Package: guix-patches;
Reported by: Paul Garlick <pgarlick <at> tourbillion-technology.com>
Date: Fri, 4 Jul 2025 12:35:02 UTC
Severity: normal
Tags: patch
Done: Andreas Enge <andreas <at> enge.fr>
Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Paul Garlick <pgarlick <at> tourbillion-technology.com> To: guix-patches <at> gnu.org Cc: Paul Garlick <pgarlick <at> tourbillion-technology.com> Subject: [PATCH] gnu: fenics: Fix build. Date: Fri, 4 Jul 2025 11:10:21 +0100
* gnu/packages/simulation.scm (fenics): Run guix style, improve
formatting.
[arguments] <phases>: Remove test module references to expired numpy
aliases in the 'pre-check' phase. Use '--deselect' instead of '--ignore'
to skip a test in the 'check' phase. Add a FIXME note to enable reading
and writing files in the binary HDF5 format.
---
gnu/packages/simulation.scm | 196 ++++++++++++++++++------------------
1 file changed, 99 insertions(+), 97 deletions(-)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index e6f86fb736..7d7668f117 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -917,108 +917,110 @@ (define-public fenics
(list fenics-dolfin
python-petsc4py
python-slepc4py
-
- ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
+ ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at runtime.
python-pkgconfig))
(arguments
- (list #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "python/setup.py"
- (("pybind11==")
- "pybind11>="))))
- (add-after 'unpack 'set-dolfin-pc-file-name
- (lambda* (#:key inputs #:allow-other-keys)
- ;; 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")))
- (substitute* "python/dolfin/jit/jit.py"
- (("pkgconfig\\.parse\\(\"dolfin\"\\)")
- (string-append "pkgconfig.parse(\"" pc-file
- "\")"))))))
- (add-after 'patch-source-shebangs 'set-paths
- (lambda _
- ;; Define paths to store locations.
- (setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
- ;; Move to python sub-directory.
- (chdir "python")))
- (add-after 'build 'mpi-setup
- #$%openmpi-setup)
- (add-before 'check 'pre-check
- (lambda _
- ;; Exclude three tests that generate
- ;; 'NotImplementedError' in matplotlib version 3.1.2.
- ;; See
- ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
- ;; 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")))
- (setenv "HOME"
- (getcwd))
- ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
- (setenv "OPENBLAS_NUM_THREADS" "1")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (with-directory-excursion "test"
- (invoke "pytest"
- "unit"
- ;; The test test_snes_set_from_options() in the file
- ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- "--ignore"
- "unit/nls/test_PETScSNES_solver.py"
- ;; Fails with a segfault.
- "--ignore"
- "unit/io/test_XDMF.py")))))
- (add-after 'install 'install-demo-files
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((demos (string-append (assoc-ref outputs "out")
- "/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)))
- (unless (equal? "." dir)
- (mkdir-p tgt-dir)
- (install-file file tgt-dir))))
- (find-files "." ".*\\.(py|gz|xdmf)$")))))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("pybind11==") "pybind11>="))))
+ (add-after 'unpack 'set-dolfin-pc-file-name
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Instead of cluttering the user's PKG_CONFIG_PATH environment
+ ;; variable, hard-code the 'dolfin.pc' absolute file name.
+ (let ((pc-file (search-input-file inputs
+ "/lib/pkgconfig/dolfin.pc")))
+ (substitute* "python/dolfin/jit/jit.py"
+ (("pkgconfig\\.parse\\(\"dolfin\"\\)")
+ (string-append "pkgconfig.parse(\"" pc-file "\")"))))))
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
+ ;; Move to python sub-directory.
+ (chdir "python")))
+ (add-after 'build 'mpi-setup
+ #$%openmpi-setup)
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Exclude three tests that generate 'NotImplementedError' in
+ ;; matplotlib v3.1.2. See
+ ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
+ ;; Also exclude tests that require meshes supplied by git-lfs.
+ (substitute* "demo/test.py"
+ (("(.*stem !.*)" line)
+ (string-append line
+ "\n"
+ "excludeList = [\n"
+ "'built-in-meshes', \n"
+ "'hyperelasticity', \n"
+ "'elasticity', \n"
+ "'multimesh-quadrature', \n"
+ "'multimesh-marking', \n"
+ "'mixed-poisson-sphere', \n"
+ "'mesh-quality', \n"
+ "'lift-drag', \n"
+ "'elastodynamics', \n"
+ "'dg-advection-diffusion', \n"
+ "'curl-curl', \n"
+ "'contact-vi-tao', \n"
+ "'contact-vi-snes', \n"
+ "'collision-detection', \n"
+ "'buckling-tao', \n"
+ "'auto-adaptive-navier-stokes', \n"
+ "'advection-diffusion', \n"
+ "'subdomains', \n"
+ "'stokes-taylor-hood', \n"
+ "'stokes-mini', \n"
+ "'navier-stokes', \n"
+ "'eigenvalue']\n"
+ "demos = ["
+ "d for d in demos if d[0].stem not "
+ "in excludeList]\n")))
+ ;; Do not test for expired numpy aliases.
+ (substitute* "test/unit/la/test_vector.py"
+ ((" numpy.float\\(42.0\\),") "")
+ (("^.*numpy.int\\(42.0\\).*$") ""))
+ (substitute* "test/unit/la/test_la_basic.py"
+ ((" int,") " ")
+ (("\\[int,") "["))
+ (setenv "HOME" (getcwd))
+ ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
+ (setenv "OPENBLAS_NUM_THREADS" "1")))
+ (replace 'check
+ (lambda* (#:key tests? #: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")))))
+ (add-after 'install 'install-demo-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((demos (string-append (assoc-ref outputs "out")
+ "/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)))
+ (unless (equal? "." dir)
+ (mkdir-p tgt-dir)
+ (install-file file tgt-dir))))
+ (find-files "." ".*\\.(py|gz|xdmf)$")))))))))
(home-page "https://fenicsproject.org/")
(synopsis "High-level environment for solving differential equations")
(description
- "@code{fenics} is a computing platform for solving general classes of
+ "@code{fenics} is a computing platform for solving general classes of
problems that involve differential equations. @code{fenics} facilitates
access to efficient methods for dealing with ordinary differential
equations (ODEs) and partial differential equations (PDEs). Systems of
--
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Copyright (C) 1999 Darren O. Benham,
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1994-97 Ian Jackson.