refactor data loader (#299)

Co-authored-by: LucaMarconato <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Luca Marconato <[email protected]>
scverse · Dec 14, 2023 · c9e7d99 · c9e7d99
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diff --git a/.readthedocs.yaml b/.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

diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -12,11 +12,8 @@ Attributes table
 ~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
-
 {% for item in attributes %}
-
     ~{{ fullname }}.{{ item }}
-
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -27,13 +24,10 @@ Methods table
 ~~~~~~~~~~~~~
 
 .. autosummary::
-
 {% for item in methods %}
-
     {%- if item != '__init__' %}
     ~{{ fullname }}.{{ item }}
     {%- endif -%}
-
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -46,7 +40,6 @@ Attributes
 {% for item in attributes %}
 
 .. autoattribute:: {{ [objname, item] | join(".") }}
-
 {%- endfor %}
 
 {% endif %}
@@ -61,7 +54,6 @@ Methods
 {%- if item != '__init__' %}
 
 .. automethod:: {{ [objname, item] | join(".") }}
-
 {%- endif -%}
 {%- endfor %}
 

diff --git a/docs/api.md b/docs/api.md
@@ -30,11 +30,10 @@ Operations on `SpatialData` objects.
     match_table_to_element
     concatenate
     rasterize
-    transform
     aggregate
 ```
 
-### Utilities
+### Operations Utilities
 
 ```{eval-rst}
 .. autosummary::
@@ -49,6 +48,7 @@ The elements (building-blocks) that consitute `SpatialData`.
 
 ```{eval-rst}
 .. currentmodule:: spatialdata.models
+
 .. autosummary::
     :toctree: generated
 
@@ -61,9 +61,11 @@ The elements (building-blocks) that consitute `SpatialData`.
     TableModel
 ```
 
-### Utilities
+### Models Utilities
 
 ```{eval-rst}
+.. currentmodule:: spatialdata.models
+
 .. autosummary::
     :toctree: generated
 
@@ -94,9 +96,11 @@ The transformations that can be defined between elements and coordinate systems
     Sequence
 ```
 
-### Utilities
+### Transformations Utilities
 
 ```{eval-rst}
+.. currentmodule:: spatialdata.transformations
+
 .. autosummary::
     :toctree: generated
 
@@ -119,7 +123,7 @@ The transformations that can be defined between elements and coordinate systems
     ImageTilesDataset
 ```
 
-## Input/output
+## Input/Output
 
 ```{eval-rst}
 .. currentmodule:: spatialdata

diff --git a/pyproject.toml b/pyproject.toml
@@ -50,7 +50,6 @@ dev = [
 docs = [
     "sphinx>=4.5",
     "sphinx-book-theme>=1.0.0",
-    "sphinx_rtd_theme",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",

diff --git a/src/spatialdata/_core/concatenate.py b/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")

diff --git a/src/spatialdata/_core/data_extent.py b/src/spatialdata/_core/data_extent.py
@@ -115,9 +115,9 @@ def get_extent(
     has_labels: bool = True,
     has_points: bool = True,
     has_shapes: bool = True,
-    # python 3.9 tests fail if we don't use Union here, see
-    # https://github.com/scverse/spatialdata/pull/318#issuecomment-1755714287
-    elements: Union[list[str], None] = None,  # noqa: UP007
+    elements: Union[  # noqa: UP007 # https://github.com/scverse/spatialdata/pull/318#issuecomment-1755714287
+        list[str], None
+    ] = None,
 ) -> BoundingBoxDescription:
     """
     Get the extent (bounding box) of a SpatialData object or a SpatialElement.
@@ -129,43 +129,50 @@ def get_extent(
 
     Returns
     -------
+    The bounding box description.
+
     min_coordinate
         The minimum coordinate of the bounding box.
     max_coordinate
         The maximum coordinate of the bounding box.
     axes
-        The names of the dimensions of the bounding box
+        The names of the dimensions of the bounding box.
     exact
-        If True, the extent is computed exactly. If False, an approximation faster to compute is given. The
-        approximation is guaranteed to contain all the data, see notes for details.
+        Whether the extent is computed exactly or not.
+
+            - If `True`, the extent is computed exactly.
+            - If `False`, an approximation faster to compute is given.
+
+        The approximation is guaranteed to contain all the data, see notes for details.
     has_images
-        If True, images are included in the computation of the extent.
+        If `True`, images are included in the computation of the extent.
     has_labels
-        If True, labels are included in the computation of the extent.
+        If `True`, labels are included in the computation of the extent.
     has_points
-        If True, points are included in the computation of the extent.
+        If `True`, points are included in the computation of the extent.
     has_shapes
-        If True, shapes are included in the computation of the extent.
+        If `True`, shapes are included in the computation of the extent.
     elements
-        If not None, only the elements with the given names are included in the computation of the extent.
+        If not `None`, only the elements with the given names are included in the computation of the extent.
 
     Notes
     -----
-    The extent of a SpatialData object is the extent of the union of the extents of all its elements. The extent of a
-    SpatialElement is the extent of the element in the coordinate system specified by the argument `coordinate_system`.
+    The extent of a `SpatialData` object is the extent of the union of the extents of all its elements.
+    The extent of a `SpatialElement` is the extent of the element in the coordinate system
+    specified by the argument `coordinate_system`.
 
-    If `exact` is False, first the extent of the SpatialElement before any transformation is computed. Then, the extent
-    is transformed to the target coordinate system. This is faster than computing the extent after the transformation,
-    since the transformation is applied to extent of the untransformed data, as opposed to transforming the data and
-    then computing the extent.
+    If `exact` is `False`, first the extent of the `SpatialElement` before any transformation is computed.
+    Then, the extent is transformed to the target coordinate system. This is faster than computing the extent
+    after the transformation, since the transformation is applied to extent of the untransformed data,
+    as opposed to transforming the data and then computing the extent.
 
-    The exact and approximate extent are the same if the transformation doesn't contain any rotation or shear, or in the
-    case in which the transformation is affine but all the corners of the extent of the untransformed data
+    The exact and approximate extent are the same if the transformation does not contain any rotation or shear, or in
+    the case in which the transformation is affine but all the corners of the extent of the untransformed data
     (bounding box corners) are part of the dataset itself. Note that this is always the case for raster data.
 
-    An extreme case is a dataset composed of the two points (0, 0) and (1, 1), rotated anticlockwise by 45 degrees. The
-    exact extent is the bounding box [minx, miny, maxx, maxy] = [0, 0, 0, 1.414], while the approximate extent is the
-    box [minx, miny, maxx, maxy] = [-0.707, 0, 0.707, 1.414].
+    An extreme case is a dataset composed of the two points `(0, 0)` and `(1, 1)`, rotated anticlockwise by 45 degrees.
+    The exact extent is the bounding box `[minx, miny, maxx, maxy] = [0, 0, 0, 1.414]`, while the approximate extent is
+    the box `[minx, miny, maxx, maxy] = [-0.707, 0, 0.707, 1.414]`.
     """
     raise ValueError("The object type is not supported.")
 
@@ -184,7 +191,9 @@ def _(
     elements: Union[list[str], None] = None,  # noqa: UP007
 ) -> BoundingBoxDescription:
     """
-    Get the extent (bounding box) of a SpatialData object: the extent of the union of the extents of all its elements.
+    Get the extent (bounding box) of a SpatialData object.
+
+    The resulting extent is the union of the extents of all its elements.
 
     Parameters
     ----------
@@ -259,7 +268,14 @@ def _get_extent_of_shapes(e: GeoDataFrame) -> BoundingBoxDescription:
 @get_extent.register
 def _(e: GeoDataFrame, coordinate_system: str = "global", exact: bool = True) -> BoundingBoxDescription:
     """
-    Compute the extent (bounding box) of a set of shapes.
+    Get the extent (bounding box) of a SpatialData object.
+
+    The resulting extent is the union of the extents of all its elements.
+
+    Parameters
+    ----------
+    e
+        The SpatialData object.
 
     Returns
     -------

diff --git a/src/spatialdata/_core/operations/aggregate.py b/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()

diff --git a/src/spatialdata/_core/operations/rasterize.py b/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)
 

diff --git a/src/spatialdata/_core/query/relational_query.py b/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:
     """

diff --git a/src/spatialdata/_core/query/spatial_query.py b/src/spatialdata/_core/query/spatial_query.py
@@ -248,7 +248,6 @@ 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)