diff options
Diffstat (limited to 'gnu/packages/simulation.scm')
| -rw-r--r-- | gnu/packages/simulation.scm | 137 |
1 files changed, 73 insertions, 64 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index 4fa2e93d81..824318bf51 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2022 Liliana Marie Prikler <liliana.prikler@gmail.com> ;;; Copyright © 2023 Reza Housseini <reza@housseini.me> ;;; Copyright © 2024 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1180,30 +1181,68 @@ command-line utility for mesh optimisation.") (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) + (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"))))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list + ;; Ignore tests which require missing packages and/or failed during + ;; tests collection. + "--ignore=tests/firedrake_adjoint/test_assignment.py" + "--ignore=tests/firedrake_adjoint/test_burgers_newton.py" + "--ignore=tests/firedrake_adjoint/test_dynamic_meshes.py" + "--ignore=tests/firedrake_adjoint/test_hessian.py" + "--ignore=tests/firedrake_adjoint/test_reduced_functional.py" + "--ignore=tests/firedrake_adjoint/test_shape_derivatives.py" + "--ignore=tests/firedrake_adjoint/test_solving.py" + "--ignore=tests/firedrake_adjoint/test_tlm.py" + "--ignore=tests/migration/burgers_newton/test_burgers_newton.py" + "--ignore=tests/migration/linear_solver/test_linear_solver.py" + "--ignore=tests/migration/optimization_scipy/test_optimization_scipy.py" + "--ignore=tests/migration/projection/test_projection.py" + "--ignore=tests/migration/reduced_functional/test_reduced_functional.py" + "--ignore=tests/migration/split/test_split.py" + "-k" (string-append "not test_read_checkpoint" + " and not test_krylov_solver_preconditioner_function_ctrl")) + #:phases + #~(modify-phases %standard-phases + (add-after 'build 'mpi-setup #$%openmpi-setup) + (add-before 'check 'set-environment-variables + (lambda _ + (setenv "HOME" (getcwd)))) + (add-after 'install 'install-doc + (lambda _ + (let* ((doc (string-append #$output "/share/doc/" #$name "-" #$version)) + (examples (string-append doc "/examples"))) + (mkdir-p examples) + (copy-recursively "examples" examples)))) + ;; Remove 'sanity-check, because it tries to import + ;; firedrake_adjoint after importing fenics_adjoint. + ;; Both load a module named 'backend' and firedrake_adjoint + ;; fails with an ImportError if it sees that the backend module + ;; has already been loaded. + (delete 'sanity-check)))) (inputs (list fenics openmpi pybind11)) (native-inputs @@ -1214,48 +1253,18 @@ command-line utility for mesh optimisation.") python-pkgconfig 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" - "-k" "not test_read_checkpoint") - (invoke "py.test" "-v" "tests/migration") - (invoke "py.test" "-v" "tests/pyadjoint"))) - #t)) - ;; Remove 'sanity-check, because it tries to import - ;; firedrake_adjoint after importing fenics_adjoint. - ;; Both load a module named 'backend' and firedrake_adjoint - ;; fails with an ImportError if it sees that the backend module - ;; has already been loaded. - (delete 'sanity-check)))) + (list python-scipy)) (home-page "https://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 + (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))) |