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gnu: fenics: Fix build.
* gnu/packages/simulation.scm (fenics): Run guix style, improve formatting. [arguments] <phases>: Remove test module references to expired numpy aliases in the 'pre-check' phase. Use '--deselect' instead of '--ignore' to skip a test in the 'check' phase. Add a FIXME note to enable reading and writing files in the binary HDF5 format. Signed-off-by: Andreas Enge <andreas@enge.fr>
This commit is contained in:
Paul Garlick
Andreas Enge
parent
d636feabcf
commit
a8769dddaa
1 changed files with 99 additions and 97 deletions
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@ -917,108 +917,110 @@ user interface to the FEniCS core components and external libraries.")
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(list fenics-dolfin
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python-petsc4py
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python-slepc4py
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;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
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;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at runtime.
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python-pkgconfig))
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(arguments
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(list #:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'relax-requirements
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(lambda _
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(substitute* "python/setup.py"
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(("pybind11==")
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"pybind11>="))))
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(add-after 'unpack 'set-dolfin-pc-file-name
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(lambda* (#:key inputs #:allow-other-keys)
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;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
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;; variable, hard-code the 'dolfin.pc' absolute file name.
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(let ((pc-file (search-input-file inputs
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"/lib/pkgconfig/dolfin.pc")))
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(substitute* "python/dolfin/jit/jit.py"
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(("pkgconfig\\.parse\\(\"dolfin\"\\)")
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(string-append "pkgconfig.parse(\"" pc-file
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"\")"))))))
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(add-after 'patch-source-shebangs 'set-paths
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(lambda _
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;; Define paths to store locations.
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(setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
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;; Move to python sub-directory.
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(chdir "python")))
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(add-after 'build 'mpi-setup
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#$%openmpi-setup)
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(add-before 'check 'pre-check
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(lambda _
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;; Exclude three tests that generate
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;; 'NotImplementedError' in matplotlib version 3.1.2.
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;; See
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;; <https://github.com/matplotlib/matplotlib/issues/15382>.
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;; Also exclude tests that require meshes supplied by
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;; git-lfs.
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(substitute* "demo/test.py"
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(("(.*stem !.*)" line)
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(string-append line
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"\n"
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"excludeList = [\n"
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"'built-in-meshes', \n"
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"'hyperelasticity', \n"
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"'elasticity', \n"
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"'multimesh-quadrature', \n"
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"'multimesh-marking', \n"
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"'mixed-poisson-sphere', \n"
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"'mesh-quality', \n"
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"'lift-drag', \n"
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"'elastodynamics', \n"
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"'dg-advection-diffusion', \n"
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"'curl-curl', \n"
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"'contact-vi-tao', \n"
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"'contact-vi-snes', \n"
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"'collision-detection', \n"
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"'buckling-tao', \n"
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"'auto-adaptive-navier-stokes', \n"
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"'advection-diffusion', \n"
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"'subdomains', \n"
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"'stokes-taylor-hood', \n"
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"'stokes-mini', \n"
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"'navier-stokes', \n"
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"'eigenvalue']\n"
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"demos = ["
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"d for d in demos if d[0].stem not in "
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"excludeList]\n")))
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(setenv "HOME"
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(getcwd))
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;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
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(setenv "OPENBLAS_NUM_THREADS" "1")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(with-directory-excursion "test"
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(invoke "pytest"
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"unit"
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;; The test test_snes_set_from_options() in the file
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;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
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"--ignore"
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"unit/nls/test_PETScSNES_solver.py"
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;; Fails with a segfault.
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"--ignore"
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"unit/io/test_XDMF.py")))))
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(add-after 'install 'install-demo-files
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((demos (string-append (assoc-ref outputs "out")
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"/share/python-dolfin/demo")))
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(mkdir-p demos)
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(with-directory-excursion "demo"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append
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demos "/" dir)))
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(unless (equal? "." dir)
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(mkdir-p tgt-dir)
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(install-file file tgt-dir))))
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(find-files "." ".*\\.(py|gz|xdmf)$")))))))))
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(list
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'relax-requirements
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(lambda _
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(substitute* "python/setup.py"
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(("pybind11==") "pybind11>="))))
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(add-after 'unpack 'set-dolfin-pc-file-name
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(lambda* (#:key inputs #:allow-other-keys)
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;; Instead of cluttering the user's PKG_CONFIG_PATH environment
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;; variable, hard-code the 'dolfin.pc' absolute file name.
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(let ((pc-file (search-input-file inputs
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"/lib/pkgconfig/dolfin.pc")))
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(substitute* "python/dolfin/jit/jit.py"
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(("pkgconfig\\.parse\\(\"dolfin\"\\)")
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(string-append "pkgconfig.parse(\"" pc-file "\")"))))))
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(add-after 'patch-source-shebangs 'set-paths
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(lambda _
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;; Define paths to store locations.
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(setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
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;; Move to python sub-directory.
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(chdir "python")))
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(add-after 'build 'mpi-setup
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#$%openmpi-setup)
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(add-before 'check 'pre-check
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(lambda _
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;; Exclude three tests that generate 'NotImplementedError' in
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;; matplotlib v3.1.2. See
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;; <https://github.com/matplotlib/matplotlib/issues/15382>.
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;; Also exclude tests that require meshes supplied by git-lfs.
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(substitute* "demo/test.py"
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(("(.*stem !.*)" line)
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(string-append line
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"\n"
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"excludeList = [\n"
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"'built-in-meshes', \n"
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"'hyperelasticity', \n"
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"'elasticity', \n"
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"'multimesh-quadrature', \n"
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"'multimesh-marking', \n"
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"'mixed-poisson-sphere', \n"
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"'mesh-quality', \n"
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"'lift-drag', \n"
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"'elastodynamics', \n"
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"'dg-advection-diffusion', \n"
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"'curl-curl', \n"
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"'contact-vi-tao', \n"
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"'contact-vi-snes', \n"
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"'collision-detection', \n"
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"'buckling-tao', \n"
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"'auto-adaptive-navier-stokes', \n"
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"'advection-diffusion', \n"
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"'subdomains', \n"
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"'stokes-taylor-hood', \n"
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"'stokes-mini', \n"
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"'navier-stokes', \n"
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"'eigenvalue']\n"
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"demos = ["
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"d for d in demos if d[0].stem not "
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"in excludeList]\n")))
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;; Do not test for expired numpy aliases.
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(substitute* "test/unit/la/test_vector.py"
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((" numpy.float\\(42.0\\),") "")
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(("^.*numpy.int\\(42.0\\).*$") ""))
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(substitute* "test/unit/la/test_la_basic.py"
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((" int,") " ")
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(("\\[int,") "["))
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(setenv "HOME" (getcwd))
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;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
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(setenv "OPENBLAS_NUM_THREADS" "1")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(with-directory-excursion "test"
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(invoke "pytest"
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"unit"
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;; This test fails and is ignored.
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"--deselect"
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"unit/nls/test_PETScSNES_solver.py::test_snes_set_from_options"
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;; FIXME: Tests with binary encoded hdf5 files fail with a
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;; segfault. See fenics-project DOLFIN commit 6fbc9fb.
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"--ignore"
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"unit/io/test_XDMF.py")))))
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(add-after 'install 'install-demo-files
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((demos (string-append (assoc-ref outputs "out")
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"/share/python-dolfin/demo")))
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(mkdir-p demos)
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(with-directory-excursion "demo"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append demos
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"/" dir)))
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(unless (equal? "." dir)
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(mkdir-p tgt-dir)
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(install-file file tgt-dir))))
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(find-files "." ".*\\.(py|gz|xdmf)$")))))))))
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(home-page "https://fenicsproject.org/")
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(synopsis "High-level environment for solving differential equations")
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(description
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"@code{fenics} is a computing platform for solving general classes of
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"@code{fenics} is a computing platform for solving general classes of
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problems that involve differential equations. @code{fenics} facilitates
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access to efficient methods for dealing with ordinary differential
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equations (ODEs) and partial differential equations (PDEs). Systems of
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