GNU bug report logs - #74974
[PATCH] gnu: python-pyvista: Update to 0.44.2.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: reza <reza <at> housseini.me>
To: guix-patches <at> gnu.org <guix-patches <at> gnu.org>
Cc: reza <reza <at> housseini.me>
Subject: [PATCH] gnu: python-pyvista: Update to 0.44.2.
Date: Thu, 19 Dec 2024 15:57:18 +0000

* gnu/packages/python-science.scm (python-pyvista): Update to 0.44.2
  [origin]: Update to 0.44.2
  [build-system]: Change to pyproject-build-system.
  [native-inputs]: Add native-inputs for testing.
  [modify-phases]: Enable sanity-check and check phase, disable failing tests
  and vtk dependency check and redirect $HOME variable.

Change-Id: I4293e99be12d096e639e47b8066116ba519909a8
---
 gnu/packages/python-science.scm | 133 +++++++++++++++++++++++++++++---
 1 file changed, 121 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index fe146717ce..5326284ce4 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2759,10 +2759,8 @@ (define-public python-plotnine
 (define-public python-pyvista
   (package
     (name "python-pyvista")
-    (version "0.42.3")
+    (version "0.44.2")
     (source
-     ;; The PyPI tarball does not contain the tests.
-     ;; (However, we don't yet actually run the tests.)
      (origin
        (method git-fetch)
        (uri (git-reference
@@ -2770,8 +2768,8 @@ (define-public python-pyvista
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1qxq0y0hc72hb60w3qq48fma8l6ffz7bdm75ymn1020bvfqrm1s4"))))
-    (build-system python-build-system)
+        (base32 "0lnh4cvf6wld7hm293015d80ny0vnsk96ckfvc2crzd1b79ch1v5"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-imageio
            python-matplotlib
@@ -2781,16 +2779,127 @@ (define-public python-pyvista
            python-pooch
            python-scooby
            vtk))
+    ;; packages needed for testing
+    (native-inputs (list python-pytest
+			 python-scipy
+			 python-ipython
+			 python-trimesh
+                         python-tqdm))
     (arguments
      '(#:phases
        (modify-phases %standard-phases
-         ;; Disable tests for now because they require several modules
-         ;; currently unpackaged in Guix.
-         (delete 'check)
-         ;; Disable the sanity check, which fails with the following error:
-         ;;
-         ;;   ...checking requirements: ERROR: pyvista==0.42.3 DistributionNotFound(Requirement.parse('vtk'), {'pyvista'})
-         (delete 'sanity-check))))
+	 ;; vtk check fails in sanity-check, comment out
+	 (add-after 'unpack 'patch-pyproject
+	   (lambda _
+	     (substitute* "pyproject.toml"
+	       (("'vtk<9\\.4\\.0'," all) (string-append "#" all)))))
+	 (add-after 'unpack 'fix-failing-tests
+	   (lambda _
+             (rename-file "tests/plotting/test_charts.py" "tests/plotting/_test_charts.py")
+	     (rename-file "tests/examples/test_download_files.py" "tests/examples/_test_download_files.py")
+	     (rename-file "tests/examples/test_downloads.py" "tests/examples/_test_downloads.py")
+             (rename-file "tests/plotting/test_texture.py" "tests/plotting/_test_texture.py")
+	     (substitute* "tests/plotting/test_plotting.py"
+	       (("\"\"\"Determine if using mesa.\"\"\"" all)
+		(string-append all "\n    return False")))
+	     (substitute* "tests/test_meshio.py"
+	       (("cow = .*$" all) (string-append "#" all "\n"))
+	       ((", cow") ""))
+	     (substitute* "tests/core/test_dataset.py"
+	       (("test_partition") "_test_partition"))
+	     (substitute* "tests/core/test_composite.py"
+	       (("test_ensight_multi_block_io") "_test_ensight_multi_block_io"))
+	     (substitute* "tests/core/test_dataset_filters.py"
+	       (("test_connectivity_.*$" all) (string-append "_" all))
+	       (("test_compute_boundary_mesh_quality") "_test_compute_boundary_mesh_quality"))
+	     (substitute* "tests/core/test_polydata_filters.py"
+	       (("test_protein_ribbon") "_test_protein_ribbon"))
+	     (substitute* "tests/core/test_validation.py"
+	       (("test_cast_to_numpy_raises") "_test_cast_to_numpy_raises"))
+	     (substitute* "tests/plotting/test_actor.py"
+	       (("test_actor_texture") "_test_actor_texture"))
+	     (substitute* "tests/plotting/test_lookup_table.py"
+	       (("test_init_cmap") "_test_init_cmap")
+	       (("test_repr") "_test_repr"))
+	     (substitute* "tests/plotting/test_plotter.py"
+	       (("test_add_multiple") "_test_add_multiple")
+	       (("test_plot_return_img_without_cpos") "_test_plot_return_img_without_cpos")
+	       (("test_plot_return_img_with_cpos") "_test_plot_return_img_with_cpos")
+	       (("test_only_screenshots_flag") "_test_only_screenshots_flag"))
+	     (substitute* "tests/plotting/test_plotting_utilities.py"
+	       (("test_gif_reader") "_test_gif_reader"))
+	     (substitute* "tests/plotting/test_render_window_interactor.py"
+	       (("test_timer") "_test_timer")
+	       (("test_add_timer_event") "_test_add_timer_event")
+	       (("test_interpolate") "_test_interpolate"))
+	     (substitute* "tests/plotting/test_renderer.py"
+	       (("test_legend_.*$" all) (string-append "_" all)))
+	     (substitute* "tests/plotting/test_theme.py"
+	       (("test_box_axes") "_test_box_axes")
+	       (("test_load_theme") "_test_load_theme")
+	       (("test_save_before_close_callback") "_test_save_before_close_callback")
+	       (("test_user_logo") "_test_user_logo"))
+	     (substitute* "tests/core/test_geometric_sources.py"
+	       (("test_translate_direction_collinear") "_test_translate_direction_collinear"))
+	     (substitute* "tests/examples/test_dataset_loader.py"
+	       (("test_dataset_loader_one_file") "_test_dataset_loader_one_file")
+	       (("test_dataset_loader_two_files_one_loadable") "_test_dataset_loader_two_files_one_loadable")
+	       (("test_dataset_loader_two_files_both_loadable") "_test_dataset_loader_two_files_both_loadable")
+	       (("test_dataset_loader_cubemap") "_test_dataset_loader_cubemap")
+	       (("test_dataset_loader_dicom") "_test_dataset_loader_dicom")
+	       (("test_dataset_loader_from_nested_files_and_directory") "_test_dataset_loader_from_nested_files_and_directory")
+	       (("test_dataset_loader_from_nested_multiblock") "_test_dataset_loader_from_nested_multiblock")
+	       (("test_load_dataset_no_reader") "_test_load_dataset_no_reader"))
+	     (substitute* "tests/core/test_reader.py"
+	       (("test_ensightreader_arrays") "_test_ensightreader_arrays")
+	       (("test_ensightreader_timepoints") "_test_ensightreader_timepoints")
+	       (("test_ensightreader_time_sets") "_test_ensightreader_time_sets")
+	       (("test_dcmreader") "_test_dcmreader")
+	       (("test_objreader") "_test_objreader")
+	       (("test_stlreader") "_test_stlreader")
+	       (("test_tecplotreader") "_test_tecplotreader")
+	       (("test_byureader") "_test_byureader")
+	       (("test_facetreader") "_test_facetreader")
+	       (("test_plot3dmetareader") "_test_plot3dmetareader")
+	       (("test_multiblockplot3dreader") "_test_multiblockplot3dreader")
+	       (("test_binarymarchingcubesreader") "_test_binarymarchingcubesreader")
+	       (("test_pvdreader") "_test_pvdreader")
+	       (("test_pvdreader_no_time_group") "_test_pvdreader_no_time_group")
+	       (("test_pvdreader_no_part_group") "_test_pvdreader_no_part_group")
+	       (("test_openfoamreader_arrays_time") "_test_openfoamreader_arrays_time")
+	       (("test_openfoamreader_active_time") "_test_openfoamreader_active_time")
+	       (("test_openfoamreader_read_data_time_value") "_test_openfoamreader_read_data_time_value")
+	       (("test_openfoamreader_read_data_time_point") "_test_openfoamreader_read_data_time_point")
+	       (("test_openfoam_skip_zero_time") "_test_openfoam_skip_zero_time")
+	       (("test_openfoam_cell_to_point_default") "_test_openfoam_cell_to_point_default")
+	       (("test_openfoam_patch_arrays") "_test_openfoam_patch_arrays")
+	       (("test_openfoam_case_type") "_test_openfoam_case_type")
+	       (("test_read_cgns") "_test_read_cgns")
+	       (("test_bmpreader") "_test_bmpreader")
+	       (("test_demreader") "_test_demreader")
+	       (("test_jpegreader") "_test_jpegreader")
+	       (("test_meta_image_reader") "_test_meta_image_reader")
+	       (("test_nifti_reader") "_test_nifti_reader")
+	       (("test_nrrd_reader") "_test_nrrd_reader")
+	       (("test_png_reader") "_test_png_reader")
+	       (("test_pnm_reader") "_test_pnm_reader")
+	       (("test_slc_reader") "_test_slc_reader")
+	       (("test_tiff_reader") "_test_tiff_reader")
+	       (("test_hdr_reader") "_test_hdr_reader")
+	       (("test_avsucd_reader") "_test_avsucd_reader")
+	       (("test_hdf_reader") "_test_hdf_reader")
+	       (("test_xdmf_reader") "_test_xdmf_reader")
+	       (("test_fluentcffreader") "_test_fluentcffreader")
+	       (("test_gambitreader") "_test_gambitreader")
+	       (("test_gaussian_cubes_reader") "_test_gaussian_cubes_reader")
+	       (("test_gesignareader") "_test_gesignareader")
+	       (("test_pdbreader") "_test_pdbreader")
+	       (("test_particle_reader") "_test_particle_reader")
+	       (("test_prostar_reader") "_test_prostar_reader"))))
+	 ;; test phase writes files to $HOME
+	 (add-before 'check 'redirect-HOME
+	   (lambda _
+	     (setenv "HOME" "/tmp"))))))
     (home-page "https://docs.pyvista.org/")
     (synopsis "3D plotting and mesh analysis through VTK")
     (description

base-commit: 20b1613484f512649f919d89285e981998592497
-- 
2.46.0

Message #8 received at 74974 <at> debbugs.gnu.org (full text, mbox):

From: Lars Bilke <lars.bilke <at> ufz.de>
To: 74974 <at> debbugs.gnu.org
Cc: mail <at> cbaines.net, reza <at> housseini.me
Subject: [PATCH] gnu: python-pyvista: Update to 0.44.2.
Date: Thu, 13 Feb 2025 16:03:03 +0100

Dear Reza,

I have checked your patch and it works perfect. The enabled tests (5921 passed, 630 skipped) are a huge improvement!

Maybe Christopher (in cc) may have a look at this patch too.

Thanks a lot!

Lars

Message #11 received at 74974 <at> debbugs.gnu.org (full text, mbox):

From: reza <reza <at> housseini.me>
To: Lars Bilke <lars.bilke <at> ufz.de>, 
 74974 <at> debbugs.gnu.org <74974 <at> debbugs.gnu.org>
Cc: mail <at> cbaines.net <mail <at> cbaines.net>
Subject: Re: [PATCH] gnu: python-pyvista: Update to 0.44.2.
Date: Tue, 18 Feb 2025 08:41:03 +0000

Dear Lars

> I have checked your patch and it works perfect. The enabled tests
> (5921 passed, 630 skipped) are a huge improvement!

Thanks for taking the time to review it. I asked on the bug tracker for
the remaining tests which mainly depend on internet access [1]. There
may be a possibility to enable more tests when downloading the test data
separately as mentioned in the issue.

Also I am now mostly disabling tests in pytest with flags --ignore for
files and --deselect for single tests, maybe I can spare some time to
send an updated patch.

> Maybe Christopher (in cc) may have a look at this patch too.
>
> Thanks a lot!
>
> Lars

Best regards,
Reza

[1] https://github.com/pyvista/pyvista/issues/7004

Message #16 received at 74974-done <at> debbugs.gnu.org (full text, mbox):

From: Christopher Baines <mail <at> cbaines.net>
To: 74974-done <at> debbugs.gnu.org
Date: Tue, 25 Feb 2025 11:49:54 +0000

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