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Add new spatial foundational types #219

Merged
merged 24 commits into from
Sep 26, 2024
Merged

Add new spatial foundational types #219

merged 24 commits into from
Sep 26, 2024

Commits on Sep 18, 2024

  1. Add new spatial datatypes to SOMA 

    - Add new MultiscaleImage
- Add new SpatialDataframe abstract base class
- Add PointCloud subclass of the SpatialDataFrame
- Add GeometryDataFrame subclass of the SpatialDataFrame
- Add shapely as a dependency
    @jp-dark
    jp-dark committed Sep 18, 2024
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  2. Update MultiscaleImage docstring and other small updates 

    * Update docstrings
* Add ValueError error messages in `SpatialRead`
* Rename method `read_level`->`read_region`
    @jp-dark
    jp-dark committed Sep 18, 2024
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  3. Move docstring updates

    @jp-dark
    jp-dark committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Update python-spec/src/somacore/spatialdata.py 

    Co-authored-by: nguyenv <vivian@tiledb.com>
    @jp-dark @nguyenv
    jp-dark and nguyenv authored Sep 19, 2024
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  2. Fix docstring for spatialdata read_region

    @jp-dark
    jp-dark committed Sep 19, 2024
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  3. Remove SpatialDataFrame from spec 

    The individual implementations may find a shared base class useful, but
it doesn't need to be included in the abstract specification.
    @jp-dark
    jp-dark committed Sep 19, 2024
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Commits on Sep 24, 2024

  1. Rename spatialdata.py -> spatialdata

    @jp-dark
    jp-dark committed Sep 24, 2024
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  2. Add coordinate space to PointCloud and GeometryDataFrame

    @jp-dark
    jp-dark committed Sep 24, 2024
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  3. Remove the extra_coords param in read_region 

    Using the `value_filter` is a less confusing API.
    @jp-dark
    jp-dark committed Sep 24, 2024
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  4. Rename param transform -> region_transform in read_region 

    The name `transform` was misleading.
    @jp-dark
    jp-dark committed Sep 24, 2024
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  5. Match axis_names order in MultiscaleImage to image_type order 

    Clarify that they should be in the same order in the docstring.
    @jp-dark
    jp-dark committed Sep 24, 2024
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  6. Fix typo in ValueError

    @jp-dark
    jp-dark committed Sep 24, 2024
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  7. Drop create_mask option from DenseArray.read_region

    @jp-dark
    jp-dark committed Sep 24, 2024
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  8. Merge branch 'main' into dark/spatial-datatypes

    @jp-dark
    jp-dark committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. Fix shapely type for SpatialRegion 

    Co-authored-by: nguyenv <vivian@tiledb.com>
    @jp-dark @nguyenv
    jp-dark and nguyenv authored Sep 25, 2024
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  2. Run linters

    @jp-dark
    jp-dark committed Sep 25, 2024
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  3. Replace 'image_type' with 'axis_types'

    @jp-dark
    jp-dark committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. Fix typo in docstring 

    Co-authored-by: Aaron Wolen <aaron@wolen.com>
    @jp-dark @aaronwolen
    jp-dark and aaronwolen authored Sep 26, 2024
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  2. Add clarity to docstring 

    Co-authored-by: Aaron Wolen <aaron@wolen.com>
    @jp-dark @aaronwolen
    jp-dark and aaronwolen authored Sep 26, 2024
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  3. Fix typos and improve clarity in docstrings 

    Co-authored-by: Aaron Wolen <aaron@wolen.com>
    @jp-dark @aaronwolen
    jp-dark and aaronwolen authored Sep 26, 2024
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  4. Rename read_region to read_spatial_region

    @jp-dark
    jp-dark committed Sep 26, 2024
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  5. Replace _transformation_ with _transform_ in method names

    @jp-dark
    jp-dark committed Sep 26, 2024
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  6. Fix incomplete docstring

    @jp-dark
    jp-dark committed Sep 26, 2024
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  7. Expand spatial dataframe docstrings (#230) 

    * Expand PointCloud doc string

* Expand GeometryDataFrame docstring

* Double back ticks
    @aaronwolen
    aaronwolen authored Sep 26, 2024
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