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gnu: Add python-dolfin-adjoint. 

* gnu/packages/simulation.scm (python-dolfin-adjoint): New variable.
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Paul Garlick 2021-07-22 09:42:37 +01:00
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commit b05a1eb5e3
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@ -42,6 +42,7 @@
#: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)
@ -49,6 +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)
@ -899,3 +901,82 @@ 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)))