From 236861847fdb098b43a99c61c562329a2fdc765c Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Wed, 15 Jan 2020 19:24:23 +0000 Subject: gnu: python-fenics-dijitso: Update to 2019.1.0. * gnu/packages/simulation.scm (python-fenics-dijitso): Update to 2019.1.0. --- gnu/packages/simulation.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index edc8d6e190..81b6e9affa 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 +;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick ;;; ;;; 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) -- cgit v1.2.3 From def588d2508644b127c49cde192c791420e113f1 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Thu, 16 Jan 2020 12:54:38 +0000 Subject: gnu: python-fenics-ufl: Update to 2019.1.0. * gnu/packages/simulation.scm (python-fenics-ufl): Update to 2019.1.0. --- gnu/packages/simulation.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 81b6e9affa..0595ad505d 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -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))) -- cgit v1.2.3 From 4dfb22c1e3c48151a1236b54637a23843b484bdc Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Fri, 17 Jan 2020 19:03:39 +0000 Subject: gnu: python-fenics-fiat: Update to 2019.1.0. * gnu/packages/simulation.scm (python-fenics-fiat): Update to 2019.1.0. --- gnu/packages/simulation.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 0595ad505d..3384c4dc55 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -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") -- cgit v1.2.3 From ec8dff89804320ba9ac237b9e479dac8c217552e Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Mon, 20 Jan 2020 11:21:24 +0000 Subject: gnu: python-fenics-ffc: Update to 2019.1.0.post0. * gnu/packages/simulation.scm (python-fenics-ffc): Update to 2019.1.0.post0. --- gnu/packages/simulation.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 3384c4dc55..8ab58c29b4 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -379,14 +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))) -- cgit v1.2.3 From 09ecd9a7944ca8af017a92228442d8ec84c15f58 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Wed, 22 Jan 2020 15:14:05 +0000 Subject: gnu: fenics-dolfin: Update to 2019.1.0.post0. * gnu/packages/simulation.scm (fenics-dolfin): Update to 2019.1.0.post0. [source](snippet): Remove three substitutions that are no longer needed. [native-inputs]: Use compatible version of CATCH. [arguments]: Use CMAKE version 3.15.5 to avoid EXCLUDE_FROM_ALL regression. See . --- gnu/packages/simulation.scm | 33 +++++++-------------------------- 1 file changed, 7 insertions(+), 26 deletions(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 8ab58c29b4..5c1931631f 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -431,7 +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) @@ -441,7 +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 @@ -452,30 +452,10 @@ FFC is part of the FEniCS Project.") (("#include.*") "#include \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 @@ -492,14 +472,15 @@ 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) ("petsc" ,petsc-openmpi) ("slepc" ,slepc-openmpi))) (arguments - `(#:configure-flags + `(#:cmake ,cmake-3.15.5 + #:configure-flags `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" "-DDOLFIN_ENABLE_HDF5:BOOL=ON" "-DDOLFIN_ENABLE_MPI:BOOL=ON" -- cgit v1.2.3 From 37bb0d1eafb3f08a204aed8c928cbf7cbc69cd19 Mon Sep 17 00:00:00 2001 From: Paul Garlick Date: Thu, 23 Jan 2020 16:00:29 +0000 Subject: gnu: fenics: Update to 2019.1.0.post0. * gnu/packages/simulation.scm (fenics): Update to 2019.1.0.post0. [arguments]: In the 'pre-check' phase, add three more demos to the list of demos that are skipped. --- gnu/packages/simulation.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'gnu/packages/simulation.scm') diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 5c1931631f..2f07e996a2 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -633,12 +633,20 @@ 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 + ;; . + ;; 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" -- cgit v1.2.3