diff options
Diffstat (limited to 'gnu/packages/simulation.scm')
| -rw-r--r-- | gnu/packages/simulation.scm | 82 |
1 files changed, 27 insertions, 55 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 23580322bb..240549be47 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -1,5 +1,6 @@ ;;; 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -100,11 +101,9 @@ ("scotch" ,pt-scotch32) ("zlib" ,zlib))) (native-inputs - `(("bison" ,bison))) + (list bison)) (propagated-inputs - `(("gzip" ,gzip) - ("gnuplot" ,gnuplot) - ("openmpi" ,openmpi))) + (list gzip gnuplot openmpi)) (outputs '("debug" ;~60MB "out")) (arguments @@ -256,12 +255,11 @@ problems for efficient solution on parallel systems.") "0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc")))) (build-system python-build-system) (inputs - `(("openmpi" ,openmpi) - ("python-numpy" ,python-numpy))) + (list openmpi python-numpy)) (native-inputs - `(("python-pytest-cov" ,python-pytest-cov))) + (list python-pytest-cov)) (propagated-inputs - `(("python-mpi4py" ,python-mpi4py))) + (list python-mpi4py)) (arguments `(#:phases (modify-phases %standard-phases @@ -270,16 +268,13 @@ problems for efficient solution on parallel systems.") (replace 'check (lambda _ (setenv "HOME" "/tmp") - (setenv "PYTHONPATH" - (string-append (getcwd) ":" (getenv "PYTHONPATH"))) (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")) - #t))))) + (invoke "./runtests.sh"))))))) (home-page "https://bitbucket.org/fenics-project/dijitso/") (synopsis "Distributed just-in-time building of shared libraries") (description @@ -307,19 +302,15 @@ the complexity of that interface. Parallel support depends on the "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p")))) (build-system python-build-system) (inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda _ - (setenv "PYTHONPATH" - (string-append (getcwd) ":" (getenv "PYTHONPATH"))) - (with-directory-excursion "test" - (invoke "py.test")) - #t))))) + (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 @@ -344,17 +335,14 @@ UFL is part of the FEniCS Project.") "13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-sympy" ,python-sympy))) + (list python-numpy python-sympy)) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda _ - (setenv "PYTHONPATH" - (string-append (getcwd) ":" (getenv "PYTHONPATH"))) (with-directory-excursion "test" ;; FIXME: three FIAT test modules are known to fail ;; with recent versions of pytest (>= 4). These are @@ -364,8 +352,7 @@ UFL is part of the FEniCS Project.") (invoke "py.test" "unit/" "--ignore=unit/test_fiat.py" "--ignore=unit/test_quadrature.py" - "--ignore=unit/test_reference_element.py")) - #t))))) + "--ignore=unit/test_reference_element.py"))))))) (home-page "https://bitbucket.org/fenics-project/fiat/") (synopsis "Tabulation of finite element function spaces") (description @@ -394,19 +381,15 @@ FIAT is part of the FEniCS Project.") "1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (propagated-inputs - `(("python-fenics-dijitso" ,python-fenics-dijitso) - ("python-fenics-fiat" ,python-fenics-fiat) - ("python-fenics-ufl" ,python-fenics-ufl))) + (list python-fenics-dijitso python-fenics-fiat python-fenics-ufl)) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda _ (setenv "HOME" (getcwd)) - (setenv "PYTHONPATH" - (string-append (getcwd) ":" (getenv "PYTHONPATH"))) (with-directory-excursion "test" ;; FIXME: the tests in subdirectory ;; 'unit/ufc/finite_element' require the ffc_factory @@ -631,8 +614,7 @@ user interface to the FEniCS core components and external libraries.") ;; Define paths to store locations. (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) ;; Move to python sub-directory. - (chdir "python") - #t)) + (chdir "python"))) (add-after 'build 'mpi-setup ,%openmpi-setup) (add-before 'check 'pre-check @@ -674,14 +656,8 @@ user interface to the FEniCS core components and external libraries.") "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)) + (setenv "OPENBLAS_NUM_THREADS" "1"))) (replace 'check (lambda _ (with-directory-excursion "test" @@ -693,8 +669,7 @@ user interface to the FEniCS core components and external libraries.") (min 3 (parallel-job-count))) "python" "-B" "-m" "pytest" "unit" "--ignore" - "unit/nls/test_PETScSNES_solver.py")) - #t)) + "unit/nls/test_PETScSNES_solver.py")))) (add-after 'install 'install-demo-files (lambda* (#:key outputs #:allow-other-keys) (let* ((demos (string-append @@ -708,8 +683,7 @@ user interface to the FEniCS core components and external libraries.") (unless (equal? "." dir) (mkdir-p tgt-dir) (install-file file tgt-dir)))) - (find-files "." ".*\\.(py|gz|xdmf)$")))) - #t))))) + (find-files "." ".*\\.(py|gz|xdmf)$"))))))))) (home-page "https://fenicsproject.org/") (synopsis "High-level environment for solving differential equations") (description @@ -745,7 +719,7 @@ FEniCS core components and external libraries.") "16v08dx7h7n4wyddzbwimazwyj74ynis12mpjfkay4243npy44b8")))) (build-system gnu-build-system) (native-inputs - `(("inetutils" ,inetutils))) ; for 'hostname', used in the check phase + (list inetutils)) ; for 'hostname', used in the check phase (arguments `(#:phases (modify-phases %standard-phases @@ -925,16 +899,14 @@ command-line utility for mesh optimisation.") #t)))) (build-system python-build-system) (inputs - `(("fenics" ,fenics) - ("openmpi" ,openmpi) - ("pybind11" ,pybind11))) + (list fenics openmpi pybind11)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-coverage" ,python-coverage) - ("python-decorator" ,python-decorator) - ("python-flake8" ,python-flake8) - ("python-pkgconfig" ,python-pkgconfig) - ("python-pytest" ,python-pytest))) + (list pkg-config + python-coverage + python-decorator + python-flake8 + python-pkgconfig + python-pytest)) (propagated-inputs `(("scipy" ,python-scipy))) (arguments |