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authorMarius Bakke <marius@gnu.org>2021-07-29 22:34:57 +0200
committerMarius Bakke <marius@gnu.org>2021-07-29 22:34:57 +0200
commitb029be2ee0f81cdcbc14240ff426408085ab0a40 (patch)
treeed6d0e1bfdadfd28e1eb804e43763b793baa0b42 /gnu/packages/simulation.scm
parentbc55f3091bac4677df0cf020381c554921fea179 (diff)
parentffb381856d0c6cc1a557b789f6b377cfa17002a0 (diff)
Merge branch 'master' into core-updates-frozen
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
Diffstat (limited to 'gnu/packages/simulation.scm')
-rw-r--r--gnu/packages/simulation.scm81
1 files changed, 81 insertions, 0 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 26e26b351e..ebf249e155 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)
@@ -879,3 +881,82 @@ 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)))