refactor data loader

.readthedocs.yaml

@@ -6,7 +6,7 @@ build:
         python: "3.10"
 sphinx:
     configuration: docs/conf.py
-    fail_on_warning: false
+    fail_on_warning: true
 python:
     install:
         - method: pip

docs/api.md

@@ -29,7 +29,6 @@ Operations on `SpatialData` objects.
     match_table_to_element
     concatenate
     rasterize
-    transform
     aggregate
 ```
 
@@ -48,6 +47,7 @@ The elements (building-blocks) that consitute `SpatialData`.
 
 ```{eval-rst}
 .. currentmodule:: spatialdata.models
+
 .. autosummary::
     :toctree: generated
 
@@ -63,6 +63,8 @@ The elements (building-blocks) that consitute `SpatialData`.
 ### Utilities
 
 ```{eval-rst}
+.. currentmodule:: spatialdata.models
+
 .. autosummary::
     :toctree: generated
 
@@ -96,6 +98,8 @@ The transformations that can be defined between elements and coordinate systems
 ### Utilities
 
 ```{eval-rst}
+.. currentmodule:: spatialdata.transformations
+
 .. autosummary::
     :toctree: generated
 

pyproject.toml

@@ -49,7 +49,6 @@ dev = [
 docs = [
     "sphinx>=4.5",
     "sphinx-book-theme>=1.0.0",
-    "sphinx_rtd_theme",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",

src/spatialdata/_core/concatenate.py

@@ -2,14 +2,12 @@
 
 from copy import copy  # Should probably go up at the top
 from itertools import chain
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import numpy as np
 from anndata import AnnData
 
-if TYPE_CHECKING:
-    from spatialdata._core.spatialdata import SpatialData
-
+from spatialdata._core.spatialdata import SpatialData
 from spatialdata.models import TableModel
 
 __all__ = [
@@ -94,8 +92,6 @@ def concatenate(
     -------
     The concatenated :class:`spatialdata.SpatialData` object.
     """
-    from spatialdata import SpatialData
-
     merged_images = {**{k: v for sdata in sdatas for k, v in sdata.images.items()}}
     if len(merged_images) != np.sum([len(sdata.images) for sdata in sdatas]):
         raise KeyError("Images must have unique names across the SpatialData objects to concatenate")

src/spatialdata/_core/operations/aggregate.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import anndata as ad
 import dask as da
@@ -20,6 +20,7 @@
 from spatialdata._core.operations.transform import transform
 from spatialdata._core.query._utils import circles_to_polygons
 from spatialdata._core.query.relational_query import get_values
+from spatialdata._core.spatialdata import SpatialData
 from spatialdata._types import ArrayLike
 from spatialdata.models import (
     Image2DModel,
@@ -32,9 +33,6 @@
 )
 from spatialdata.transformations import BaseTransformation, Identity, get_transformation
 
-if TYPE_CHECKING:
-    from spatialdata import SpatialData
-
 __all__ = ["aggregate"]
 
 
@@ -236,7 +234,6 @@ def _create_sdata_from_table_and_shapes(
     instance_key: str,
     deepcopy: bool,
 ) -> SpatialData:
-    from spatialdata import SpatialData
     from spatialdata._utils import _deepcopy_geodataframe
 
     table.obs[instance_key] = table.obs_names.copy()

src/spatialdata/_core/operations/rasterize.py

@@ -207,8 +207,6 @@ def _(
     target_height: Optional[float] = None,
     target_depth: Optional[float] = None,
 ) -> SpatialData:
-    from spatialdata import SpatialData
-
     min_coordinate = _parse_list_into_array(min_coordinate)
     max_coordinate = _parse_list_into_array(max_coordinate)
 

src/spatialdata/_core/query/relational_query.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import dask.array as da
 import numpy as np
@@ -11,6 +11,7 @@
 from multiscale_spatial_image import MultiscaleSpatialImage
 from spatial_image import SpatialImage
 
+from spatialdata._core.spatialdata import SpatialData
 from spatialdata._utils import _inplace_fix_subset_categorical_obs
 from spatialdata.models import (
     Labels2DModel,
@@ -22,9 +23,6 @@
     get_model,
 )
 
-if TYPE_CHECKING:
-    from spatialdata import SpatialData
-
 
 def _filter_table_by_coordinate_system(table: AnnData | None, coordinate_system: str | list[str]) -> AnnData | None:
     """

src/spatialdata/_core/query/spatial_query.py

@@ -305,7 +305,6 @@ def _(
     target_coordinate_system: str,
     filter_table: bool = True,
 ) -> SpatialData:
-    from spatialdata import SpatialData
     from spatialdata._core.query.relational_query import _filter_table_by_elements
 
     min_coordinate = _parse_list_into_array(min_coordinate)

src/spatialdata/_core/spatialdata.py

@@ -18,27 +18,17 @@
 from pyarrow.parquet import read_table
 from spatial_image import SpatialImage
 
-from spatialdata._io import (
-    write_image,
-    write_labels,
-    write_points,
-    write_shapes,
-    write_table,
-)
-from spatialdata._io._utils import get_backing_files
 from spatialdata._logging import logger
 from spatialdata._types import ArrayLike
-from spatialdata._utils import _natural_keys
-from spatialdata.models import (
+from spatialdata.models._utils import SpatialElement, get_axes_names
+from spatialdata.models.models import (
     Image2DModel,
     Image3DModel,
     Labels2DModel,
     Labels3DModel,
     PointsModel,
     ShapesModel,
-    SpatialElement,
     TableModel,
-    get_axes_names,
     get_model,
 )
 
@@ -653,6 +643,9 @@ def add_image(
         -----
         If the SpatialData object is backed by a Zarr storage, the image will be written to the Zarr storage.
         """
+        from spatialdata._io._utils import get_backing_files
+        from spatialdata._io.io_raster import write_image
+
         if self.is_backed():
             files = get_backing_files(image)
             assert self.path is not None
@@ -736,6 +729,9 @@ def add_labels(
         -----
         If the SpatialData object is backed by a Zarr storage, the image will be written to the Zarr storage.
         """
+        from spatialdata._io._utils import get_backing_files
+        from spatialdata._io.io_raster import write_labels
+
         if self.is_backed():
             files = get_backing_files(labels)
             assert self.path is not None
@@ -820,6 +816,9 @@ def add_points(
         -----
         If the SpatialData object is backed by a Zarr storage, the image will be written to the Zarr storage.
         """
+        from spatialdata._io._utils import get_backing_files
+        from spatialdata._io.io_points import write_points
+
         if self.is_backed():
             files = get_backing_files(points)
             assert self.path is not None
@@ -902,6 +901,8 @@ def add_shapes(
         -----
         If the SpatialData object is backed by a Zarr storage, the image will be written to the Zarr storage.
         """
+        from spatialdata._io.io_shapes import write_shapes
+
         self._add_shapes_in_memory(name=name, shapes=shapes, overwrite=overwrite)
         if self.is_backed():
             elem_group = self._init_add_element(name=name, element_type="shapes", overwrite=overwrite)
@@ -918,6 +919,8 @@ def write(
         storage_options: JSONDict | list[JSONDict] | None = None,
         overwrite: bool = False,
     ) -> None:
+        from spatialdata._io import write_image, write_labels, write_points, write_shapes, write_table
+
         """Write the SpatialData object to Zarr."""
         if isinstance(file_path, str):
             file_path = Path(file_path)
@@ -1113,6 +1116,8 @@ def table(self, table: AnnData) -> None:
         The table needs to pass validation (see :class:`~spatialdata.TableModel`).
         If the SpatialData object is backed by a Zarr storage, the table will be written to the Zarr storage.
         """
+        from spatialdata._io.io_table import write_table
+
         TableModel().validate(table)
         if self.table is not None:
             raise ValueError("The table already exists. Use del sdata.table to remove it first.")
@@ -1199,6 +1204,7 @@ def _gen_repr(
         -------
             The string representation of the SpatialData object.
         """
+        from spatialdata._utils import _natural_keys
 
         def rreplace(s: str, old: str, new: str, occurrence: int) -> str:
             li = s.rsplit(old, occurrence)

src/spatialdata/_io/_utils.py

@@ -8,7 +8,7 @@
 from collections.abc import Generator, Mapping
 from contextlib import contextmanager
 from functools import singledispatch
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import zarr
 from dask.dataframe.core import DataFrame as DaskDataFrame
@@ -18,6 +18,7 @@
 from spatial_image import SpatialImage
 from xarray import DataArray
 
+from spatialdata._core.spatialdata import SpatialData
 from spatialdata._utils import iterate_pyramid_levels
 from spatialdata.models._utils import (
     MappingToCoordinateSystem_t,
@@ -30,9 +31,6 @@
     _get_current_output_axes,
 )
 
-if TYPE_CHECKING:
-    from spatialdata import SpatialData
-
 
 # suppress logger debug from ome_zarr with context manager
 @contextmanager
@@ -196,8 +194,6 @@ def _are_directories_identical(
 
 
 def _compare_sdata_on_disk(a: SpatialData, b: SpatialData) -> bool:
-    from spatialdata import SpatialData
-
     if not isinstance(a, SpatialData) or not isinstance(b, SpatialData):
         return False
     # TODO: if the sdata object is backed on disk, don't create a new zarr file

src/spatialdata/_io/io_zarr.py

@@ -7,7 +7,7 @@
 from anndata import AnnData
 from anndata import read_zarr as read_anndata_zarr
 
-from spatialdata import SpatialData
+from spatialdata._core.spatialdata import SpatialData
 from spatialdata._io._utils import ome_zarr_logger
 from spatialdata._io.io_points import _read_points
 from spatialdata._io.io_raster import _read_multiscale

src/spatialdata/_utils.py

@@ -3,7 +3,7 @@
 import re
 from collections.abc import Generator
 from copy import deepcopy
-from typing import TYPE_CHECKING, Union
+from typing import Union
 
 import numpy as np
 import pandas as pd
@@ -26,9 +26,6 @@
 # I was using "from numbers import Number" but this led to mypy errors, so I switched to the following:
 Number = Union[int, float]
 
-if TYPE_CHECKING:
-    pass
-
 
 def _parse_list_into_array(array: list[Number] | ArrayLike) -> ArrayLike:
     if isinstance(array, list):

src/spatialdata/dataloader/__init__.py

@@ -1,6 +1,4 @@
-import contextlib
-
-with contextlib.suppress(ImportError):
+try:
     from spatialdata.dataloader.datasets import ImageTilesDataset
-
-__all__ = ["ImageTilesDataset"]
+except ImportError:
+    ImageTilesDataset = None  # type: ignore[assignment, misc]