guix/gnu/packages/simulation.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;;
;;; 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 flex)
  #:use-module (gnu packages gettext)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages gtk)
  #: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 pkg-config)
  #: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 readline)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages version-control)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (guix download)
  #: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 python)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (ice-9 ftw)
  #:use-module (ice-9 regex)
  #:use-module (srfi srfi-1))

(define-public openfoam
  (package
    (name "openfoam")
    (version "4.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://dl.openfoam.org/source/"
             (string-map (lambda (x) (if (eq? x #\.) #\- x)) version)))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d"))
       (patches (search-patches "openfoam-4.1-cleanup.patch"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides
           ;; 'major' and 'minor'.
           (substitute* "src/OSspecific/POSIX/fileStat.C"
             (("#include <unistd\\.h>")
              "#include <unistd.h>\n#include <sys/sysmacros.h>\n"))
           #t))))
    (build-system gnu-build-system)
    (inputs
     `(("boost" ,boost)
       ("cgal" ,cgal)
       ("flex" ,flex)
       ("git" ,git)
       ("gmp" ,gmp)
       ("libxt" ,libxt)
       ("metis" ,metis)
       ("mpfr" ,mpfr)
       ("ncurses" ,ncurses)
       ("readline" ,readline)
       ("scotch" ,pt-scotch32)
       ("zlib" ,zlib)))
    (native-inputs
     (list bison))
    (propagated-inputs
     (list gzip gnuplot openmpi))
    (outputs '("debug"                  ;~60MB
               "out"))
    (arguments
     `( ;; Executable files and shared libraries are located in the 'platforms'
       ;; subdirectory.
       #:strip-directories (list (string-append
                                  "lib/OpenFOAM-" ,version
                                  "/platforms/linux64GccDPInt32Opt/bin")
                                 (string-append
                                  "lib/OpenFOAM-" ,version
                                  "/platforms/linux64GccDPInt32Opt/lib"))
       #:tests? #f                                ; no tests to run

       #:modules ((ice-9 ftw)
                  (ice-9 regex)
                  (guix build gnu-build-system)
                  (guix build utils))

       #:phases (modify-phases %standard-phases
                  (add-after 'unpack 'rename-build-directory
                    (lambda _
                      (chdir "..")
                      ;; Use 'OpenFOAM-version' convention to match the file
                      ;; name expectations in the build phase.
                      (let ((unpack-dir (string-append
                                         (getcwd) "/"
                                         (list-ref (scandir (getcwd) (lambda (name)
                                                                       (string-match "^OpenFOAM" name))) 0)))
                            (build-dir (string-append
                                        (getcwd) "/OpenFOAM-" ,version)))
                        (rename-file unpack-dir build-dir) ; rename build directory
                        (chdir (basename build-dir))) ; move to build directory
                      #t))
                  (delete 'configure)             ; no configure phase
                  (replace 'build
                    (lambda _
                      (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))
                        ;; set variables to define store paths
                        (for-each (lambda (library)
                                    (setenv (string-append
                                             (string-upcase library) "_ROOT")
                                            (assoc-ref %build-inputs library))) libraries))
                      ;; set variables to define package versions
                      (setenv "SCOTCHVERSION" ,(package-version scotch))
                      (setenv "METISVERSION" ,(package-version metis))
                      ;; set variable to pass extra 'rpath' arguments to linker
                      (setenv "LDFLAGS"
                              (string-append
                               "-Wl,"
                               "-rpath=" %output "/lib/OpenFOAM-" ,version
                               "/platforms/linux64GccDPInt32Opt/lib,"
                               "-rpath=" %output "/lib/OpenFOAM-" ,version
                               "/platforms/linux64GccDPInt32Opt/lib/dummy"))
                      ;; compile OpenFOAM libraries and applications
                      (zero? (system (format #f
                                             "source ./etc/bashrc && ./Allwmake -j~a"
                                             (parallel-job-count))))))
                  (add-after 'build 'update-configuration-files
                    (lambda _
                      ;; record store paths and package versions in
                      ;; configuration files
                      (substitute* "etc/config.sh/CGAL"
                        (("$BOOST_ROOT") (getenv "BOOST_ROOT")))
                      (substitute* "etc/config.sh/CGAL"
                        (("$CGAL_ROOT") (getenv "CGAL_ROOT")))
                      (substitute* "etc/config.sh/metis"
                        (("$METIS_ROOT") (getenv "METIS_ROOT")))
                      (substitute* "etc/config.sh/metis"
                        (("$METISVERSION") (getenv "METISVERSION")))
                      (substitute* "etc/config.sh/scotch"
                        (("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT")))
                      (substitute* "etc/config.sh/scotch"
                        (("$SCOTCHVERSION") (getenv "SCOTCHVERSION")))
                      (substitute* "etc/config.sh/settings"
                        (("$GMP_ROOT") (getenv "GMP_ROOT")))
                      (substitute* "etc/config.sh/settings"
                        (("$MPFR_ROOT") (getenv "MPFR_ROOT")))
                      ;; reset lockDir variable to refer to write-enabled
                      ;; directory
                      (substitute* "wmake/wmake"
                        (("        lockDir=.*$")
                         "        lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
                      (substitute* "wmake/wmakeScheduler"
                        (("lockDir=.*$")
                         "lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
                      (substitute* "wmake/wmakeSchedulerUptime"
                        (("lockDir=.*$")
                         "lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
                      #t))
                  (add-after 'build 'cleanup
                    ;; Avoid unncessary, voluminous object and dep files.
                    (lambda _
                      (delete-file-recursively
                       "platforms/linux64GccDPInt32Opt/src")
                      (delete-file-recursively
                       "platforms/linux64GccDPInt32OptSYSTEMOPENMPI")
                      (for-each delete-file (find-files "." "\\.o$"))
                      #t))
                  (replace 'install
                    (lambda _
                      ;; use 'OpenFOAM-version' convention
                      (let ((install-dir (string-append
                                          %output "/lib/OpenFOAM-" ,version)))
                        (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 _
                      ;; add symbolic link for standard 'bin' directory
                      (symlink
                       (string-append "./lib/OpenFOAM-" ,version
                                      "/platforms/linux64GccDPInt32Opt/bin")
                       (string-append %output "/bin"))
                      #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 $GUIX_PROFILE/lib/OpenFOAM-4.1/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 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")))
            #t))))
    (build-system cmake-build-system)
    (inputs
     `(("blas" ,openblas)
       ("boost" ,boost)
       ("eigen" ,eigen)
       ("hdf5" ,hdf5-parallel-openmpi)
       ("lapack" ,lapack)
       ("libxml2" ,libxml2)
       ("openmpi" ,openmpi)
       ("python" ,python-3)
       ("scotch" ,pt-scotch32)
       ("suitesparse" ,suitesparse)
       ("sundials" ,sundials-openmpi)
       ("zlib" ,zlib)))
    (native-inputs
     `(("catch" ,catch-framework2-1)
       ("pkg-config" ,pkg-config)))
    (propagated-inputs
     `(("ffc" ,python-fenics-ffc)
       ("petsc" ,petsc-openmpi)
       ("slepc" ,slepc-openmpi)))
    (arguments
     `(#:configure-flags
       `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
         "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
         "-DDOLFIN_ENABLE_MPI:BOOL=ON"
         "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
         "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
         "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
         "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
       #:phases
       (modify-phases %standard-phases
         (add-after 'patch-usr-bin-file 'mpi-setup
           ,%openmpi-setup)
         (add-after 'patch-source-shebangs 'set-paths
           (lambda _
             ;; Define paths to store locations.
             (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas"))
             (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
             (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
             (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
             (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
             (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
             (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
             (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
             #t))
         (add-before 'check 'pre-check
           (lambda _
             ;; The Dolfin repository uses git-lfs, whereby web links are
             ;; substituted for large files.  Guix does not currently support
             ;; git-lfs, so only the links are downloaded.  The tests that
             ;; require the absent meshes cannot run and are skipped.
             ;;
             ;; 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)))
             #t))
         (replace 'check
           (lambda _
             (and (invoke "make" "unittests")
                  (invoke "make" "demos")
                  (invoke "ctest" "-R" "unittests")
                  (invoke "ctest" "-R" "demo" "-R" "serial")
                  (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
    (home-page "https://bitbucket.org/fenics-project/dolfin/")
    (synopsis "Problem solving environment for differential equations")
    (description
      "DOLFIN is a computational framework for finding numerical
solutions to problems described by differential equations.  Numerical
models in DOLFIN are constructed using general families of finite
elements.  Data structures are provided for discretizing the governing
system on a computational mesh.  A compact syntax, similar to
mathematical notation, is made available for defining function spaces
and expressing variational forms.  Interfaces to specialized matrix
solvers are provided for solving the resultant linear systems.

@code{fenics-dolfin} is part of the FEniCS project.  It is the C++
user interface to the FEniCS core components and external libraries.")
    ;; The source code for the DOLFIN C++ library is licensed under the
    ;; GNU Lesser General Public License, version 3 or later, with the
    ;; following exceptions:
    ;;
    ;; public-domain: dolfin/geometry/predicates.cpp
    ;;                dolfin/geometry/predicates.h
    ;;
    ;; zlib:          dolfin/io/base64.cpp
    ;;                dolfin/io/base64.h
    ;;
    ;; expat:         dolfin/io/pugiconfig.hpp
    ;;                dolfin/io/pugixml.cpp
    ;;                dolfin/io/pugixml.hpp
    (license (list license:public-domain
                   license:zlib
                   license:expat
                   license:lgpl3+))))

(define-public fenics
  (package/inherit fenics-dolfin
    (name "fenics")
    (build-system python-build-system)
    (inputs
     `(("pybind11" ,pybind11)
       ("python-matplotlib" ,python-matplotlib)
       ,@(alist-delete "python" (package-inputs fenics-dolfin))))
    (native-inputs
     `(("cmake" ,cmake-minimal)
       ("ply" ,python-ply)
       ("pytest" ,python-pytest)
       ("python-decorator" ,python-decorator)
       ("python-pkgconfig" ,python-pkgconfig)
       ,@(package-native-inputs fenics-dolfin)))
    (propagated-inputs
     `(("dolfin" ,fenics-dolfin)
       ("petsc4py" ,python-petsc4py)
       ("slepc4py" ,python-slepc4py)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'patch-source-shebangs 'set-paths
           (lambda _
             ;; Define paths to store locations.
             (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
             ;; Move to python sub-directory.
             (chdir "python")))
         (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 _
             (with-directory-excursion "test"
               ;; Note: The test test_snes_set_from_options() in the file
               ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
               ;; Limit the number of jobs to 3 as 500 MiB of memory is used
               ;; per process.
               (invoke "mpirun" "-np" (number->string
                                       (min 3 (parallel-job-count)))
                       "python" "-B" "-m"
                       "pytest" "unit" "--ignore"
                       "unit/nls/test_PETScSNES_solver.py"))))
         (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 "4.4.6")
    (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "meshio" version))
        (sha256
          (base32
           "0kv832s2vyff30zz8yqypw5jifwdanvh5x56d2bzkvy94h4jlddy"))
        (snippet
         '(begin
            (let ((file (open-file "setup.py" "a")))
              (display "from setuptools import setup\nsetup()" file)
              (close-port file))
            #t))))
    (build-system python-build-system)
    (inputs
     `(("h5py" ,python-h5py)
       ("netcdf4" ,python-netcdf4)))
    (native-inputs
     `(("pytest" ,python-pytest)))
    (propagated-inputs
     `(("importlib-metadata" ,python-importlib-metadata)
       ("numpy" ,python-numpy)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key outputs inputs #:allow-other-keys)
             (add-installed-pythonpath inputs outputs)
             (invoke "python" "-m" "pytest" "-v" "tests")
             #t)))))
    (home-page "https://github.com/nschloe/meshio")
    (synopsis "I/O for mesh files")
    (description "There are various file formats available for
representing unstructured meshes and mesh data.  The @code{meshio}
package is able to read and write mesh files in many formats and to
convert files from one format to another.  Formats such as cgns, h5m,
gmsh, xdmf and vtk are supported.  The package provides command-line
tools and a collection of Python modules for programmatic use.")
    (license license:expat)))

(define-public python-pygmsh
  (package
    (name "python-pygmsh")
    (version "7.1.11")
    (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/nschloe/pygmsh")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
          (base32
           "0g4yllmxks7yb50vild5xi1cma0yl16vsq6rfvdwmqaj4hwxcabk"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            (let ((file (open-file "setup.py" "a")))
              (display "from setuptools import setup\nsetup()" file)
              (close-port file))
            ;; A reference to setuptools in the configuration file
            ;; triggers an attempt to download the package from pypi.
            ;; The reference is not needed since the package is
            ;; provided by the build system.
            (substitute* "setup.cfg"
              (("^[[:blank:]]+setuptools>=42\n") ""))
            #t))))
    (build-system python-build-system)
    (native-inputs
     `(("pytest" ,python-pytest)
       ("wheel" ,python-wheel)))
    (propagated-inputs
     `(("importlib-metadata" ,python-importlib-metadata)
       ("gmsh" ,gmsh)
       ("meshio" ,python-meshio)
       ("numpy" ,python-numpy)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (invoke "python" "-m" "pytest" "-v" "tests"))
             #t)))))
    (home-page "https://github.com/nschloe/pygmsh")
    (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:lgpl3)))

(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")
                    (invoke "py.test" "-v" "tests/migration")
                    (invoke "py.test" "-v" "tests/pyadjoint")))
             #t)))))
    (home-page "http://www.dolfin-adjoint.org")
    (synopsis "Automatic differentiation library")
    (description "@code{python-dolfin-adjoint} is a solver of
differential equations associated with a governing system and a
functional of interest.  Working from the forward model the solver
automatically derives the discrete adjoint and tangent linear models.
These additional models are key ingredients in many algorithms such as
data assimilation, optimal control, sensitivity analysis, design
optimisation and error estimation.  The dolfin-adjoint project
provides the necessary tools and data structures for cases where the
forward model is implemented in @code{fenics} or
@url{https://firedrakeproject.org,firedrake}.")
    (license license:lgpl3)))