diff options
Diffstat (limited to 'gnu/packages/simulation.scm')
| -rw-r--r-- | gnu/packages/simulation.scm | 68 |
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" |