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gnu: python-pyvista: Improve package style.

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* gnu/packages/python-science.scm (python-pyvista): Use G-Expressions,
fix indentation, remove necessary comments.
[arguments] <test-flags>: Utilize Pytest option to ignore and skip
tests instead modifying test files.
[phases]{fix-failing-tests}: Keep file modifications which can't be
skipped with Pytest options.

Change-Id: I51cbf14a9572bd096d409fa6b4b7b9c8bef5eea1
This commit is contained in:
Sharlatan Hellseher
2025-10-08 21:09:25 +01:00
parent 66e814c8f0
commit 19f80dff85
1 changed files with 114 additions and 124 deletions
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238
gnu/packages/python-science.scm
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@@ -5150,16 +5150,127 @@ and aims to provide a similar API and functionality in Python.")
(name "python-pyvista")
(version "0.44.2")
(source
;; The PyPI tarball does not contain the tests.
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pyvista/pyvista")
(commit (string-append "v" version))))
(url "https://github.com/pyvista/pyvista")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0lnh4cvf6wld7hm293015d80ny0vnsk96ckfvc2crzd1b79ch1v5"))))
(build-system pyproject-build-system)
(arguments
(list
;; tests: 5891 passed, 623 skipped, 355 deselected, 3 xfailed, 167 warnings
#:test-flags
;; TODO: Find out what's going on with skipped tests.
#~(list "--ignore=tests/plotting/test_charts.py"
"--ignore=tests/examples/test_download_files.py"
"--ignore=tests/examples/test_downloads.py"
"--ignore=tests/plotting/test_texture.py"
"-k" (string-join
(list "not test_actor_texture"
"test_add_multiple"
"test_add_timer_event"
"test_avsucd_reader"
"test_binarymarchingcubesreader"
"test_bmpreader"
"test_box_axes"
"test_byureader"
"test_cast_to_numpy_raises"
"test_compute_boundary_mesh_quality"
"test_connectivity_"
"test_dataset_loader_cubemap"
"test_dataset_loader_dicom"
"test_dataset_loader_from_nested_files_and_directory"
"test_dataset_loader_from_nested_multiblock"
"test_dataset_loader_one_file"
"test_dataset_loader_two_files_both_loadable"
"test_dataset_loader_two_files_one_loadable"
"test_dcmreader"
"test_demreader"
"test_ensight_multi_block_io"
"test_ensightreader_arrays"
"test_ensightreader_time_sets"
"test_ensightreader_timepoints"
"test_facetreader"
"test_fluentcffreader"
"test_gambitreader"
"test_gaussian_cubes_reader"
"test_gesignareader"
"test_gif_reader"
"test_hdf_reader"
"test_hdr_reader"
"test_init_cmap"
"test_interpolate"
"test_jpegreader"
"test_legend_"
"test_load_dataset_no_reader"
"test_load_theme"
"test_meta_image_reader"
"test_multiblockplot3dreader"
"test_nifti_reader"
"test_nrrd_reader"
"test_objreader"
"test_only_screenshots_flag"
"test_openfoam_case_type"
"test_openfoam_cell_to_point_default"
"test_openfoam_patch_arrays"
"test_openfoam_skip_zero_time"
"test_openfoamreader_active_time"
"test_openfoamreader_arrays_time"
"test_openfoamreader_read_data_time_point"
"test_openfoamreader_read_data_time_value"
"test_particle_reader"
"test_partition"
"test_pdbreader"
"test_plot3dmetareader"
"test_plot_return_img_with_cpos"
"test_plot_return_img_without_cpos"
"test_png_reader"
"test_pnm_reader"
"test_prostar_reader"
"test_protein_ribbon"
"test_pvdreader"
"test_pvdreader_no_part_group"
"test_pvdreader_no_time_group"
"test_read_cgns"
"test_repr"
"test_save_before_close_callback"
"test_slc_reader"
"test_stlreader"
"test_tecplotreader"
"test_tiff_reader"
"test_timer"
"test_translate_direction_collinear"
"test_user_logo"
"test_xdmf_reader")
" and not "))
#:phases
#~(modify-phases %standard-phases
;; 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 _
(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") ""))))
;; test phase writes files to $HOME
(add-before 'check 'redirect-HOME
(lambda _
(setenv "HOME" "/tmp"))))))
(native-inputs
(list python-ipython
python-pytest
python-scipy
python-tqdm
python-trimesh))
(propagated-inputs
(list python-imageio
python-matplotlib
@@ -5169,127 +5280,6 @@ and aims to provide a similar API and functionality in Python.")
python-pooch
python-scooby
vtk))
;; packages needed for testing
(native-inputs (list python-pytest
python-scipy
python-ipython
python-trimesh
python-tqdm))
(arguments
'(#:phases
(modify-phases %standard-phases
;; vtk check fails in sanity-check, comment out
(add-after 'unpack 'patch-pyproject
(lambda _
(substitute* "pyproject.toml"
(("'vtk<9\\.4\\.0'," all) (string-append "#" all)))))
(add-after 'unpack 'fix-failing-tests
(lambda _
(rename-file "tests/plotting/test_charts.py" "tests/plotting/_test_charts.py")
(rename-file "tests/examples/test_download_files.py" "tests/examples/_test_download_files.py")
(rename-file "tests/examples/test_downloads.py" "tests/examples/_test_downloads.py")
(rename-file "tests/plotting/test_texture.py" "tests/plotting/_test_texture.py")
(substitute* "tests/plotting/test_plotting.py"
(("\"\"\"Determine if using mesa.\"\"\"" all)
(string-append all "\n return False")))
(substitute* "tests/test_meshio.py"
(("cow = .*$" 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