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gnu: fenics: Switch to pyproject.

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* 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 <sharlatanus@gmail.com>
This commit is contained in:
Nicolas Graves
2025-11-23 11:44:29 +01:00
committed by Sharlatan Hellseher
parent 99e0ae2431
commit c63083b2a1
1 changed files with 61 additions and 60 deletions
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gnu/packages/simulation.scm
+61 -60
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@@ -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