfoam "/etc/bashrc")
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(string-append etc "/bashrc"))) #t))
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(add-after 'add-symbolic-link 'wrap
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(lambda* (#:key python inputs outputs #:allow-other-keys)
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(let* ((bin (string-append #$output "/bin"))
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(openfoam-version #$(package-version this-package))
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(openfoam-root (string-append #$output "/share/OpenFOAM-"
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openfoam-version))
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(openmpi-version #$(package-version (this-package-input
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"openmpi")))
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(paraview-version #$(package-version (this-package-input
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"paraview")))
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(paraview-version-major+minor #$(version-major+minor (package-version
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(this-package-input
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"paraview")))))
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(for-each (lambda (program)
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;; wrap the programs with all the variables created by sourcing
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;; etc/bashrc
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(wrap-program program
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`("WM_PROJECT_INST_DIR" =
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(,openfoam-root))
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`("WM_PROJECT_DIR" =
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(,openfoam-root))
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'("WM_PROJECT" =
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("OpenFOAM"))
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`("WM_PROJECT_VERSION" =
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(,openfoam-version))
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'("WM_COMPILER_TYPE" =
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("system"))
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'("WM_COMPILER" =
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("Gcc"))
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'("WM_ARCH_OPTION" =
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("64"))
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'("WM_PRECISION_OPTION" =
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("DP"))
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'("WM_LABEL_SIZE" =
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("32"))
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'("WM_COMPILE_OPTION" =
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("Opt"))
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'("WM_MPLIB" =
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("SYSTEMOPENMPI"))
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'("WM_OSTYPE" =
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("POSIX"))
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'("WM_OPTIONS" =
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("linux64GccDPInt32Opt"))
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`("WM_PROJECT_USER_DIR" =
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(,(string-append "$HOME/OpenFOAM/$USER-"
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openfoam-version)))
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`("WM_THIRD_PARTY_DIR" =
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(,(string-append openfoam-root "/ThirdParty-"
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openfoam-version)))
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'("WM_LABEL_OPTION" =
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("Int32"))
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'("WM_LINK_LANGUAGE" =
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("c++"))
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'("WM_COMPILER_LIB_ARCH" =
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("64"))
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`("WM_DIR" =
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(,(string-append openfoam-root "/wmake")))
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'("WM_LDFLAGS" =
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("-m64"))
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'("WM_CC" =
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("gcc"))
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'("WM_CFLAGS" =
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("-m64 -fPIC"))
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'("WM_CXX" =
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("g++"))
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'("WM_CXXFLAGS" =
|
|
("-m64 -fPIC -std=c++0x"))
|
|
|
|
`("FOAM_INST_DIR" =
|
|
(,openfoam-root))
|
|
`("FOAM_APP" =
|
|
(,(string-append openfoam-root "/applications")))
|
|
`("FOAM_SRC" =
|
|
(,(string-append openfoam-root "/src")))
|
|
`("FOAM_ETC" =
|
|
(,(string-append openfoam-root "/etc")))
|
|
`("FOAM_TUTORIALS" =
|
|
(,(string-append openfoam-root "/tutorials")))
|
|
`("FOAM_UTILITIES" =
|
|
(,(string-append openfoam-root
|
|
"/applications/utilities")))
|
|
`("FOAM_SOLVERS" =
|
|
(,(string-append openfoam-root
|
|
"/applications/solvers")))
|
|
`("FOAM_MPI" =
|
|
(,(string-append "openmpi-" openmpi-version)))
|
|
`("FOAM_RUN" =
|
|
(,(string-append "$HOME/OpenFOAM/$USER-"
|
|
openfoam-version "/run")))
|
|
`("FOAM_EXT_LIBBIN" =
|
|
(,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32/lib")))
|
|
`("FOAM_APPBIN" =
|
|
(,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/bin")))
|
|
`("FOAM_JOB_DIR" =
|
|
(,(string-append openfoam-root "/jobControl")))
|
|
`("FOAM_LIBBIN" =
|
|
(,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/lib")))
|
|
`("FOAM_SITE_LIBBIN" =
|
|
(,(string-append openfoam-root "/site/"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/lib")))
|
|
`("FOAM_SITE_APPBIN" =
|
|
(,(string-append openfoam-root "/site/"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/bin")))
|
|
`("FOAM_USER_LIBBIN" =
|
|
(,(string-append "$HOME/OpenFOAM/$USER-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/lib")))
|
|
`("FOAM_USER_APPBIN" =
|
|
(,(string-append "$HOME/OpenFOAM/$USER-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/bin")))
|
|
`("FOAM_MODULES" =
|
|
(,(string-append openfoam-root
|
|
"/applications/modules")))
|
|
'("FOAM_SIGFPE" =
|
|
(""))
|
|
'("FOAM_SETTINGS" =
|
|
(""))
|
|
|
|
`("ParaView_INCLUDE_DIR" =
|
|
(,(string-append #$(this-package-input
|
|
"paraview")
|
|
"/include/paraview-"
|
|
paraview-version-major+minor)))
|
|
'("ParaView_GL" =
|
|
("mesa"))
|
|
`("ParaView_VERSION" =
|
|
(,paraview-version))
|
|
`("ParaView_MAJOR" =
|
|
(,paraview-version-major+minor))
|
|
`("ParaView_DIR" =
|
|
(,#$(this-package-input "paraview")))
|
|
`("PV_PLUGIN_PATH" =
|
|
(,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/lib/paraview-"
|
|
paraview-version-major+minor)))
|
|
|
|
`("MPI_ARCH_PATH" =
|
|
(,#$(this-package-input "openmpi")))
|
|
`("OPAL_PREFIX" =
|
|
(,#$(this-package-input "openmpi")))
|
|
'("MPI_BUFFER_SIZE" =
|
|
("20000000"))
|
|
|
|
`("LD_LIBRARY_PATH" prefix
|
|
(,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64Gcc/gperftools-svn/lib") ,
|
|
(string-append #$(this-package-input
|
|
"paraview") "/lib")
|
|
,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/lib/openmpi-"
|
|
openmpi-version)
|
|
,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32/lib/openmpi-"
|
|
openmpi-version)
|
|
,(string-append #$(this-package-input
|
|
"openmpi") "/lib")
|
|
,(string-append #$(this-package-input
|
|
"openmpi") "/lib64")
|
|
,(string-append "$HOME/OpenFOAM/$USER-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/lib")
|
|
,(string-append openfoam-root "/site/"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/lib")
|
|
,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/lib")
|
|
,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32/lib")
|
|
,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/lib/openmpi-system")))
|
|
`("PATH" prefix
|
|
(,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64Gcc/gperftools-svn/bin") ,
|
|
(string-append #$(this-package-input
|
|
"paraview") "/bin")
|
|
,(string-append openfoam-root "/ThirdParty-"
|
|
openfoam-version
|
|
"/platforms/linux64Gcc/cmake-*/bin")
|
|
,(string-append #$(this-package-input
|
|
"openmpi") "/bin")
|
|
,(string-append openfoam-root "/bin")
|
|
,(string-append openfoam-root "/wmake")
|
|
,(string-append "$HOME/OpenFOAM/$USER-"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/bin")
|
|
,(string-append openfoam-root "/site/"
|
|
openfoam-version
|
|
"/platforms/linux64GccDPInt32Opt/bin")
|
|
,(string-append openfoam-root
|
|
"/platforms/linux64GccDPInt32Opt/bin")))))
|
|
(find-files bin))))))))
|
|
;; Note:
|
|
;; Tutorial files are installed read-only in /gnu/store.
|
|
;; To allow write permissions on files copied from the store a
|
|
;; 'chmod' step is needed before running the applications. For
|
|
;; example, from a user's login:
|
|
;; $ source $(foamEtcFile bashrc)
|
|
;; $ mkdir -p $FOAM_RUN
|
|
;; $ cd $FOAM_RUN
|
|
;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
|
|
;; $ cd pitzDaily
|
|
;; $ chmod -R u+w .
|
|
;; $ blockMesh
|
|
(home-page "https://openfoam.org")
|
|
(synopsis "Framework for numerical simulation of fluid flow")
|
|
(description
|
|
"OpenFOAM provides a set of solvers and methods for tackling
|
|
problems in the field of Computational Fluid Dynamics (CFD). It is written in
|
|
C++. Governing equations such as the Navier-Stokes equations can be solved in
|
|
integral form. Physical processes such as phase change, droplet transport and
|
|
chemical reaction can be modelled. Numerical methods are included to deal with
|
|
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+)))
|
|
|
|
(define-public openfoam-com
|
|
;; This is a fork of 'openfoam-org', maintained separately.
|
|
(package
|
|
(inherit openfoam-org)
|
|
(name "openfoam-com")
|
|
(version "2506")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://gitlab.com/openfoam/core/openfoam")
|
|
(commit (string-append "OpenFOAM-v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "1g8cjiqkk4yp5kmxyv8z43aaalr5459i54yaqmkn6qr38cjrhnd2"))))
|
|
(arguments
|
|
;; Since 'arguments' is a function of the package's version, define
|
|
;; 'parent' such that the 'arguments' thunk gets to see the right
|
|
;; version.
|
|
(let ((parent (package
|
|
(inherit openfoam-org)
|
|
(version (package-version this-package)))))
|
|
(substitute-keyword-arguments (package-arguments parent)
|
|
((#:phases phases)
|
|
#~(modify-phases #$phases
|
|
(delete 'disable-failing-tests))))))
|
|
(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 pyproject-build-system)
|
|
(arguments '())
|
|
(native-inputs
|
|
(modify-inputs (package-native-inputs open-simulation-interface)
|
|
(append python-pytest python-setuptools)))
|
|
(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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'build 'mpi-setup
|
|
#$%openmpi-setup)
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(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"))))))))
|
|
(native-inputs
|
|
(list python-pytest
|
|
python-pytest-cov
|
|
python-setuptools
|
|
python-wheel))
|
|
(inputs
|
|
(list openmpi python-numpy))
|
|
(propagated-inputs
|
|
(list python-mpi4py))
|
|
(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 "2025.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics_ufl" version))
|
|
(sha256
|
|
(base32 "1k2r7s1c7dqlgkah4jr08lqy4z17h49r94yxjm7ca16vgvqvq1xg"))))
|
|
(build-system pyproject-build-system)
|
|
(inputs (list python-numpy))
|
|
(native-inputs (list python-pytest python-setuptools))
|
|
(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-ufl-2019
|
|
(package/inherit python-fenics-ufl
|
|
(name "python-fenics-ufl")
|
|
(version "2019.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "fenics-ufl" version))
|
|
(sha256
|
|
(base32 "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))))
|
|
|
|
;; XXX: This package is quite dated and upstream no longer maintains it: "This
|
|
;; repository was archived by the owner on Feb 21, 2022. It is now read-only."
|
|
;; <https://bitbucket.org/fenics-project/fiat> ->
|
|
;; <https://github.com/FEniCS/fiat> while providing a new refactored fork
|
|
;; <https://github.com/firedrakeproject/fiat>.
|
|
(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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
#~(list
|
|
;; 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/.
|
|
"--ignore=test/regression/"
|
|
"--ignore=test/unit/test_quadrature.py"
|
|
"--ignore=test/unit/test_reference_element.py"
|
|
"-k" (string-join
|
|
(list "not test_nodality"
|
|
"test_basis_values")
|
|
" and not "))))
|
|
(native-inputs
|
|
(list python-pytest
|
|
python-setuptools
|
|
python-wheel))
|
|
(propagated-inputs
|
|
(list python-numpy
|
|
python-sympy))
|
|
(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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#: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 "pytest" "unit/" "--ignore=unit/ufc/")
|
|
(with-directory-excursion "uflacs"
|
|
(invoke "pytest" "unit/"))))))))
|
|
(native-inputs (list python-pytest python-setuptools))
|
|
(propagated-inputs (list python-fenics-dijitso python-fenics-fiat
|
|
python-fenics-ufl-2019))
|
|
(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"
|
|
"fenics-dolfin-hdf5-version-check.patch"
|
|
"fenics-dolfin-integer-types.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-1.83
|
|
eigen
|
|
hdf5-parallel-openmpi
|
|
libxml2
|
|
openmpi
|
|
python-3
|
|
pt-scotch32
|
|
suitesparse
|
|
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=OFF"
|
|
"-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"
|
|
#$(this-package-input "scotch"))
|
|
(setenv "UMFPACK_DIR"
|
|
#$(this-package-input "suitesparse"))))
|
|
(add-before 'check 'pre-check
|
|
(lambda _
|
|
;; The Dolfin repository uses git-lfs, whereby web links are
|
|
;; substituted for large files. 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 "
|
|
"demo_stokes-iterative_mpi"
|
|
")\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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
#~(list
|
|
"unit"
|
|
;; This test fails and is ignored.
|
|
"--deselect"
|
|
"unit/nls/test_PETScSNES_solver.py::test_snes_set_from_options"
|
|
;; These tests are flaky.
|
|
"--deselect=unit/common/test_timer.py::test_context_manager_named"
|
|
"--deselect=unit/common/test_timer.py::test_context_manager_anonymous"
|
|
;; FIXME: Tests with binary encoded hdf5 files fail with a
|
|
;; segfault. See fenics-project DOLFIN commit 6fbc9fb.
|
|
"--ignore=unit/io/test_XDMF.py")
|
|
#: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 v3.1.2. See
|
|
;; <https://github.com/matplotlib/matplotlib/issues/15382>.
|
|
;; Also exclude tests that require meshes supplied by git-lfs.
|
|
(substitute* "demo/test.py"
|
|
(("(.*stem !.*)" line)
|
|
(format #f "~a
|
|
excludeList = [~{ '~a',~% ~}]
|
|
demos = [d for d in demos if d[0].stem not in excludeList]~%"
|
|
line
|
|
(list "built-in-meshes"
|
|
"hyperelasticity"
|
|
"elasticity"
|
|
"multimesh-quadrature"
|
|
"multimesh-marking"
|
|
"mixed-poisson-sphere"
|
|
"mesh-quality"
|
|
"lift-drag"
|
|
"elastodynamics"
|
|
"dg-advection-diffusion"
|
|
"curl-curl"
|
|
"contact-vi-tao"
|
|
"contact-vi-snes"
|
|
"collision-detection"
|
|
"buckling-tao"
|
|
"auto-adaptive-navier-stokes"
|
|
"advection-diffusion"
|
|
"subdomains"
|
|
"stokes-taylor-hood"
|
|
"stokes-mini"
|
|
"navier-stokes"
|
|
"eigenvalue"))))
|
|
;; Do not test for expired numpy aliases.
|
|
(substitute* "test/unit/la/test_vector.py"
|
|
((" numpy.float\\(42.0\\),") "")
|
|
(("^.*numpy.int\\(42.0\\).*$") ""))
|
|
(substitute* "test/unit/la/test_la_basic.py"
|
|
((" int,") " ")
|
|
(("\\[int,") "["))
|
|
(setenv "HOME" (getcwd))
|
|
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
|
|
(setenv "OPENBLAS_NUM_THREADS" "1")))
|
|
(replace 'check
|
|
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
|
(when tests?
|
|
(with-directory-excursion "test"
|
|
(apply invoke "pytest" test-flags)))))
|
|
(add-after 'install 'install-demo-files
|
|
(lambda _
|
|
(let* ((demos (string-append #$output
|
|
"/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)$")))))))))
|
|
(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
|
|
python-setuptools)))
|
|
(propagated-inputs
|
|
(list fenics-dolfin
|
|
python-petsc4py
|
|
python-slepc4py
|
|
;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at runtime.
|
|
python-pkgconfig))
|
|
(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 "5.3.5")
|
|
(source
|
|
(origin
|
|
;; Using PyPI rather than git because some test files must be
|
|
;; downloaded through git-fls.
|
|
(method url-fetch)
|
|
(uri (pypi-uri "meshio" version))
|
|
(sha256
|
|
(base32 "0vaqhygr2d186qixvfckzqf4447674ylnc0rl5pa16zjv6mh27zj"))))
|
|
(build-system pyproject-build-system)
|
|
(inputs (list python-h5py python-netcdf4))
|
|
(native-inputs (list python-pytest python-setuptools))
|
|
(propagated-inputs (list python-numpy python-rich))
|
|
(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-simpy
|
|
(package
|
|
(name "python-simpy")
|
|
(version "4.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "simpy" version))
|
|
(sha256
|
|
(base32 "19h1a3wxygyi819njmnl8cbmzvflqv3hpki0iq71xcc4g057bl06"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
;; tests: 141 passed, 10 deselected, 10 warnings
|
|
#:test-flags
|
|
;; Doctests require deprecated python-py.
|
|
#~(list "--ignore=docs/")))
|
|
(native-inputs
|
|
(list python-pytest
|
|
python-setuptools
|
|
python-setuptools-scm))
|
|
(home-page "https://gitlab.com/team-simpy/simpy")
|
|
(synopsis "Process-based discrete-event simulation framework")
|
|
(description
|
|
"SimPy is a process-based discrete-event simulation framework based
|
|
on standard Python. Processes in SimPy are defined by Python generator
|
|
functions and can, for example, be used to model active components like
|
|
customers, vehicles or agents. SimPy also provides various types of shared
|
|
resources to model limited capacity congestion points (like servers, checkout
|
|
counters and tunnels).")
|
|
(license license:bsd-2)))
|
|
|
|
(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.
|
|
"--import-mode=importlib"
|
|
"--ignore=tests/firedrake_adjoint"
|
|
"--ignore=tests/fenics_adjoint/test_dynamic_meshes.py"
|
|
"-k" (string-append "not test_sin_weak_spatial and "
|
|
"not test_shape_hessian and "
|
|
"not test_read_checkpoint and "
|
|
"not test_lu_solver and "
|
|
"not test_lu_solver_function_ctrl and "
|
|
"not test_dirichletbc_subspace"))
|
|
#: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
|
|
python-setuptools
|
|
python-wheel))
|
|
(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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
#~(list "--ignore=scripts/test_vehicle.py" ; import error
|
|
"-k" "not test_std") ; flaky
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(native-inputs
|
|
(list python-matplotlib
|
|
python-pytest
|
|
python-scipy
|
|
python-setuptools))
|
|
(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 pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:tests? #f ; No tests.
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("protobuf==3.20.1") "protobuf >= 3.20.1"))
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(propagated-inputs (list python-commonroad-vehicle-models
|
|
python-iso3166
|
|
python-lxml
|
|
python-matplotlib
|
|
python-networkx
|
|
python-numpy
|
|
python-omegaconf
|
|
python-pillow
|
|
python-protobuf
|
|
python-rtree
|
|
python-scipy
|
|
python-shapely
|
|
python-tqdm))
|
|
(native-inputs (list python-lxml python-setuptools))
|
|
(home-page "https://commonroad.in.tum.de/")
|
|
(synopsis "Read, write, and visualize CommonRoad scenarios")
|
|
(description "This package provides methods to read, write, and visualize
|
|
CommonRoad scenarios and planning problems. It can be used as a framework for
|
|
implementing motion planning algorithms to solve CommonRoad Benchmarks
|
|
and is the basis for other tools of the CommonRoad Framework.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-commonroad-route-planner
|
|
(package
|
|
(name "python-commonroad-route-planner")
|
|
(version "2022.3")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://gitlab.lrz.de/tum-cps/commonroad-route-planner")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0xn0l7bzmj56d4mlqacvbl8mdvsffkg2fn2lzfmis5jl4vp99ipf"))))
|
|
(arguments
|
|
(list
|
|
#:tests? #f ; No tests.
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-setup.py
|
|
(lambda _
|
|
#$%commonroad-dont-install-license-at-root)))))
|
|
(build-system pyproject-build-system)
|
|
(native-inputs (list python-setuptools))
|
|
(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-1.8 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+))))
|