general fixes to adapt table model

.github/workflows/test_and_deploy.yaml

@@ -63,7 +63,7 @@ jobs:
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
-                  pytest -v --cov --color=yes --cov-report=xml
+                  pytest --cov --color=yes --cov-report=xml
             - name: Upload coverage to Codecov
               uses: codecov/[email protected]
               with:

.pre-commit-config.yaml

@@ -9,25 +9,25 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.10.1
+      rev: 23.12.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.3
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
       rev: 1.16.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.6.1
+      rev: v1.7.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.3
+      rev: v0.1.8
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

.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/_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 %}
 

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

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",

src/spatialdata/_core/_elements.py

@@ -0,0 +1,116 @@
+"""SpatialData elements."""
+from __future__ import annotations
+
+from collections import UserDict
+from collections.abc import Iterable
+from typing import Any
+from warnings import warn
+
+from anndata import AnnData
+from dask.dataframe.core import DataFrame as DaskDataFrame
+from datatree import DataTree
+from geopandas import GeoDataFrame
+
+from spatialdata._types import Raster_T
+from spatialdata._utils import multiscale_spatial_image_from_data_tree
+from spatialdata.models import (
+    Image2DModel,
+    Image3DModel,
+    Labels2DModel,
+    Labels3DModel,
+    PointsModel,
+    ShapesModel,
+    TableModel,
+    get_axes_names,
+    get_model,
+)
+
+
+class Elements(UserDict[str, Any]):
+    def __init__(self, shared_keys: set[str | None]) -> None:
+        self._shared_keys = shared_keys
+        super().__init__()
+
+    @staticmethod
+    def _check_key(key: str, element_keys: Iterable[str], shared_keys: set[str | None]) -> None:
+        if key in element_keys:
+            warn(f"Key `{key}` already exists. Overwriting it.", UserWarning, stacklevel=2)
+        else:
+            if key in shared_keys:
+                raise KeyError(f"Key `{key}` already exists.")
+
+    def __setitem__(self, key: str, value: Any) -> None:
+        self._shared_keys.add(key)
+        super().__setitem__(key, value)
+
+    def __delitem__(self, key: str) -> None:
+        self._shared_keys.remove(key)
+        super().__delitem__(key)
+
+
+class Images(Elements):
+    def __setitem__(self, key: str, value: Raster_T) -> None:
+        self._check_key(key, self.keys(), self._shared_keys)
+        if isinstance(value, (DataTree)):
+            value = multiscale_spatial_image_from_data_tree(value)
+        schema = get_model(value)
+        if schema not in (Image2DModel, Image3DModel):
+            raise TypeError(f"Unknown element type with schema: {schema!r}.")
+        ndim = len(get_axes_names(value))
+        if ndim == 3:
+            Image2DModel().validate(value)
+            super().__setitem__(key, value)
+        elif ndim == 4:
+            Image3DModel().validate(value)
+            super().__setitem__(key, value)
+        else:
+            NotImplementedError("TODO: implement for ndim > 4.")
+
+
+class Labels(Elements):
+    def __setitem__(self, key: str, value: Raster_T) -> None:
+        self._check_key(key, self.keys(), self._shared_keys)
+        if isinstance(value, (DataTree)):
+            value = multiscale_spatial_image_from_data_tree(value)
+        schema = get_model(value)
+        if schema not in (Labels2DModel, Labels3DModel):
+            raise TypeError(f"Unknown element type with schema: {schema!r}.")
+        ndim = len(get_axes_names(value))
+        if ndim == 2:
+            Labels2DModel().validate(value)
+            super().__setitem__(key, value)
+        elif ndim == 3:
+            Labels3DModel().validate(value)
+            super().__setitem__(key, value)
+        else:
+            NotImplementedError("TODO: implement for ndim > 3.")
+
+
+class Shapes(Elements):
+    def __setitem__(self, key: str, value: GeoDataFrame) -> None:
+        self._check_key(key, self.keys(), self._shared_keys)
+        schema = get_model(value)
+        if schema != ShapesModel:
+            raise TypeError(f"Unknown element type with schema: {schema!r}.")
+        ShapesModel().validate(value)
+        super().__setitem__(key, value)
+
+
+class Points(Elements):
+    def __setitem__(self, key: str, value: DaskDataFrame) -> None:
+        self._check_key(key, self.keys(), self._shared_keys)
+        schema = get_model(value)
+        if schema != PointsModel:
+            raise TypeError(f"Unknown element type with schema: {schema!r}.")
+        PointsModel().validate(value)
+        super().__setitem__(key, value)
+
+
+class Tables(Elements):
+    def __setitem__(self, key: str, value: AnnData) -> None:
+        self._check_key(key, self.keys(), self._shared_keys)
+        schema = get_model(value)
+        if schema != TableModel:
+            raise TypeError(f"Unknown element type with schema: {schema!r}.")
+        TableModel().validate(value)
+        super().__setitem__(key, value)

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__ = [
@@ -25,6 +23,8 @@ def _concatenate_tables(
 ) -> AnnData:
     import anndata as ad
 
+    if not all(TableModel.ATTRS_KEY in table.uns for table in tables):
+        raise ValueError("Not all tables are annotating a spatial element")
     region_keys = [table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY] for table in tables]
     instance_keys = [table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY] for table in tables]
     regions = [table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY] for table in tables]
@@ -73,6 +73,7 @@ def concatenate(
     sdatas: list[SpatialData],
     region_key: str | None = None,
     instance_key: str | None = None,
+    concatenate_table: bool = True,
     **kwargs: Any,
 ) -> SpatialData:
     """
@@ -87,15 +88,15 @@ def concatenate(
         If all region_keys are the same, the `region_key` is used.
     instance_key
         The key to use for the instance column in the concatenated object.
+    concatenate_table
+        Whether to merge the tables in case of having the same element name.
     kwargs
         See :func:`anndata.concat` for more details.
 
     Returns
     -------
     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")
@@ -108,20 +109,29 @@ def concatenate(
     merged_shapes = {**{k: v for sdata in sdatas for k, v in sdata.shapes.items()}}
     if len(merged_shapes) != np.sum([len(sdata.shapes) for sdata in sdatas]):
         raise KeyError("Shapes must have unique names across the SpatialData objects to concatenate")
+    # TODO: finish
 
     assert isinstance(sdatas, list), "sdatas must be a list"
     assert len(sdatas) > 0, "sdatas must be a non-empty list"
 
-    merged_table = _concatenate_tables(
-        [sdata.table for sdata in sdatas if sdata.table is not None], region_key, instance_key, **kwargs
-    )
+    if not concatenate_table:
+        merged_tables = {**{k: v for sdata in sdatas for k, v in sdata.tables.items()}}
+        if len(merged_shapes) != np.sum([len(sdata.tables) for sdata in sdatas]):
+            raise KeyError(
+                "Tables must have unique names across the SpatialData objects to concatenate unless"
+                "concatenate_table is set to True."
+            )
+    else:
+        merged_tables = _concatenate_tables(
+            [sdata.table for sdata in sdatas if sdata.table is not None], region_key, instance_key, **kwargs
+        )
 
     return SpatialData(
         images=merged_images,
         labels=merged_labels,
         points=merged_points,
         shapes=merged_shapes,
-        table=merged_table,
+        tables=merged_tables,
     )