;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2022 Liliana Marie Prikler <liliana.prikler@gmail.com>
;;; Copyright © 2023 Reza Housseini <reza@housseini.me>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages simulation)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages admin)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages engineering)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages fontutils)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages geo)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages image)
  #:use-module (gnu packages iso-codes)
  #:use-module (gnu packages image-processing)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages m4)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages qt)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages version-control)
  #:use-module (gnu packages video)
  #:use-module (gnu packages xiph)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix svn-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system pyproject)
  #:use-module (guix build-system python)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #:use-module (guix utils)
  #:use-module (ice-9 ftw)
  #:use-module (ice-9 match)
  #:use-module (ice-9 regex)
  #:use-module (srfi srfi-1))

(define-public openfoam-org
  (package
    (name "openfoam-org")
    (version "10.20230119")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url (string-append "https://github.com/OpenFOAM/OpenFOAM-"
                                        (version-major version)))
                    (commit (second (string-split version #\.)))))
              (sha256
               (base32
                "0icvwg7s6vnkgmdiczivia9pbrgx8nanw9a4j080fzfvdv9vxhzp"))
              (file-name (git-file-name name version))
              (modules '((guix build utils)))
              (snippet `(begin
                          ;; patch shell paths
                          (substitute* (list "wmake/src/Makefile"
                                             "wmake/makefiles/general")
                            (("/bin/sh")
                             "sh"))
                          (substitute* "etc/bashrc"
                            ;; only go back one folder level
                            (("\\$\\(dirname \\$\\{BASH_SOURCE:-\\$0\\}\\)/../..")
                             "$(dirname ${BASH_SOURCE:-$0})/..")
                            ;; do not use openfoam folder convention
                            (("^export WM_PROJECT_DIR=.*$")
                             (string-append
                              "export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR\n"))
                            ;; do not source bash_completion (gives error)
                            (("^.*bash_completion.*$" all)
                             (string-append "#" all))
                            ;; set same version as guix package
                            (("^export WM_PROJECT_VERSION=.*$")
                             (string-append "export WM_PROJECT_VERSION="
                                            ,version "\n")))
                          ;; add expand flag to RunFunctions
                          (substitute* "bin/tools/RunFunctions"
                            (("foamDictionary (.*)" all args)
                             (string-append "foamDictionary -expand " args)))
                          ;; disable failing test
                          (substitute* "test/postProcessing/channel/Allrun"
                            (("^.*getApplication.*$" all)
                             (string-append "#" all "\n")))))))
    (build-system gnu-build-system)
    (inputs (list boost
                  cgal
                  git
                  gmp
                  libxt
                  metis
                  mpfr
                  ncurses
                  openmpi
                  openssh
                  paraview
                  pt-scotch32
                  readline
                  zlib))
    (native-inputs (list bison
                         flex
                         ;; paraview plugin dependencies
                         cli11
                         cmake-minimal
                         cgns
                         curl
                         double-conversion
                         eigen
                         expat
                         ffmpeg
                         fmt
                         freetype
                         gdal
                         gl2ps
                         glew
                         gmsh
                         hdf5
                         jsoncpp
                         libjpeg-turbo
                         libogg
                         libpng
                         libharu
                         libtheora
                         libtiff
                         libx11
                         libxml2
                         lz4
                         netcdf
                         nlohmann-json
                         proj
                         protobuf
                         pugixml
                         python
                         python-mpi4py
                         qtbase-5
                         qtsvg-5
                         qttools-5
                         qtwebengine-5
                         qtxmlpatterns
                         utfcpp
                         vtk
                         xz))
    (propagated-inputs (list gnuplot))
    (outputs '("debug" ;~60MB
               "out"))
    (arguments
     (list
      ;; Executable files and shared libraries are located in the 'platforms'
      ;; subdirectory.
      #:strip-directories
      #~(list "share/OpenFOAM/platforms/linux64GccDPInt32Opt/bin"
              "share/OpenFOAM/platforms/linux64GccDPInt32Opt/lib")

      #:modules
      '((ice-9 ftw)
        (ice-9 regex)
        (ice-9 string-fun)
        (srfi srfi-1)
        (guix build gnu-build-system)
        (guix build utils))

      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'patch-HOME-path
            (lambda _
              (setenv "HOME" "/tmp")))
          (add-before 'build 'rename-self
            (lambda _
              ;; The script 'bin/foamEtcFile' derives the version name based
              ;; on the current directory name (!), so make sure to follow the
              ;; expected naming convention.
              (let ((here (canonicalize-path "."))
                    (target #$(string-append
                               "OpenFOAM-"
                               (string-map (match-lambda
                                             (#\. #\-)
                                             (chr chr))
                                           (package-version this-package)))))
                (chdir "..")
                (format #t "renaming '~a' to '~a'~%"
                        here target)
                (rename-file here target)
                (chdir target))))
          (add-before 'build 'patch-scotch
            (lambda _
              (substitute* "etc/config.sh/scotch"
                (("^export SCOTCH_VERSION=scotch_.*$")
                 (string-append "export SCOTCH_VERSION=scotch_"
                                #$(package-version pt-scotch32) "\n"))
                (("^export SCOTCH_ARCH_PATH=.*$")
                 (string-append "export SCOTCH_ARCH_PATH="
                                (assoc-ref %build-inputs "pt-scotch32")
                                "\n"))) #t))
          (add-before 'build 'patch-mpi
            (lambda _
              (let* ((mpi-path (assoc-ref %build-inputs "openmpi"))
                     (mpi-version #$(package-version openmpi)))
                ;; specify openmpi type
                (substitute* "etc/bashrc"
                  (("WM_MPLIB=SYSTEMOPENMPI")
                   "WM_MPLIB=OPENMPI"))
                (substitute* "etc/config.sh/mpi"
                  (("export FOAM_MPI=openmpi-.*$")
                   (string-append "export FOAM_MPI=openmpi-"
                                  mpi-version "\n"))
                  (("export MPI_ARCH_PATH=.*\\$FOAM_MPI.*$")
                   (string-append "export MPI_ARCH_PATH=" mpi-path
                                  "\n")))) #t))
          (add-before 'build 'patch-paraview
            (lambda _
              (substitute* "etc/config.sh/paraview"
                (("^export ParaView_VERSION=.*$")
                 (string-append "export ParaView_VERSION="
                                #$(package-version paraview) "\n"))
                (("^export ParaView_DIR=.*$")
                 (string-append "export ParaView_DIR="
                                (assoc-ref %build-inputs "paraview")
                                "\n"))) #t))
          (add-before 'build 'add-rpaths
            (lambda _
              (letrec* ((libraries '("boost" "cgal"
                                     "gmp"
                                     "metis"
                                     "mpfr"
                                     "pt-scotch32"
                                     "openmpi"
                                     "zlib"
                                     "paraview"))
                        (rpaths
                         (fold-right (lambda (library rpaths)
                                       (string-append rpaths
                                                      "-rpath="
                                                      (assoc-ref
                                                       %build-inputs library)
                                                      "/lib,")) "" libraries))
                        (openfoam-lib
                         (string-append #$output
                                        "/share/OpenFOAM/platforms/linux64GccDPInt32Opt/lib"))
                        (ldflags
                         (string-append "-Wl,"
                                        rpaths
                                        "-rpath="
                                        openfoam-lib
                                        ","
                                        "-rpath="
                                        openfoam-lib
                                        "/dummy,"
                                        "-rpath="
                                        openfoam-lib
                                        "/paraview-"
                                        #$(version-major+minor (package-version
                                                                paraview)))))
                (substitute* "wmake/rules/linux64Gcc/c++"
                  (("\\$\\(LIB_HEADER_DIRS\\) -fPIC" all)
                   (string-append all " " ldflags)))) #t))
          (add-before 'build 'add-vtk-include-path
            (lambda _
              (let* ((vtk-version #$(version-major+minor
                                     (package-version vtk)))
                     (vtk-root (assoc-ref %build-inputs "vtk"))
                     (vtk-inc (string-append vtk-root "/include/vtk-" vtk-version))
                     (vtk-inc-flag (string-append "-I" vtk-inc)))
                (substitute* "wmake/rules/linux64Gcc/c++"
                  (("\\$\\(LIB_HEADER_DIRS\\)" all)
                   (string-append all " " vtk-inc-flag " "))))
              #t))
          (delete 'configure) ;no configure phase
          (replace 'build
            (lambda _
              ;; compile OpenFOAM libraries and applications
              (invoke "bash" "-c"
                      (format #f
                              "source ./etc/bashrc && ./Allwmake -j~a"
                              (parallel-job-count)))))
          (add-after 'build 'cleanup
            ;; Avoid unnecessary, voluminous object and dep files.
            (lambda _
              (when (file-exists? "platforms/linux64GccDPInt32Opt/src")
                (delete-file-recursively
                 "platforms/linux64GccDPInt32Opt/src"))
              (when (file-exists?
                     "platforms/linux64GccDPInt32OptOPENMPI")
                (delete-file-recursively
                 "platforms/linux64GccDPInt32OptOPENMPI"))
              (for-each delete-file
                        (find-files "." "\\.o$")) #t))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
                (when (file-exists? "test")
                  (with-directory-excursion "test"
                    (invoke "bash" "-c"
                            (format #f
                                    "source ../etc/bashrc && ./Allrun -j~a"
                                    (parallel-job-count)))))
                ;; too many tutorials are failing
                ;; (with-directory-excursion "tutorials"
                ;; (invoke "bash" "-c" "source ../etc/bashrc && ./Alltest"))
                ) #t))
          (replace 'install
            (lambda _
              (let ((install-dir (string-append #$output
                                                "/share/OpenFOAM")))
                (mkdir-p install-dir) ;create install directory
                ;; move contents of build directory to install directory
                (copy-recursively "." install-dir))))
          (add-after 'install 'add-symbolic-link
            (lambda _
              (let* ((bin (string-append #$output "/bin"))
                     (lib (string-append #$output "/lib"))
                     (openfoam (string-append #$output
                                              "/share/OpenFOAM"))
                     (build-bin (string-append openfoam
                                               "/platforms/linux64GccDPInt32Opt/bin"))
                     (build-lib (string-append openfoam
                                               "/platforms/linux64GccDPInt32Opt/lib"))
                     (foam-bin (string-append openfoam "/bin")))
                ;; add symbolic links in standard 'bin' directory
                (mkdir-p bin)
                (for-each (lambda (file)
                            (unless (member file
                                            '("." ".."))
                              (symlink (string-append build-bin "/"
                                                      file)
                                       (string-append bin "/" file))))
                          (scandir build-bin))
                (for-each (lambda (file)
                            (unless (member file
                                            '("." ".."))
                              (symlink (string-append foam-bin "/"
                                                      file)
                                       (string-append bin "/" file))))
                          (scandir foam-bin))
                ;; add symbolic link for standard 'lib' directory
                (symlink build-lib lib)) #t)))))
    (native-search-paths
     (list (search-path-specification
            (variable "WM_PROJECT_DIR")
            (separator #f)
            (files '("share/OpenFOAM")))))
    ;; 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 $(dirname $(which blockMesh))/../../../etc/bashrc
    ;; $ mkdir -p $FOAM_RUN
    ;; $ cd $FOAM_RUN
    ;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
    ;; $ cd pitzDaily
    ;; $ chmod -R u+w .
    ;; $ blockMesh
    (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+)
    (home-page "https://openfoam.org")))

(define-public openfoam
  (deprecated-package "openfoam" openfoam-org))

(define-public openfoam-com
  ;; This is a fork of 'openfoam-org', maintained separately.
  (package
    (inherit openfoam-org)
    (name "openfoam-com")
    (version "2212")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://develop.openfoam.com"
                                  "/Development/openfoam/-/archive/OpenFOAM-v"
                                  version
                                  "/openfoam-OpenFOAM-v"
                                  version
                                  ".tar.gz"))
              (sha256
               (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="
					    ,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* (openfoam-package source version name home-page synopsis)
  (let* ((install-path (string-append "share/OpenFOAM-" version))
         (paraview-version (version-major+minor (package-version paraview)))
         (pv-plugin-path
          (string-append install-path
                         "/platforms/linux64GccDPInt32Opt/lib/paraview-"
                         paraview-version)))
    (package
      (name name)
      (version version)
      (source source)
      (build-system gnu-build-system)
      (native-search-paths
       (list (search-path-specification
	      (variable "WM_PROJECT_DIR")
	      (files `(,install-path)))
             ;; add PV_PLUGIN_PATH to LD_LIBRARY_PATH so paraview
             ;; finds the OpenFOAM PV plugins
             (search-path-specification
	      (variable "LD_LIBRARY_PATH")
	      (files `(,pv-plugin-path)))))
      (inputs (list boost
		    cgal
		    git
		    gmp
		    libxt
		    metis
		    mpfr
		    ncurses
		    openmpi
		    openssh
		    paraview
		    pt-scotch32
		    readline
		    scotch
		    zlib))
      (native-inputs (list bison
		           flex
		           ;; paraview plugin dependencies
		           cli11
		           cmake-minimal
		           cgns
		           curl
		           double-conversion
		           eigen
		           expat
		           ffmpeg
		           fmt
		           freetype
		           gdal
		           gl2ps
		           glew
		           gmsh
		           hdf5
		           jsoncpp
		           libjpeg-turbo
		           libogg
		           libpng
		           libharu
		           libtheora
		           libtiff
		           libx11
		           libxml2
		           lz4
		           netcdf
		           nlohmann-json
		           proj
		           protobuf
		           pugixml
		           python
		           python-mpi4py
		           qtbase-5
		           qtsvg-5
		           qttools-5
		           qtwebengine-5
		           qtxmlpatterns
		           utfcpp
		           vtk
		           xz))
      (propagated-inputs (list gnuplot))
      (outputs '("debug" ;~60MB
	         "out"))
      (arguments
       (list
        ;; Executable files and shared libraries are located in the 'platforms'
        ;; subdirectory.
        #:strip-directories
        #~(list (string-append "OpenFOAM-" #$version "/platforms/linux64GccDPInt32Opt/bin")
	        (string-append "OpenFOAM-" #$version "/platforms/linux64GccDPInt32Opt/lib"))

        #:modules
        '((ice-9 ftw)
          (ice-9 regex)
          (ice-9 string-fun)
          (srfi srfi-1)
          (guix build gnu-build-system)
          (guix build utils))

        #:phases
        #~(modify-phases %standard-phases
	    (add-before 'build 'patch-HOME-path
	      (lambda _
	        (setenv "HOME" "/tmp") #t))
	    (add-before 'build 'patch-scotch
	      (lambda _
	        (substitute* "etc/config.sh/scotch"
	          (("^export SCOTCH_VERSION=scotch_.*$")
	           (string-append "export SCOTCH_VERSION=scotch_"
			          #$(package-version pt-scotch32) "\n"))
	          (("^export SCOTCH_ARCH_PATH=.*$")
	           (string-append "export SCOTCH_ARCH_PATH=" #$pt-scotch32 "\n")))
	        #t))
	    (add-before 'build 'patch-mpi
	      (lambda _
	        (let* ((mpi-version #$(package-version openmpi)))
	          ;; specify openmpi type
	          (substitute* "etc/bashrc"
		    (("WM_MPLIB=SYSTEMOPENMPI")
		     "WM_MPLIB=OPENMPI"))
	          (substitute* "etc/config.sh/mpi"
		    (("export FOAM_MPI=openmpi-.*$")
		     (string-append "export FOAM_MPI=openmpi-"
				    mpi-version "\n"))
		    (("export MPI_ARCH_PATH=.*\\$FOAM_MPI.*$")
		     (string-append "export MPI_ARCH_PATH=" #$openmpi "\n"))))
	        #t))
	    (add-before 'build 'patch-paraview
	      (lambda _
	        (substitute* "etc/config.sh/paraview"
	          (("^export ParaView_VERSION=.*$")
	           (string-append "export ParaView_VERSION="
			          #$(package-version paraview) "\n"))
	          (("^export ParaView_DIR=.*$")
	           (string-append "export ParaView_DIR=" #$paraview "\n"))
                  (("export ParaView_GL=mesa") "export ParaView_GL=system"))
	        #t))
	    (add-before 'build 'add-rpaths
	      (lambda _
	        (letrec* ((libraries '("boost"
				       "cgal"
				       "gmp"
				       "metis"
				       "mpfr"
				       "scotch"
				       "pt-scotch32"
 				       "openmpi"
				       "zlib"
				       "paraview"))
		          (rpaths
		           (fold-right (lambda (lib rpaths)
				         (string-append rpaths
						        "-rpath="
						        (assoc-ref %build-inputs lib)
						        "/lib,")) "" libraries))
		          (openfoam-lib
		           (string-append #$output
				          "/share/OpenFOAM-" #$version
				          "/platforms/linux64GccDPInt32Opt/lib"))
		          (ldflags
		           (string-append "-Wl,"
				          rpaths
				          "-rpath="
				          openfoam-lib
				          ","
				          "-rpath="
				          openfoam-lib
				          "/dummy,"
				          "-rpath="
				          openfoam-lib
				          "/paraview-"
				          #$(version-major+minor (package-version
							          paraview)))))
	          (substitute* "wmake/rules/linux64Gcc/c++"
		    (("\\$\\(LIB_HEADER_DIRS\\) -fPIC" all)
		     (string-append all " " ldflags)))) #t))
	    (add-before 'build 'add-vtk-include-path
	      (lambda _
	        (let* ((vtk-version #$(version-major+minor
				       (package-version vtk)))
		       (vtk-inc (string-append #$vtk "/include/vtk-" vtk-version))
		       (vtk-inc-flag (string-append "-I" vtk-inc)))
	          (substitute* "wmake/rules/linux64Gcc/c++"
		    (("\\$\\(LIB_HEADER_DIRS\\)" all)
		     (string-append all " " vtk-inc-flag " "))))
	        #t))
	    (delete 'configure) ;no configure phase
	    (replace 'build
	      (lambda _
	        ;; compile OpenFOAM libraries and applications
	        (invoke "bash" "-c"
		        (format #f
			        "source ./etc/bashrc && ./Allwmake -j~a"
			        (parallel-job-count)))))
	    (add-after 'build 'cleanup
	      ;; Avoid unnecessary, voluminous object and dep files.
	      (lambda _
	        (when (file-exists? "platforms/linux64GccDPInt32Opt/src")
	          (delete-file-recursively
	           "platforms/linux64GccDPInt32Opt/src"))
	        (when (file-exists?
		       "platforms/linux64GccDPInt32OptOPENMPI")
	          (delete-file-recursively
	           "platforms/linux64GccDPInt32OptOPENMPI"))
	        (for-each delete-file
		          (find-files "." "\\.o$"))
                ;; Remove spurious files in src tree
                (invoke "bash" "-c" "source ./etc/bashrc && wclean all")
                #t))
	    (replace 'check
	      (lambda* (#:key tests? #:allow-other-keys)
	        (when tests?
	          (when (file-exists? "test")
		    (with-directory-excursion "test"
		      (invoke "bash" "-c"
			      (format #f
				      "source ../etc/bashrc && ./Allrun -j~a"
				      (parallel-job-count)))
                      ;; cleanup
                      (invoke "bash" "-c"
			      "source ../etc/bashrc && ./Allclean")))
	          ;; too many tutorials are failing
	          ;; (with-directory-excursion "tutorials"
	          ;; (invoke "bash" "-c" "source ../etc/bashrc && ./Alltest"))
	          ) #t))
	    (add-before 'install 'set-paths
	      (lambda _
	        (let ((install-path (string-append #$output
					           "/share/OpenFOAM-" #$version)))
	          (substitute* "etc/bashrc"
		    (("^\\[ \"\\$BASH\".*$") "")
		    (("^export FOAM_INST_DIR=\\$\\(cd.*$")
		     (string-append "export FOAM_INST_DIR=" install-path "\n"))
		    (("^export FOAM_INST_DIR=\\$HOME.*$") "")))
	        #t))
	    (replace 'install
	      (lambda* (#:key outputs inputs #:allow-other-keys)
	        (let ((install-path (string-append #$output
					           "/share/OpenFOAM-" #$version)))
	          (mkdir-p install-path) ;create install directory
	          ;; move contents of build directory to install directory
	          (copy-recursively "." install-path))))
	    (add-after 'install 'add-symbolic-link
	      (lambda _
	        (let* ((bin (string-append #$output "/bin"))
		       (lib (string-append #$output "/lib"))
		       (openfoam (string-append #$output
					        "/share/OpenFOAM-" #$version))
		       (build-bin (string-append openfoam
					         "/platforms/linux64GccDPInt32Opt/bin"))
		       (build-lib (string-append openfoam
					         "/platforms/linux64GccDPInt32Opt/lib"))
		       (foam-bin (string-append openfoam "/bin")))
	          ;; add symbolic links in standard 'bin' directory
	          (mkdir-p bin)
	          (for-each (lambda (file)
			      (unless (member file
					      '("." ".."))
			        (symlink (string-append build-bin "/"
						        file)
				         (string-append bin "/" file))))
			    (scandir build-bin))
	          (for-each (lambda (file)
			      (unless (member file
					      '("." ".."))
			        (symlink (string-append foam-bin "/"
						        file)
				         (string-append bin "/" file))))
			    (scandir foam-bin))
	          ;; add symbolic link for standard 'lib' directory
	          (symlink build-lib lib)) #t)))))
      ;; 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 $WM_PROJECT_DIR/etc/bashrc
      ;; $ mkdir -p $FOAM_RUN
      ;; $ cd $FOAM_RUN
      ;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
      ;; $ cd pitzDaily
      ;; $ chmod -R u+w .
      ;; $ blockMesh
      (synopsis synopsis)
      (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+)
      (home-page home-page))))

(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 "2.27.1")
    (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"
                                       "esmini-no-clutter-log.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
                "07ccydz7kxy5jc52f8fmxg4nkr1spshfnpzcv0wgd5lqz9ghjahz"))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags #~(list "-DDYN_PROTOBUF=TRUE")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'fix-cmake
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (substitute* "CMakeLists.txt"
                (("\\$\\{CMAKE_HOME_DIRECTORY\\}/bin")
                 (string-append (assoc-ref outputs "out") "/bin")))
              (substitute* "EnvironmentSimulator/CMakeLists.txt"
                (("\\$\\{OSI_DIR\\}/(include|lib)(-dyn)?" all what)
                 (search-input-directory
                  inputs
                  (string-append what "/osi"
                                 #$(version-major
                                    (package-version
                                     (this-package-input
                                      "open-simulation-interface"))))))
                (("\\$\\{SUMO_BASE_DIR\\}/\\$\\{EXT_DIR_NAME\\}")
                 #$(this-package-input "sumo")))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (with-directory-excursion "EnvironmentSimulator/Unittest/"
                (for-each invoke (find-files "_test$")))))
          (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 "." "\\.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
                              "$ENV{CATCH_DIR}/include" back "\n")))))))
    (build-system cmake-build-system)
    (inputs
     (list openblas
           boost
           eigen
           hdf5-parallel-openmpi
           lapack
           libxml2
           openmpi
           python-3
           pt-scotch32
           suitesparse
           sundials-openmpi
           zlib))
    (native-inputs
     (list catch-framework pkg-config))
    (propagated-inputs
     (list python-fenics-ffc petsc-openmpi slepc-openmpi))
    (arguments
     (list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
                                 "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
                                 "-DDOLFIN_ENABLE_MPI:BOOL=ON"
                                 "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
                                 "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
                                 "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
                                 "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
           #:phases
           #~(modify-phases %standard-phases
               (add-after 'patch-usr-bin-file 'mpi-setup
                 #$%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"
                           #$(this-package-input "lapack"))
                   (setenv "PETSC_DIR"
                           #$(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")
            #t))))
    (build-system python-build-system)
    (inputs
     (list fenics openmpi pybind11))
    (native-inputs
     (list pkg-config
           python-coverage
           python-decorator
           python-flake8
           python-pkgconfig
           python-pytest))
    (propagated-inputs
     `(("scipy" ,python-scipy)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'build 'mpi-setup
                    ,%openmpi-setup)
         (add-after 'install 'install-doc
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((doc (string-append (assoc-ref outputs "out")
                                        "/share/doc/" ,name "-"
                                        ,version))
                    (examples (string-append doc "/examples")))
               (mkdir-p examples)
               (copy-recursively "examples" examples))
             #t))
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (setenv "HOME" (getcwd))
               (and (invoke "py.test" "-v" "tests/fenics_adjoint"
                            "-k" "not test_read_checkpoint")
                    (invoke "py.test" "-v" "tests/migration")
                    (invoke "py.test" "-v" "tests/pyadjoint")))
             #t))
         ;; 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))))
    (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 _
                   #$%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+))))