Subject: [PATCH v2 9/9] gnu: Add fenics.

From: Paul Garlick <[email-masked]>
Date: Mon, 12 Nov 2018 16:00:41 +0000

* gnu/packages/simulation.scm (fenics): New variable.
---
 gnu/packages/simulation.scm | 117 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)

diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index bd139d3..6144e23 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -592,3 +592,120 @@ user interface to the FEniCS core components and external libraries.")
                    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)
+       ("ply" ,python-ply)
+       ("pytest" ,python-pytest)
+       ("python-decorator" ,python-decorator)
+       ("python-pkgconfig" ,python-pkgconfig)
+       ,@(package-native-inputs fenics-dolfin)))
+    (propagated-inputs
+     `(("dolfin" ,fenics-dolfin)
+       ("petsc4py" ,python-petsc4py)
+       ("slepc4py" ,python-slepc4py)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'patch-source-shebangs 'set-paths
+           (lambda _
+             ;; Define paths to store locations.
+             (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
+             ;; Move to python sub-directory.
+             (chdir "python")
+             #t))
+         (add-after 'build 'mpi-setup
+           ,%openmpi-setup)
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Exclude tests that require meshes supplied by git-lfs.
+             (substitute* "demo/test.py"
+               (("(.*stem !.*)" line)
+                (string-append
+                 line "\n"
+                 "excludeList = [\n"
+                 "'multimesh-quadrature', \n"
+                 "'multimesh-marking', \n"
+                 "'mixed-poisson-sphere', \n"
+                 "'mesh-quality', \n"
+                 "'lift-drag', \n"
+                 "'elastodynamics', \n"
+                 "'dg-advection-diffusion', \n"
+                 "'contact-vi-tao', \n"
+                 "'contact-vi-snes', \n"
+                 "'collision-detection', \n"
+                 "'buckling-tao', \n"
+                 "'auto-adaptive-navier-stokes', \n"
+                 "'advection-diffusion', \n"
+                 "'subdomains', \n"
+                 "'stokes-taylor-hood', \n"
+                 "'stokes-mini', \n"
+                 "'navier-stokes', \n"
+                 "'eigenvalue']\n"
+                 "demos = ["
+                 "d for d in demos if d[0].stem not in "
+                 "excludeList]\n")))
+             (setenv "HOME" (getcwd))
+             (setenv "PYTHONPATH"
+                     (string-append
+                      (getcwd) "/build/lib.linux-x86_64-"
+                      ,(version-major+minor (package-version python)) ":"
+                      (getenv "PYTHONPATH")))
+             ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
+             (setenv "OPENBLAS_NUM_THREADS" "1")
+             #t))
+         (replace 'check
+           (lambda _
+             (with-directory-excursion "test"
+               ;; Note: The test test_snes_set_from_options() in the file
+               ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+               (and (invoke "py.test" "unit" "--ignore"
+                            "unit/nls/test_PETScSNES_solver.py")
+                    (invoke "mpirun" "-np" "3" "python" "-B" "-m"
+                            "pytest" "unit" "--ignore"
+                            "unit/nls/test_PETScSNES_solver.py")))
+             (with-directory-excursion "demo"
+               ;; Check demos.
+               (invoke "python" "generate-demo-files.py")
+               (and (invoke "python" "-m" "pytest" "-v" "test.py")
+                    (invoke "python" "-m" "pytest" "-v" "test.py"
+                            "--mpiexec=mpiexec" "--num-proc=3")))
+             #t))
+         (add-after 'install 'install-demo-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((demos (string-append
+                            (assoc-ref outputs "out")
+                            "/share/python-dolfin/demo")))
+               (mkdir-p demos)
+               (with-directory-excursion "demo"
+                 (for-each (lambda (file)
+                             (let* ((dir (dirname file))
+                                    (tgt-dir (string-append demos "/" dir)))
+                               (unless (equal? "." dir)
+                                 (mkdir-p tgt-dir)
+                                 (install-file file tgt-dir))))
+                           (find-files "." ".*\\.(py|gz|xdmf)$"))))
+             #t)))))
+    (home-page "https://fenicsproject.org/")
+    (synopsis "High-level environment for solving differential equations")
+    (description
+      "@code{fenics} is a computing platform for solving general classes of
+problems that involve differential equations.  @code{fenics} facilitates
+access to efficient methods for dealing with ordinary differential
+equations (ODEs) and partial differential equations (PDEs).  Systems of
+equations such as these are commonly encountered in areas of engineering,
+mathematics and the physical sciences.  It is particularly well-suited to
+problems that can be solved using the Finite Element Method (FEM).
+
+@code{fenics} is the top level of the set of packages that are developed
+within the FEniCS project.  It provides the python user interface to the
+FEniCS core components and external libraries.")
+    (license license:lgpl3+)))
-- 
1.8.3.1