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-rw-r--r--gnu/packages/simulation.scm82
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
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-21 22:37:44 +0000