spatialdata-io 0.5.0__tar.gz → 0.5.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (73) hide show
  1. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/PKG-INFO +1 -1
  2. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/_version.py +2 -2
  3. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/visium_hd.py +8 -0
  4. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.bumpversion.cfg +0 -0
  5. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.codecov.yaml +0 -0
  6. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.editorconfig +0 -0
  7. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.github/codecov.yml +0 -0
  8. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.github/release.yml +0 -0
  9. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.github/workflows/prepare_test_data.yaml +0 -0
  10. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.github/workflows/release.yaml +0 -0
  11. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.github/workflows/test.yaml +0 -0
  12. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.gitignore +0 -0
  13. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.mypy.ini +0 -0
  14. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.pre-commit-config.yaml +0 -0
  15. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.readthedocs.yaml +0 -0
  16. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/LICENSE +0 -0
  17. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/README.md +0 -0
  18. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/Makefile +0 -0
  19. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/_static/.gitkeep +0 -0
  20. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/_templates/.gitkeep +0 -0
  21. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/_templates/autosummary/class.rst +0 -0
  22. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/api.md +0 -0
  23. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/changelog.md +0 -0
  24. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/cli.md +0 -0
  25. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/conf.py +0 -0
  26. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/contributing.md +0 -0
  27. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/extensions/.gitkeep +0 -0
  28. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/extensions/typed_returns.py +0 -0
  29. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/index.md +0 -0
  30. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/make.bat +0 -0
  31. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/references.bib +0 -0
  32. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/docs/references.md +0 -0
  33. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/pyproject.toml +0 -0
  34. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/__init__.py +0 -0
  35. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/__main__.py +0 -0
  36. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/_constants/__init__.py +0 -0
  37. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/_constants/_constants.py +0 -0
  38. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/_constants/_enum.py +0 -0
  39. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/_docs.py +0 -0
  40. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/_utils.py +0 -0
  41. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/converters/__init__.py +0 -0
  42. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/converters/generic_to_zarr.py +0 -0
  43. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/converters/legacy_anndata.py +0 -0
  44. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/experimental/__init__.py +0 -0
  45. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/__init__.py +0 -0
  46. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/_utils/__init__.py +0 -0
  47. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/_utils/_read_10x_h5.py +0 -0
  48. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/_utils/_utils.py +0 -0
  49. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/codex.py +0 -0
  50. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/cosmx.py +0 -0
  51. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/curio.py +0 -0
  52. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/dbit.py +0 -0
  53. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/generic.py +0 -0
  54. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/iss.py +0 -0
  55. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/macsima.py +0 -0
  56. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/mcmicro.py +0 -0
  57. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/merscope.py +0 -0
  58. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/seqfish.py +0 -0
  59. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/steinbock.py +0 -0
  60. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/stereoseq.py +0 -0
  61. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/visium.py +0 -0
  62. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/xenium.py +0 -0
  63. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/__init__.py +0 -0
  64. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/_utils.py +0 -0
  65. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/conftest.py +0 -0
  66. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/converters/__init__.py +0 -0
  67. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/converters/test_legacy_anndata.py +0 -0
  68. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_basic.py +0 -0
  69. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_generic.py +0 -0
  70. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_macsima.py +0 -0
  71. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_seqfish.py +0 -0
  72. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_visium_hd.py +0 -0
  73. {spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/tests/test_xenium.py +0 -0
{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: spatialdata-io
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- Version: 0.5.0
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+ Version: 0.5.1
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  Summary: SpatialData IO for common techs
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  Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
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  Project-URL: Source, https://github.com/scverse/spatialdata-io
{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/_version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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- __version__ = version = '0.5.0'
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- __version_tuple__ = version_tuple = (0, 5, 0)
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+ __version__ = version = '0.5.1'
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+ __version_tuple__ = version_tuple = (0, 5, 1)
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  __commit_id__ = commit_id = None
{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/src/spatialdata_io/readers/visium_hd.py RENAMED
@@ -133,6 +133,14 @@ def visium_hd(
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  CELL_GEOJSON_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.CELL_SEGMENTATION_GEOJSON_PATH
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  NUCLEUS_GEOJSON_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.NUCLEUS_SEGMENTATION_GEOJSON_PATH
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  SCALE_FACTORS_PATH = SEGMENTED_OUTPUTS_PATH / VisiumHDKeys.SPATIAL / VisiumHDKeys.SCALEFACTORS_FILE
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+ if not SCALE_FACTORS_PATH.exists():
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+ # Visium HD 3.0.0 does not have the SEGMENTATION_OUTPUTS folder
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+ scale_factors_file = next(
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+ (file for file in path.rglob("*") if file.name.endswith(VisiumHDKeys.SCALEFACTORS_FILE)),
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+ None,
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+ )
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+ assert scale_factors_file is not None, "Scale factors file not found in any of the subdirectories."
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+ SCALE_FACTORS_PATH = scale_factors_file
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  BARCODE_MAPPINGS_PATH = next(
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  (file for file in path.rglob("*") if file.name.endswith(VisiumHDKeys.BARCODE_MAPPINGS_FILE)),
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  None,
{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/.mypy.ini RENAMED
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{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/LICENSE RENAMED
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{spatialdata_io-0.5.0 → spatialdata_io-0.5.1}/README.md RENAMED
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