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Merged
merged 82 commits into from
Jul 18, 2025

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This pull request introduces significant updates to the napari_stress package, focusing on restructuring the approximation module, improving documentation, and deprecating outdated methods. The changes enhance the clarity of the API, add new functionality for spherical harmonics expansion, and ensure consistency across the codebase.

Documentation Updates:

  • Removed the api.rst file, reorganizing its contents into individual submodule files for better modularity. (docs/05_API/api.rst, docs/05_API/api.rstL1-L11)
  • Updated the approximation.rst file to reflect the new structure and added individual documentation files for EllipsoidExpander, EllipsoidImageExpander, SphericalHarmonicsExpander, and LebedevExpander. (docs/05_API/approximation.rst, [1]; docs/05_API/approximation/EllipsoidExpander.rst, [2]; docs/05_API/approximation/EllipsoidImageExpander.rst, [3]; docs/05_API/approximation/LebedevExpander.rst, [4]; docs/05_API/approximation/SphericalHarmonicsExpander.rst, [5]
  • Updated the table of contents in docs/_toc.yml to include the new documentation structure. (docs/_toc.yml, docs/_toc.ymlL63-R73)

Code Enhancements:

  • Added new methods for spherical harmonics expansion using Lebedev quadrature (expand_spherical_harmonics_on_lebedev_grid) and integrated them into the approximation module. (src/napari_stress/_approximation/expansion_napari.py, src/napari_stress/_approximation/expansion_napari.pyR90-R163)
  • Introduced new attributes and examples for the EllipsoidImageExpander class to improve usability and clarity. (src/napari_stress/_approximation/expansion_ellipsoid.py, [1] [2]

Deprecations:

  • Deprecated older methods in the spherical harmonics module (stress_spherical_harmonics_expansion, lebedev_quadrature, create_manifold, get_normals_on_manifold, and calculate_mean_curvature_on_manifold) in favor of the new API. (src/napari_stress/_spherical_harmonics/spherical_harmonics.py, [1] [2] [3] [4] [5]
  • Deprecated corresponding functions in the spherical_harmonics_napari.py file. (src/napari_stress/_spherical_harmonics/spherical_harmonics_napari.py, [1] [2]

Dependency Updates:

  • Updated the version requirement for napari-timelapse-processor in pyproject.toml. (pyproject.toml, pyproject.tomlL33-R33)

YAML Configuration:

  • Added entries for the new expand_spherical_harmonics_on_lebedev_grid functionality in the napari.yaml contributions section. (src/napari_stress/napari.yaml, [1] [2]

@jo-mueller jo-mueller added the enhancement New feature or request label Jun 16, 2025
jo-mueller and others added 28 commits June 26, 2025 14:37
@jo-mueller jo-mueller merged commit 6e71333 into campaslab:main Jul 18, 2025
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@jo-mueller jo-mueller deleted the introduce-lebedev-expander branch July 18, 2025 12:08
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