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-rw-r--r--gnu/packages/simulation.scm68
1 files changed, 32 insertions, 36 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index edc8d6e190..8d5788545f 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -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"