diff options
Diffstat (limited to 'gnu/packages/simulation.scm')
| -rw-r--r-- | gnu/packages/simulation.scm | 112 |
1 files changed, 93 insertions, 19 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 26e26b351e..f5fe3fcf1d 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-build) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages tls) @@ -50,6 +51,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix svn-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -821,33 +823,29 @@ tools and a collection of Python modules for programmatic use.") (define-public python-pygmsh (package (name "python-pygmsh") - (version "7.1.9") + (version "7.1.11") (source (origin - (method url-fetch) - (uri (pypi-uri "pygmsh" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/nschloe/pygmsh") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1q7nr0cq581wlif537y6awj7vz9jywxg14c8znmsx5ip8x24754j")) + "0g4yllmxks7yb50vild5xi1cma0yl16vsq6rfvdwmqaj4hwxcabk")) (modules '((guix build utils))) (snippet '(begin (let ((file (open-file "setup.py" "a"))) (display "from setuptools import setup\nsetup()" file) (close-port file)) - ;; setuptools is supplied by the build system. An extra - ;; reference in the original configuration file triggers - ;; an attempt to download the package again. This fails. - ;; The extra reference is unnecessary and is removed. + ;; A reference to setuptools in the configuration file + ;; triggers an attempt to download the package from pypi. + ;; The reference is not needed since the package is + ;; provided by the build system. (substitute* "setup.cfg" (("^[[:blank:]]+setuptools>=42\n") "")) - ;; FIXME: gmsh version 4.7.0 introduces new field option - ;; names. See gmsh commit 6eab8028. pygmsh needs to use - ;; one of the old option names for compatibility with gmsh - ;; version 4.6.0. - (with-directory-excursion "pygmsh/common" - (substitute* "size_field.py" - (("NumPointsPerCurve") "NNodesByEdge"))) #t)))) (build-system python-build-system) (native-inputs @@ -865,10 +863,7 @@ tools and a collection of Python modules for programmatic use.") (lambda* (#:key inputs outputs tests? #:allow-other-keys) (when tests? (add-installed-pythonpath inputs outputs) - ;; The readme test is skipped. It requires the exdown - ;; module which is not available. - (invoke "python" "-m" "pytest" "-v" "test" - "--ignore" "test/test_readme.py")) + (invoke "python" "-m" "pytest" "-v" "tests")) #t))))) (home-page "https://github.com/nschloe/pygmsh") (synopsis "Python frontend for Gmsh") @@ -879,3 +874,82 @@ way the meshing of complex geometries using high-level abstractions is made possible. The package provides a Python library together with a command-line utility for mesh optimisation.") (license license:lgpl3))) + +(define-public python-dolfin-adjoint + (package + (name "python-dolfin-adjoint") + (version "2019.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dolfin-adjoint/pyadjoint") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn")) + (modules '((guix build utils))) + (snippet + '(begin + ;; One of the migration tests attempts to call openmpi + ;; recursively and fails. See + ;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the + ;; test sequentially instead. + (with-directory-excursion "tests/migration/optimal_control_mms" + (substitute* "test_optimal_control_mms.py" + (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") ""))) + ;; Result files are regenerated in the check phase. + (delete-file-recursively + "tests/migration/viscoelasticity/test-results") + #t)))) + (build-system python-build-system) + (inputs + `(("fenics" ,fenics) + ("openmpi" ,openmpi) + ("pybind11" ,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))) + (propagated-inputs + `(("scipy" ,python-scipy))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-after 'install 'install-doc + (lambda* (#:key outputs #:allow-other-keys) + (let* ((doc (string-append (assoc-ref outputs "out") + "/share/doc/" ,name "-" + ,version)) + (examples (string-append doc "/examples"))) + (mkdir-p examples) + (copy-recursively "examples" examples)) + #t)) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (setenv "HOME" (getcwd)) + (and (invoke "py.test" "-v" "tests/fenics_adjoint") + (invoke "py.test" "-v" "tests/migration") + (invoke "py.test" "-v" "tests/pyadjoint"))) + #t))))) + (home-page "http://www.dolfin-adjoint.org") + (synopsis "Automatic differentiation library") + (description "@code{python-dolfin-adjoint} is a solver of +differential equations associated with a governing system and a +functional of interest. Working from the forward model the solver +automatically derives the discrete adjoint and tangent linear models. +These additional models are key ingredients in many algorithms such as +data assimilation, optimal control, sensitivity analysis, design +optimisation and error estimation. The dolfin-adjoint project +provides the necessary tools and data structures for cases where the +forward model is implemented in @code{fenics} or +@url{https://firedrakeproject.org,firedrake}.") + (license license:lgpl3))) |