gnu: fenics-dolfin, fenics: Remove input labels.
* gnu/packages/simulation.scm (fenics-dolfin)[inputs, native-inputs] [propagated-inputs]: Remove labels. Replace CATCH2-1, which was actually unused, by CATCH-FRAMEWORK. [arguments]: Rewrite using gexps. Adjust 'set-paths' phase accordingly. (fenics): Likewise.master
Ludovic Courtès
Ludovic Courtès
parent
9a86e2e97f
commit
eb64632422
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@ -569,108 +569,111 @@ FFC is part of the FEniCS Project.")
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"$ENV{CATCH_DIR}/include" back "\n")))))))
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(build-system cmake-build-system)
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(inputs
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`(("blas" ,openblas)
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("boost" ,boost)
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("eigen" ,eigen)
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("hdf5" ,hdf5-parallel-openmpi)
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("lapack" ,lapack)
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("libxml2" ,libxml2)
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("openmpi" ,openmpi)
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("python" ,python-3)
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("scotch" ,pt-scotch32)
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("suitesparse" ,suitesparse)
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("sundials" ,sundials-openmpi)
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("zlib" ,zlib)))
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(list openblas
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boost
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eigen
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hdf5-parallel-openmpi
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lapack
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libxml2
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openmpi
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python-3
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pt-scotch32
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suitesparse
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sundials-openmpi
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zlib))
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(native-inputs
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`(("catch" ,catch2-1)
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("pkg-config" ,pkg-config)))
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(list catch-framework pkg-config))
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(propagated-inputs
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`(("ffc" ,python-fenics-ffc)
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("petsc" ,petsc-openmpi)
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("slepc" ,slepc-openmpi)))
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(list python-fenics-ffc petsc-openmpi slepc-openmpi))
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(arguments
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`(#:configure-flags
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`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
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"-DDOLFIN_ENABLE_HDF5:BOOL=ON"
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"-DDOLFIN_ENABLE_MPI:BOOL=ON"
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"-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
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"-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
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"-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
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"-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
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#:phases
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(modify-phases %standard-phases
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(add-after 'patch-usr-bin-file 'mpi-setup
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,%openmpi-setup)
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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 "BLAS_DIR" (assoc-ref %build-inputs "blas"))
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(setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
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(setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
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(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
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(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
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(setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
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(setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
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(setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))))
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(add-before 'check 'pre-check
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(lambda _
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;; The Dolfin repository uses git-lfs, whereby web links are
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;; substituted for large files. Guix does not currently support
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;; git-lfs, so only the links are downloaded. The tests that
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;; require the absent meshes cannot run and are skipped.
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;;
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;; One serial test fails and is skipped.
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;; i) demo_multimesh-stokes_serial:
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;; Warning: Found no facets matching domain for boundary
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;; condition.
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;;
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;; One mpi test fails and is skipped.
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;; i) demo_stokes-iterative_mpi:
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;; The MPI_Comm_rank() function was called before MPI_INIT was
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;; invoked
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(call-with-output-file "CTestCustom.cmake"
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(lambda (port)
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(display
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(string-append
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"set(CTEST_CUSTOM_TESTS_IGNORE "
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"demo_bcs_serial "
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"demo_bcs_mpi "
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"demo_eigenvalue_serial "
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"demo_eigenvalue_mpi "
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"demo_navier-stokes_serial "
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"demo_navier-stokes_mpi "
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"demo_stokes-taylor-hood_serial "
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"demo_stokes-taylor-hood_mpi "
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"demo_subdomains_serial "
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"demo_advection-diffusion_serial "
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"demo_advection-diffusion_mpi "
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"demo_auto-adaptive-navier-stokes_serial "
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"demo_contact-vi-snes_serial "
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"demo_contact-vi-snes_mpi "
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"demo_contact-vi-tao_serial "
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"demo_contact-vi-tao_mpi "
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"demo_curl-curl_serial "
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"demo_curl-curl_mpi "
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"demo_dg-advection-diffusion_serial "
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"demo_dg-advection-diffusion_mpi "
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"demo_elasticity_serial "
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"demo_elasticity_mpi "
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"demo_elastodynamics_serial "
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"demo_elastodynamics_mpi "
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"demo_lift-drag_serial "
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"demo_lift-drag_mpi "
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"demo_mesh-quality_serial "
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"demo_mesh-quality_mpi "
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"demo_multimesh-stokes_serial "
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")\n") port)))))
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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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(invoke "make" "unittests")
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(invoke "make" "demos")
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(invoke "ctest" "-R" "unittests")
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(invoke "ctest" "-R" "demo" "-R" "serial")
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(invoke "ctest" "-R" "demo" "-R" "mpi")))))))
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(list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
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"-DDOLFIN_ENABLE_HDF5:BOOL=ON"
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"-DDOLFIN_ENABLE_MPI:BOOL=ON"
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"-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
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"-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
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"-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
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"-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'patch-usr-bin-file 'mpi-setup
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#$%openmpi-setup)
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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 "BLAS_DIR"
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#$(this-package-input "openblas"))
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(setenv "CATCH_DIR"
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#$(this-package-input "catch"))
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(setenv "LAPACK_DIR"
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#$(this-package-input "lapack"))
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(setenv "PETSC_DIR"
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#$(this-package-input "petsc"))
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(setenv "SLEPC_DIR"
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#$(this-package-input "slepc"))
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(setenv "SCOTCH_DIR"
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#$(this-package-input "scotch"))
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(setenv "SUNDIALS_DIR"
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#$(this-package-input "sundials"))
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(setenv "UMFPACK_DIR"
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#$(this-package-input "suitesparse"))))
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(add-before 'check 'pre-check
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(lambda _
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;; The Dolfin repository uses git-lfs, whereby web links are
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;; substituted for large files. Guix does not currently support
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;; git-lfs, so only the links are downloaded. The tests that
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;; require the absent meshes cannot run and are skipped.
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;;
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;; One serial test fails and is skipped.
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;; i) demo_multimesh-stokes_serial:
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;; Warning: Found no facets matching domain for boundary
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;; condition.
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;;
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;; One mpi test fails and is skipped.
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;; i) demo_stokes-iterative_mpi:
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;; The MPI_Comm_rank() function was called before MPI_INIT was
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;; invoked
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(call-with-output-file "CTestCustom.cmake"
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(lambda (port)
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(display (string-append
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"set(CTEST_CUSTOM_TESTS_IGNORE "
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"demo_bcs_serial "
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"demo_bcs_mpi "
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"demo_eigenvalue_serial "
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"demo_eigenvalue_mpi "
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"demo_navier-stokes_serial "
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"demo_navier-stokes_mpi "
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"demo_stokes-taylor-hood_serial "
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"demo_stokes-taylor-hood_mpi "
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"demo_subdomains_serial "
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"demo_advection-diffusion_serial "
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"demo_advection-diffusion_mpi "
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"demo_auto-adaptive-navier-stokes_serial "
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"demo_contact-vi-snes_serial "
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"demo_contact-vi-snes_mpi "
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"demo_contact-vi-tao_serial "
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"demo_contact-vi-tao_mpi "
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"demo_curl-curl_serial "
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"demo_curl-curl_mpi "
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"demo_dg-advection-diffusion_serial "
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"demo_dg-advection-diffusion_mpi "
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"demo_elasticity_serial "
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"demo_elasticity_mpi "
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"demo_elastodynamics_serial "
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"demo_elastodynamics_mpi "
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"demo_lift-drag_serial "
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"demo_lift-drag_mpi "
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"demo_mesh-quality_serial "
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"demo_mesh-quality_mpi "
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"demo_multimesh-stokes_serial "
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")\n") port)))))
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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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(invoke "make" "unittests")
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(invoke "make" "demos")
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(invoke "ctest" "-R" "unittests")
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(invoke "ctest" "-R" "demo" "-R" "serial")
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(invoke "ctest" "-R" "demo" "-R" "mpi")))))))
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(home-page "https://bitbucket.org/fenics-project/dolfin/")
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(synopsis "Problem solving environment for differential equations")
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(description
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@ -708,112 +711,114 @@ user interface to the FEniCS core components and external libraries.")
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(name "fenics")
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(build-system python-build-system)
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(inputs
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`(("pybind11" ,pybind11)
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("python-matplotlib" ,python-matplotlib)
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,@(alist-delete "python" (package-inputs fenics-dolfin))))
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(modify-inputs (package-inputs fenics-dolfin)
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(delete "python")
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(prepend pybind11 python-matplotlib)))
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(native-inputs
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`(("cmake" ,cmake-minimal)
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("ply" ,python-ply)
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("pytest" ,python-pytest)
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("python-decorator" ,python-decorator)
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,@(package-native-inputs fenics-dolfin)))
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(modify-inputs (package-native-inputs fenics-dolfin)
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(prepend cmake-minimal python-ply python-pytest python-decorator)))
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(propagated-inputs
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`(("dolfin" ,fenics-dolfin)
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("petsc4py" ,python-petsc4py)
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("slepc4py" ,python-slepc4py)
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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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("python-pkgconfig" ,python-pkgconfig)))
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;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
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python-pkgconfig))
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(arguments
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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" (assoc-ref %build-inputs "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
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line "\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" (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
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"pytest" "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" "unit/nls/test_PETScSNES_solver.py"
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;; Fails with a segfault.
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"--ignore" "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
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(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 "/" 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)$")))))))))
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(list #:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'relax-requirements
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(lambda _
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(substitute* "python/setup.py"
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(("pybind11==")
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"pybind11>="))))
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(add-after 'unpack 'set-dolfin-pc-file-name
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(lambda* (#:key inputs #:allow-other-keys)
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;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
|
||||
;; variable, hard-code the 'dolfin.pc' absolute file name.
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(let ((pc-file (search-input-file inputs
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"/lib/pkgconfig/dolfin.pc")))
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(substitute* "python/dolfin/jit/jit.py"
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(("pkgconfig\\.parse\\(\"dolfin\"\\)")
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(string-append "pkgconfig.parse(\"" pc-file
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"\")"))))))
|
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(add-after 'patch-source-shebangs 'set-paths
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||||
(lambda _
|
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;; Define paths to store locations.
|
||||
(setenv "PYBIND11_DIR" #$(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)
|
||||
(add-before 'check 'pre-check
|
||||
(lambda _
|
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;; 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.
|
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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"
|
||||
"'elasticity', \n"
|
||||
"'multimesh-quadrature', \n"
|
||||
"'multimesh-marking', \n"
|
||||
"'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 "
|
||||
"excludeList]\n")))
|
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(setenv "HOME"
|
||||
(getcwd))
|
||||
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
|
||||
(setenv "OPENBLAS_NUM_THREADS" "1")))
|
||||
(replace 'check
|
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(lambda* (#:key tests? #:allow-other-keys)
|
||||
(when tests?
|
||||
(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.
|
||||
"--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
|
||||
|
|
|
|||
Reference in New Issue