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>
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From: help-debbugs <at> gnu.org (GNU bug Tracking System) To: Andreas Enge <andreas <at> enge.fr> Cc: tracker <at> debbugs.gnu.org Subject: bug#78954: closed ([PATCH] gnu: fenics: Fix build.) Date: Sat, 05 Jul 2025 14:47:03 +0000
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Your message dated Sat, 5 Jul 2025 16:46:27 +0200 with message-id <aGk6w5KXBGxGFSMU <at> jurong> and subject line Re: [PATCH] gnu: fenics: Fix build. has caused the debbugs.gnu.org bug report #78954, regarding [PATCH] gnu: fenics: Fix build. to be marked as done. (If you believe you have received this mail in error, please contact help-debbugs <at> gnu.org.) -- 78954: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=78954 GNU Bug Tracking System Contact help-debbugs <at> gnu.org with problems
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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 -- 2.39.5
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From: Andreas Enge <andreas <at> enge.fr> To: Paul Garlick <pgarlick <at> tourbillion-technology.com> Cc: 78954-done <at> debbugs.gnu.org Subject: Re: [PATCH] gnu: fenics: Fix build. Date: Sat, 5 Jul 2025 16:46:27 +0200Thanks a lot for your detective work! I could build the package locally and have pushed to master. Andreas
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