changes to adapt to SCE

CHANGELOG.md

@@ -1,47 +1,52 @@
 # Changelog
 
+## Version 0.1.0
+
+- Migrating changes from SCE, replace `validate` with `_validate`.
+
 ## Version 0.0.11-0.0.13
+
 - BUGFIX: `to_anndata()` only populates `obsm` with spatial coordinates if the original `SpatialExperiment` has spatial coordinates (PR #53, #54)
 - Enhance docstring for `to_anndata()` to describe the structure of returned AnnData object (PR #55)
 
-
 ## Version 0.0.10
+
 - Add an affine function that computes a `rasterio.Affine` object given a `scale_factor`. This assumes a simple scaling where the origin is (0,0) in the spatial coordinate system corresponding to the top-left pixel (0,0). More complex alignments would require explicit affine transforms.
 - Ensure img_raster() consistently returns a PIL.Image.Image.
 - Add to_numpy() method.
 - Changes to how caching works in remote images.
 
-
 ## Version 0.0.9
-- Added `to_anndata()` in main `SpatialExperiment` class (PR #50)
 
+- Added `to_anndata()` in main `SpatialExperiment` class (PR #50)
 
 ## Version 0.0.8
-- Set the expected column names for image data slot (PR #46)
 
+- Set the expected column names for image data slot (PR #46)
 
 ## Version 0.0.7
+
 - Added `img_source` function in main SpatialExperiment class and child classes of VirtualSpatialExperiment (PR #36)
 - Added `remove_img` function (PR #34)
 - Refactored `get_img_idx` for improved maintainability
 - Disambiguated `get_img_data` between `_imgutils.py` and `SpatialExperiment.py`
 - Moved `SpatialFeatureExperiment` into its own package
 
-
 ## Version 0.0.6
+
 - Added `read_tenx_visium()` function to load 10x Visium data as SpatialExperiment
 - Added `combine_columns` function
 - Implemented `__eq__` override for `SpatialImage` subclasses
 
-
 ## Version 0.0.5
-- Implementing a placeholder `SpatialFeatureExperiment` class. This version only implements the data structure to hold various geometries but none of the methods except for slicing.
 
+- Implementing a placeholder `SpatialFeatureExperiment` class. This version only implements the data structure to hold various geometries but none of the methods except for slicing.
 
 ## Version 0.0.3 - 0.0.4
-- Streamlining the `SpatialImage` class implementations.
 
+- Streamlining the `SpatialImage` class implementations.
 
 ## Version 0.0.1 - 0.0.2
+
 - Initial version of the SpatialExperiment class with the additional slots.
 - Allow spatial coordinates to be a numpy array

setup.cfg

@@ -49,9 +49,9 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    biocframe>=0.6.3
-    biocutils>=0.2
-    singlecellexperiment>=0.5.7
+    biocframe>=0.7.2
+    biocutils>=0.3.3
+    singlecellexperiment>=0.6.0
     pillow>=11.0
     requests
     scipy~=1.13

src/spatialexperiment/spatialexperiment.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Sequence, Union, Tuple
+from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
 from urllib.parse import urlparse
 from warnings import warn
 
@@ -30,10 +32,10 @@
     _validate_spatial_coords_names,
 )
 from .spatialimage import (
-    VirtualSpatialImage,
-    StoredSpatialImage,
-    RemoteSpatialImage,
     LoadedSpatialImage,
+    RemoteSpatialImage,
+    StoredSpatialImage,
+    VirtualSpatialImage,
     construct_spatial_image_class,
 )
 
@@ -60,7 +62,7 @@ def __init__(
         column_data: Optional[BiocFrame] = None,
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         reduced_dims: Optional[Dict[str, Any]] = None,
         main_experiment_name: Optional[str] = None,
         alternative_experiments: Optional[Dict[str, Any]] = None,
@@ -69,7 +71,7 @@ def __init__(
         column_pairs: Optional[Any] = None,
         spatial_coords: Optional[Union[BiocFrame, np.ndarray]] = None,
         img_data: Optional[BiocFrame] = None,
-        validate: bool = True,
+        _validate: bool = True,
         **kwargs,
     ) -> None:
         """Initialize a spatial experiment.
@@ -179,7 +181,7 @@ def __init__(
                 Image data are coerced to a
                 :py:class:`~biocframe.BiocFrame.BiocFrame`. Defaults to None.
 
-            validate:
+            _validate:
                 Internal use only.
         """
         super().__init__(
@@ -196,7 +198,7 @@ def __init__(
             row_pairs=row_pairs,
             column_pairs=column_pairs,
             alternative_experiment_check_dim_names=alternative_experiment_check_dim_names,
-            validate=validate,
+            _validate=_validate,
             **kwargs,
         )
 
@@ -217,7 +219,7 @@ def __init__(
         self._cols = column_data
         self._spatial_coords = spatial_coords
 
-        if validate:
+        if _validate:
             _validate_column_data(column_data=column_data)
             _validate_img_data(img_data=img_data)
             _validate_sample_ids(column_data=column_data, img_data=img_data)
@@ -265,6 +267,7 @@ def __deepcopy__(self, memo=None, _nil=[]):
             column_pairs=_col_pair_copy,
             spatial_coords=_spatial_coords_copy,
             img_data=_img_data_copy,
+            _validate=False,
         )
 
     def __copy__(self):
@@ -288,6 +291,7 @@ def __copy__(self):
             column_pairs=self._column_pairs,
             spatial_coords=self._spatial_coords,
             img_data=self._img_data,
+            _validate=False,
         )
 
     def copy(self):
@@ -399,7 +403,7 @@ def set_spatial_coordinates(
         self,
         spatial_coords: Optional[Union[BiocFrame, np.ndarray]],
         in_place: bool = False,
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Set new spatial coordinates.
 
         Args:
@@ -434,7 +438,7 @@ def set_spatial_coords(
         self,
         spatial_coords: Optional[Union[BiocFrame, np.ndarray]],
         in_place: bool = False,
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Alias for :py:meth:`~set_spatial_coordinates`."""
         return self.set_spatial_coordinates(spatial_coords=spatial_coords, in_place=in_place)
 
@@ -487,7 +491,7 @@ def get_spatial_coords_names(self) -> List[str]:
 
     def set_spatial_coordinates_names(
         self, spatial_coords_names: List[str], in_place: bool = False
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Set new spatial coordinates names.
 
         Args:
@@ -514,7 +518,7 @@ def set_spatial_coordinates_names(
         output._spatial_coords = new_spatial_coords
         return output
 
-    def set_spatial_coords_names(self, spatial_coords_names: List[str], in_place: bool = False) -> "SpatialExperiment":
+    def set_spatial_coords_names(self, spatial_coords_names: List[str], in_place: bool = False) -> SpatialExperiment:
         """Alias for :py:meth:`~set_spatial_coordinates_names`."""
         return self.set_spatial_coordinates_names(spatial_coords_names=spatial_coords_names, in_place=in_place)
 
@@ -562,7 +566,7 @@ def get_img_data(self) -> BiocFrame:
         """Alias for :py:meth:`~get_image_data`."""
         return self.get_image_data()
 
-    def set_image_data(self, img_data: Optional[BiocFrame], in_place: bool = False) -> "SpatialExperiment":
+    def set_image_data(self, img_data: Optional[BiocFrame], in_place: bool = False) -> SpatialExperiment:
         """Set new image data.
 
         Args:
@@ -591,7 +595,7 @@ def set_image_data(self, img_data: Optional[BiocFrame], in_place: bool = False)
         output._img_data = img_data
         return output
 
-    def set_img_data(self, img_data: BiocFrame, in_place: bool = False) -> "SpatialExperiment":
+    def set_img_data(self, img_data: BiocFrame, in_place: bool = False) -> SpatialExperiment:
         """Alias for :py:meth:`~set_image_data`."""
         return self.set_image_data(img_data=img_data, in_place=in_place)
 
@@ -666,7 +670,7 @@ def set_column_data(
         cols: Optional[BiocFrame],
         replace_column_names: bool = False,
         in_place: bool = False,
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Override: Set sample data.
 
         Args:
@@ -710,7 +714,7 @@ def get_slice(
         self,
         rows: Optional[Union[str, int, bool, Sequence]],
         columns: Optional[Union[str, int, bool, Sequence]],
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Alias for :py:attr:`~__getitem__`."""
 
         spe = super().get_slice(rows=rows, columns=columns)
@@ -820,7 +824,7 @@ def add_img(
         image_id: Union[str, bool, None],
         load: bool = True,
         in_place: bool = False,
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Add a new image entry.
 
         Args:
@@ -883,7 +887,7 @@ def add_img(
 
     def remove_img(
         self, sample_id: Union[str, bool, None] = None, image_id: Union[str, bool, None] = None, in_place: bool = False
-    ) -> "SpatialExperiment":
+    ) -> SpatialExperiment:
         """Remove an image entry.
 
         Args:
@@ -1083,11 +1087,11 @@ def to_anndata(
     #######>> combine ops <<########
     ################################
 
-    def relaxed_combine_columns(self, *other) -> "SpatialExperiment":
+    def relaxed_combine_columns(self, *other) -> SpatialExperiment:
         """Wrapper around :py:func:`~relaxed_combine_columns`."""
         return relaxed_combine_columns(self, *other)
 
-    def combine_columns(self, *other) -> "SpatialExperiment":
+    def combine_columns(self, *other) -> SpatialExperiment:
         """Wrapper around :py:func:`~combine_columns`."""
         return combine_columns(self, *other)
 

src/spatialexperiment/spatialimage.py

@@ -1,6 +1,6 @@
 import shutil
 import tempfile
-from abc import ABC, abstractmethod
+from abc import abstractmethod
 from functools import lru_cache
 from pathlib import Path
 from typing import Optional, Tuple, Union
@@ -19,11 +19,11 @@
 
 
 # Keeping the same names as the R classes
-class VirtualSpatialImage(ABC):
+class VirtualSpatialImage(ut.BiocObject):
     """Base class for spatial images."""
 
     def __init__(self, metadata: Optional[dict] = None):
-        self._metadata = metadata if metadata is not None else {}
+        super().__init__(metadata=metadata)
 
     #########################
     ######>> Equality <<#####
@@ -40,54 +40,6 @@ def __hash__(self):
         # Generally, these classes are mutable and shouldn't be used as dict keys or in sets.
         return hash(frozenset(self._metadata.items()))
 
-    ###########################
-    ######>> metadata <<#######
-    ###########################
-
-    def get_metadata(self) -> dict:
-        """
-        Returns:
-            Dictionary of metadata for this object.
-        """
-        return self._metadata
-
-    def set_metadata(self, metadata: dict, in_place: bool = False) -> "VirtualSpatialImage":
-        """Set additional metadata.
-
-        Args:
-            metadata:
-                New metadata for this object.
-
-            in_place:
-                Whether to modify the ``VirtualSpatialImage`` in place.
-
-        Returns:
-            A modified ``VirtualSpatialImage`` object, either as a copy of the original
-            or as a reference to the (in-place-modified) original.
-        """
-        if not isinstance(metadata, dict):
-            raise TypeError(f"`metadata` must be a dictionary, provided {type(metadata)}.")
-        output = self._define_output(in_place)
-        output._metadata = metadata
-        return output
-
-    @property
-    def metadata(self) -> dict:
-        """Alias for :py:attr:`~get_metadata`."""
-        return self.get_metadata()
-
-    @metadata.setter
-    def metadata(self, metadata: dict):
-        """Alias for :py:attr:`~set_metadata` with ``in_place = True``.
-
-        As this mutates the original object, a warning is raised.
-        """
-        warn(
-            "Setting property 'metadata' is an in-place operation, use 'set_metadata' instead",
-            UserWarning,
-        )
-        self.set_metadata(metadata, in_place=True)
-
     ##################################
     ######>> Spatial Props <<#########
     ##################################