guix_mirror_bot pushed a commit to branch master
in repository guix.
commit c63083b2a14bbeb973c20c2a00d1cc58b19ad5f3
Author: Nicolas Graves <[email protected]>
AuthorDate: Sun Nov 23 11:44:29 2025 +0100
gnu: fenics: Switch to pyproject.
* gnu/packages/simulation.scm (fenics):
[build-system]: Switch to pyproject-build-system.
[arguments]: Relocate field, improve style.
<#:test-flags>: Use them, and skip flaky tests.
[native-inputs]: Add python-setuptools.
Change-Id: I85825ec6aa2a68db74cb7b5864103bbf34c33031
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/simulation.scm | 121 ++++++++++++++++++++++----------------------
1 file changed, 61 insertions(+), 60 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 00bf74d0f0..e558bc2d2c 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -902,22 +902,21 @@ user interface to the FEniCS core components and external
libraries.")
(define-public fenics
(package/inherit fenics-dolfin
(name "fenics")
- (build-system python-build-system)
- (inputs
- (modify-inputs (package-inputs fenics-dolfin)
- (delete "python")
- (prepend pybind11 python-matplotlib)))
- (native-inputs
- (modify-inputs (package-native-inputs fenics-dolfin)
- (prepend cmake-minimal python-ply python-pytest python-decorator)))
- (propagated-inputs
- (list fenics-dolfin
- python-petsc4py
- python-slepc4py
- ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at runtime.
- python-pkgconfig))
+ (build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ #~(list
+ "unit"
+ ;; This test fails and is ignored.
+ "--deselect"
+ "unit/nls/test_PETScSNES_solver.py::test_snes_set_from_options"
+ ;; These tests are flaky.
+ "--deselect=unit/common/test_timer.py::test_context_manager_named"
+ "--deselect=unit/common/test_timer.py::test_context_manager_anonymous"
+ ;; FIXME: Tests with binary encoded hdf5 files fail with a
+ ;; segfault. See fenics-project DOLFIN commit 6fbc9fb.
+ "--ignore=unit/io/test_XDMF.py")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
@@ -929,7 +928,7 @@ user interface to the FEniCS core components and external
libraries.")
;; Instead of cluttering the user's PKG_CONFIG_PATH environment
;; variable, hard-code the 'dolfin.pc' absolute file name.
(let ((pc-file (search-input-file inputs
- "/lib/pkgconfig/dolfin.pc")))
+ "/lib/pkgconfig/dolfin.pc")))
(substitute* "python/dolfin/jit/jit.py"
(("pkgconfig\\.parse\\(\"dolfin\"\\)")
(string-append "pkgconfig.parse(\"" pc-file "\")"))))))
@@ -939,8 +938,7 @@ user interface to the FEniCS core components and external
libraries.")
(setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
;; Move to python sub-directory.
(chdir "python")))
- (add-after 'build 'mpi-setup
- #$%openmpi-setup)
+ (add-after 'build 'mpi-setup #$%openmpi-setup)
(add-before 'check 'pre-check
(lambda _
;; Exclude three tests that generate 'NotImplementedError' in
@@ -949,34 +947,32 @@ user interface to the FEniCS core components and external
libraries.")
;; Also exclude tests that require meshes supplied by git-lfs.
(substitute* "demo/test.py"
(("(.*stem !.*)" line)
- (string-append line
- "\n"
- "excludeList = [\n"
- "'built-in-meshes', \n"
- "'hyperelasticity', \n"
- "'elasticity', \n"
- "'multimesh-quadrature', \n"
- "'multimesh-marking', \n"
- "'mixed-poisson-sphere', \n"
- "'mesh-quality', \n"
- "'lift-drag', \n"
- "'elastodynamics', \n"
- "'dg-advection-diffusion', \n"
- "'curl-curl', \n"
- "'contact-vi-tao', \n"
- "'contact-vi-snes', \n"
- "'collision-detection', \n"
- "'buckling-tao', \n"
- "'auto-adaptive-navier-stokes', \n"
- "'advection-diffusion', \n"
- "'subdomains', \n"
- "'stokes-taylor-hood', \n"
- "'stokes-mini', \n"
- "'navier-stokes', \n"
- "'eigenvalue']\n"
- "demos = ["
- "d for d in demos if d[0].stem not "
- "in excludeList]\n")))
+ (format #f "~a
+excludeList = [~{ '~a',~% ~}]
+demos = [d for d in demos if d[0].stem not in excludeList]~%"
+ line
+ (list "built-in-meshes"
+ "hyperelasticity"
+ "elasticity"
+ "multimesh-quadrature"
+ "multimesh-marking"
+ "mixed-poisson-sphere"
+ "mesh-quality"
+ "lift-drag"
+ "elastodynamics"
+ "dg-advection-diffusion"
+ "curl-curl"
+ "contact-vi-tao"
+ "contact-vi-snes"
+ "collision-detection"
+ "buckling-tao"
+ "auto-adaptive-navier-stokes"
+ "advection-diffusion"
+ "subdomains"
+ "stokes-taylor-hood"
+ "stokes-mini"
+ "navier-stokes"
+ "eigenvalue"))))
;; Do not test for expired numpy aliases.
(substitute* "test/unit/la/test_vector.py"
((" numpy.float\\(42.0\\),") "")
@@ -988,32 +984,37 @@ user interface to the FEniCS core components and external
libraries.")
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
(setenv "OPENBLAS_NUM_THREADS" "1")))
(replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
(when tests?
(with-directory-excursion "test"
- (invoke "pytest"
- "unit"
- ;; This test fails and is ignored.
- "--deselect"
-
"unit/nls/test_PETScSNES_solver.py::test_snes_set_from_options"
- ;; FIXME: Tests with binary encoded hdf5 files fail with a
- ;; segfault. See fenics-project DOLFIN commit 6fbc9fb.
- "--ignore"
- "unit/io/test_XDMF.py")))))
+ (apply invoke "pytest" test-flags)))))
(add-after 'install 'install-demo-files
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((demos (string-append (assoc-ref outputs "out")
- "/share/python-dolfin/demo")))
+ (lambda _
+ (let* ((demos (string-append #$output
+ "/share/python-dolfin/demo")))
(mkdir-p demos)
(with-directory-excursion "demo"
(for-each (lambda (file)
(let* ((dir (dirname file))
- (tgt-dir (string-append demos
- "/" dir)))
+ (tgt-dir (string-append demos "/" dir)))
(unless (equal? "." dir)
(mkdir-p tgt-dir)
(install-file file tgt-dir))))
(find-files "." ".*\\.(py|gz|xdmf)$")))))))))
+ (inputs
+ (modify-inputs (package-inputs fenics-dolfin)
+ (delete "python")
+ (prepend pybind11 python-matplotlib)))
+ (native-inputs
+ (modify-inputs (package-native-inputs fenics-dolfin)
+ (prepend cmake-minimal python-ply python-pytest python-decorator
+ python-setuptools)))
+ (propagated-inputs
+ (list fenics-dolfin
+ python-petsc4py
+ python-slepc4py
+ ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at runtime.
+ python-pkgconfig))
(home-page "https://fenicsproject.org/";)
(synopsis "High-level environment for solving differential equations")
(description
