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Merge branch 'staging' into core-updates

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Marius Bakke 2020-01-23 23:11:11 +01:00
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68
gnu/packages/simulation.scm
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@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -241,14 +241,14 @@ problems for efficient solution on parallel systems.")
(define-public python-fenics-dijitso
(package
(name "python-fenics-dijitso")
(version "2018.1.0")
(version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-dijitso" version))
(sha256
(base32
"1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9"))))
"0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc"))))
(build-system python-build-system)
(inputs
`(("openmpi" ,openmpi)
@ -292,14 +292,14 @@ the complexity of that interface. Parallel support depends on the
(define-public python-fenics-ufl
(package
(name "python-fenics-ufl")
(version "2018.1.0")
(version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-ufl" version))
(sha256
(base32
"1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla"))))
"10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p"))))
(build-system python-build-system)
(inputs
`(("python-numpy" ,python-numpy)))
@ -329,14 +329,14 @@ UFL is part of the FEniCS Project.")
(define-public python-fenics-fiat
(package
(name "python-fenics-fiat")
(version "2018.1.0")
(version "2019.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-fiat" version))
(sha256
(base32
"0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc"))))
"13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
@ -351,7 +351,15 @@ UFL is part of the FEniCS Project.")
(setenv "PYTHONPATH"
(string-append (getcwd) ":" (getenv "PYTHONPATH")))
(with-directory-excursion "test"
(invoke "py.test" "unit/"))
;; FIXME: three FIAT test modules are known to fail
;; with recent versions of pytest (>= 4). These are
;; skipped for FIAT version 2019.1.0 pending an
;; upstream pull request. For details see request #59
;; at https://bitbucket.org/fenics-project/fiat/.
(invoke "py.test" "unit/"
"--ignore=unit/test_fiat.py"
"--ignore=unit/test_quadrature.py"
"--ignore=unit/test_reference_element.py"))
#t)))))
(home-page "https://bitbucket.org/fenics-project/fiat/")
(synopsis "Tabulation of finite element function spaces")
@ -371,14 +379,14 @@ FIAT is part of the FEniCS Project.")
(define-public python-fenics-ffc
(package
(name "python-fenics-ffc")
(version "2018.1.0")
(version "2019.1.0.post0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fenics-ffc" version))
(sha256
(base32
"1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9"))))
"1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9"))))
(build-system python-build-system)
(native-inputs
`(("python-pytest" ,python-pytest)))
@ -423,7 +431,7 @@ FFC is part of the FEniCS Project.")
(define-public fenics-dolfin
(package
(name "fenics-dolfin")
(version "2018.1.0.post1")
(version "2019.1.0.post0")
(source
(origin
(method url-fetch)
@ -433,7 +441,7 @@ FFC is part of the FEniCS Project.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya"))
"1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
(modules '((guix build utils)))
(snippet
'(begin
@ -444,30 +452,10 @@ FFC is part of the FEniCS Project.")
(("#include.*")
"#include <catch.hpp>\n"))
(substitute* "test/unit/cpp/CMakeLists.txt"
;; Add extra include directories required by the unit tests.
(("(^target_link_libraries.*)" line)
(string-append line "\n"
"target_include_directories("
"unittests PRIVATE "
"${DOLFIN_SOURCE_DIR} "
"${DOLFIN_SOURCE_DIR}/dolfin "
"${DOLFIN_BINARY_DIR})\n"))
;; Specify directory to find the header file.
(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
(string-append front
"$ENV{CATCH_DIR}"
"/include" back "\n")))
(substitute* "demo/CMakeLists.txt"
;; Add extra include directories required by the demo tests.
(("(^#find_package.*)" line)
(string-append line "\n"
"include_directories("
"${DOLFIN_SOURCE_DIR} "
"${DOLFIN_SOURCE_DIR}/dolfin "
"${DOLFIN_BINARY_DIR})\n")))
(substitute* "dolfin/nls/PETScSNESSolver.cpp"
;; Remove SNESTEST mapping. The SNESTEST symbol was removed
;; from PETSc at version 3.10.3.
((".*SNESTEST.*") "" ))
"$ENV{CATCH_DIR}/include" back "\n")))
#t))))
(build-system cmake-build-system)
(inputs
@ -484,7 +472,7 @@ FFC is part of the FEniCS Project.")
("sundials" ,sundials-openmpi)
("zlib" ,zlib)))
(native-inputs
`(("catch" ,catch-framework2)
`(("catch" ,catch-framework2-1)
("pkg-config" ,pkg-config)))
(propagated-inputs
`(("ffc" ,python-fenics-ffc)
@ -644,12 +632,20 @@ user interface to the FEniCS core components and external libraries.")
,%openmpi-setup)
(add-before 'check 'pre-check
(lambda _
;; Exclude tests that require meshes supplied by git-lfs.
;; 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.
(substitute* "demo/test.py"
(("(.*stem !.*)" line)
(string-append
line "\n"
"excludeList = [\n"
"'built-in-meshes', \n"
"'hyperelasticity', \n"
"'elasticity', \n"
"'multimesh-quadrature', \n"
"'multimesh-marking', \n"
"'mixed-poisson-sphere', \n"