diff options
Diffstat (limited to 'gnu/packages/simulation.scm')
| -rw-r--r-- | gnu/packages/simulation.scm | 183 |
1 files changed, 182 insertions, 1 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index e1de78402d..23580322bb 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, 2019, 2020 Paul Garlick <[email protected]> +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,6 +41,8 @@ #:use-module (gnu packages ncurses) #: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) @@ -48,6 +50,7 @@ #: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) @@ -792,3 +795,181 @@ areas in the model. A semi-implicit method is used to advance the solution in time. The tool is typically applied to the modelling of river flooding.") (license license:cecill)))) + +(define-public python-meshio + (package + (name "python-meshio") + (version "4.4.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "meshio" version)) + (sha256 + (base32 + "0kv832s2vyff30zz8yqypw5jifwdanvh5x56d2bzkvy94h4jlddy")) + (snippet + '(begin + (let ((file (open-file "setup.py" "a"))) + (display "from setuptools import setup\nsetup()" file) + (close-port file)) + #t)))) + (build-system python-build-system) + (inputs + `(("h5py" ,python-h5py) + ("netcdf4" ,python-netcdf4))) + (native-inputs + `(("pytest" ,python-pytest))) + (propagated-inputs + `(("importlib-metadata" ,python-importlib-metadata) + ("numpy" ,python-numpy))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key outputs inputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "pytest" "-v" "tests") + #t))))) + (home-page "https://github.com/nschloe/meshio") + (synopsis "I/O for mesh files") + (description "There are various file formats available for +representing unstructured meshes and mesh data. The @code{meshio} +package is able to read and write mesh files in many formats and to +convert files from one format to another. Formats such as cgns, h5m, +gmsh, xdmf and vtk are supported. The package provides command-line +tools and a collection of Python modules for programmatic use.") + (license license:expat))) + +(define-public python-pygmsh + (package + (name "python-pygmsh") + (version "7.1.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nschloe/pygmsh") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0g4yllmxks7yb50vild5xi1cma0yl16vsq6rfvdwmqaj4hwxcabk")) + (modules '((guix build utils))) + (snippet + '(begin + (let ((file (open-file "setup.py" "a"))) + (display "from setuptools import setup\nsetup()" file) + (close-port file)) + ;; 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") "")) + #t)))) + (build-system python-build-system) + (native-inputs + `(("pytest" ,python-pytest) + ("wheel" ,python-wheel))) + (propagated-inputs + `(("importlib-metadata" ,python-importlib-metadata) + ("gmsh" ,gmsh) + ("meshio" ,python-meshio) + ("numpy" ,python-numpy))) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "pytest" "-v" "tests")) + #t))))) + (home-page "https://github.com/nschloe/pygmsh") + (synopsis "Python frontend for Gmsh") + (description "The goal of @code{pygmsh} is to combine the power of +Gmsh with the versatility of Python. The package generalises many of +the methods and functions that comprise the Gmsh Python API. In this +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))) |