napari-spatialdata 0.3.0__tar.gz → 0.4.0__tar.gz

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.9.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
   - repo: https://github.com/psf/black
-    rev: 23.10.1
+    rev: 24.3.0
     hooks:
       - id: black
         additional_dependencies: [toml]
   - 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/pre-commit/pre-commit-hooks
@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.4
+    rev: v0.3.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/.readthedocs.yaml

@@ -15,3 +15,4 @@ python:
         - "doc"
         - "all"
         - "readthedocs"
+        - "pre"

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/CHANGELOG.md

@@ -8,7 +8,27 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [0.3.1] - TBD
+## [0.4.0] - 2023-03-24
+
+### Added
+
+- Multi table support #199 @melonora
+- Color shapes and points by values in dataframe in addition to tables #216
+
+### Fixed
+
+- Avoid exception when registering shortcuts #201 @aeisenbarth
+- Fix wrong point size when affine specified #193
+- Wrong element visiblity when changing coordinate system #207
+- Cleaned up data model #180
+- Fixes correct matching of geometies and annoations via join #208
+- Better docstrings #219
+
+## [0.3.1] - 2023-11-11
+
+### Fix
+
+- removed npe (napari plugin engine) dependency
 
 ## [0.3.0] - 2023-11-09
 

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.3.0
+Version: 0.4.0
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -30,15 +30,15 @@ Requires-Dist: dask
 Requires-Dist: geopandas
 Requires-Dist: loguru
 Requires-Dist: matplotlib
-Requires-Dist: napari
+Requires-Dist: napari>=0.4.19
 Requires-Dist: napari-matplotlib
-Requires-Dist: napari-plugin-engine
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: packaging
 Requires-Dist: pandas
 Requires-Dist: pillow
 Requires-Dist: qtpy
+Requires-Dist: scanpy
 Requires-Dist: scipy
 Requires-Dist: shapely
 Requires-Dist: scikit-learn
@@ -67,9 +67,10 @@ Requires-Dist: sphinx-copybutton; extra == "doc"
 Requires-Dist: sphinx-qt-documentation; extra == "doc"
 Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: squidpy; extra == "doc"
-Requires-Dist: scanpy; extra == "doc"
 Provides-Extra: readthedocs
 Requires-Dist: pydantic<2; extra == "readthedocs"
+Provides-Extra: pre
+Requires-Dist: spatialdata>=0.1.0-pre0; extra == "pre"
 Provides-Extra: all
 Requires-Dist: PyQt5; extra == "all"
 
@@ -110,6 +111,11 @@ pip install napari-spatialdata
 
 You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).
 
+## Using napari-spatialdata as default zarr reader
+
+If you would like to use the plugin as the default zarr reader, in napari please go to `File` -> `Preferences`
+-> `Plugins` and follow the instructions under `File extension readers`.
+
 ## Development Version
 
 You can install `napari-spatialdata` from Github with:
@@ -145,6 +151,10 @@ Distributed under the terms of the [BSD-3] license,
 
 If you encounter any problems, please file an [issue] along with a detailed description.
 
+## Citation
+
+Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x
+
 [napari]: https://github.com/napari/napari
 [cookiecutter]: https://github.com/audreyr/cookiecutter
 [@napari]: https://github.com/napari

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/README.md

@@ -35,6 +35,11 @@ pip install napari-spatialdata
 
 You can find more details on this in the [installation instructions](https://spatialdata.scverse.org/en/latest/installation.html).
 
+## Using napari-spatialdata as default zarr reader
+
+If you would like to use the plugin as the default zarr reader, in napari please go to `File` -> `Preferences`
+-> `Plugins` and follow the instructions under `File extension readers`.
+
 ## Development Version
 
 You can install `napari-spatialdata` from Github with:
@@ -70,6 +75,10 @@ Distributed under the terms of the [BSD-3] license,
 
 If you encounter any problems, please file an [issue] along with a detailed description.
 
+## Citation
+
+Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x
+
 [napari]: https://github.com/napari/napari
 [cookiecutter]: https://github.com/audreyr/cookiecutter
 [@napari]: https://github.com/napari

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/docs/conf.py

@@ -135,7 +135,7 @@ nitpick_ignore = [
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.insertAction"),
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.scroll"),
     # ("py:obj", "napari_spatialdata.QtAdataViewWidget.setTabOrder"),
-    # ("py:class", "napari_spatialdata._model.ImageModel"),
+    # ("py:class", "napari_spatialdata._model.DataModel"),
     # ("py:obj", "napari_spatialdata.QtAdataScatterWidget.scroll"),
     # ("py:obj", "napari_spatialdata.QtAdataScatterWidget.insertAction"),
     # If building the documentation fails because of a missing link that is outside your control,

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/pyproject.toml

@@ -37,6 +37,9 @@ exclude = [
     "dist",
     "setup.py",
 ]
+line-length = 120
+target-version = "py38"
+[tool.ruff.lint]
 ignore = [
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -56,7 +59,6 @@ ignore = [
     # Missing docstring in magic method
     "D105",
 ]
-line-length = 120
 select = [
     "D", # flake8-docstrings
     "I", # isort
@@ -76,8 +78,9 @@ select = [
     "RET", # flake8-raise
 ]
 unfixable = ["B", "UP", "C4", "BLE", "T20", "RET"]
-target-version = "py38"
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+[tool.ruff.lint.per-file-ignores]
     "tests/*" = ["D", "PT", "B024"]
     "*/__init__.py" = ["F401", "D104", "D107"]
     "docs/*" = ["D","B","E","A"]
@@ -86,5 +89,3 @@ target-version = "py38"
     "src/napari_spatialdata/_constants/_utils.py" = ["D101","D102", "B024"]
     "src/napari_spatialdata/_widgets.py" = ["D"]
     "src/napari_spatialdata/_scatterwidgets.py" = ["D"]
-[tool.ruff.pydocstyle]
-convention = "numpy"

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/setup.cfg

@@ -37,15 +37,15 @@ install_requires =
 	geopandas
 	loguru
 	matplotlib
-	napari
+	napari>=0.4.19
 	napari-matplotlib
-	napari-plugin-engine
 	numba
 	numpy
 	packaging
 	pandas
 	pillow
 	qtpy
+	scanpy
 	scipy
 	shapely
 	scikit-learn
@@ -78,9 +78,10 @@ doc =
 	sphinx-qt-documentation
 	myst-nb
 	squidpy
-	scanpy
 readthedocs = 
 	pydantic<2
+pre = 
+	spatialdata>=0.1.0-pre0
 all = 
 	PyQt5
 

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/__main__.py

@@ -32,6 +32,8 @@ def view(path: tuple[str], headless: bool) -> None:
     ----------
     path
         Path to one or more SpatialData datasets.
+    headless
+        Whether to run the napari application or to run in headless mode.
     """
     assert type(path) == tuple
 

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/_constants/_constants.py

@@ -1,4 +1,5 @@
 """Constants that user deals with."""
+
 from enum import unique
 
 from napari_spatialdata._constants._utils import ModeEnum

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/_constants/_pkg_constants.py

@@ -1,4 +1,5 @@
 """Internal constants not exposed to the user."""
+
 from typing import Any, Callable, Optional
 
 from anndata import AnnData

napari-spatialdata-0.4.0/src/napari_spatialdata/_constants/config.py

@@ -0,0 +1,2 @@
+POLYGON_THRESHOLD = 100
+POINT_THRESHOLD = 100000

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/_interactive.py

@@ -34,6 +34,19 @@ class Interactive:
     """
 
     def add_element(self, element: str, element_coordinate_system: str, view_element_system: bool = False) -> None:
+        """
+        Add an element of a spatial data object being visualized with interactive to the viewer.
+
+        Parameters
+        ----------
+        element
+            The name of the element in the spatial data object to add as napari layer.
+        element_coordinate_system
+            The coordinate system in which the layer should be visualized.
+        view_element_system
+            Whether to switch to element_coordinate_system or to switch back to current active coordinate system
+            after adding an element as layer.
+        """
         duplicate_element_names, _ = get_duplicate_element_names(self._sdata)
         elements, name_to_add = get_elements_meta_mapping(
             self._sdata, element_coordinate_system, duplicate_element_names, element
@@ -58,6 +71,7 @@ class Interactive:
             raise ValueError(f"Element {element} not found in coordinate system {element_coordinate_system}.")
 
     def switch_coordinate_system(self, coordinate_system: str) -> None:
+        """Switch to a coordinate system present in the spatialdata object(s)."""
         widget_item = get_itemindex_by_text(self._sdata_widget.coordinate_system_widget, coordinate_system)
         if widget_item:
             self._sdata_widget.coordinate_system_widget.setCurrentItem(widget_item)
@@ -80,7 +94,9 @@ class Interactive:
             self.run()
 
     def run(self) -> None:
+        """Run the napari application."""
         napari.run()
 
     def screenshot(self) -> NDArrayA | Any:
+        """Take a screenshot of the viewer in its current state."""
         return self._viewer.screenshot(canvas_only=False)

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/_model.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass, field
-from typing import TYPE_CHECKING, Any, Optional, Tuple, Union
+from typing import Any, Optional, Sequence, Tuple, Union
 
 import numpy as np
 import pandas as pd
@@ -8,65 +8,63 @@ from napari.layers import Layer
 from napari.utils.events import EmitterGroup, Event
 
 from napari_spatialdata._constants._constants import Symbol
-from napari_spatialdata._constants._pkg_constants import Key
 from napari_spatialdata.utils._utils import NDArrayA, _ensure_dense_vector
 
-__all__ = ["ImageModel"]
+__all__ = ["DataModel"]
 
 
 @dataclass
-class ImageModel:
+class DataModel:
     """Model which holds the data for interactive visualization."""
 
     events: EmitterGroup = field(init=False, default=None, repr=True)
+    _table_names: Sequence[Optional[str]] = field(default_factory=list, init=False)
+    _active_table_name: Optional[str] = field(default=None, init=False, repr=True)
     _layer: Layer = field(init=False, default=None, repr=True)
     _adata: Optional[AnnData] = field(init=False, default=None, repr=True)
-    _spatial_key: str = field(default=Key.obsm.spatial, repr=False)
     _adata_layer: Optional[str] = field(init=False, default=None, repr=False)
-    _label_key: Optional[str] = field(default=None, repr=True)
-    _coordinates: Optional[NDArrayA] = field(init=False, default=None, repr=True)
-    _points_coordinates: Optional[NDArrayA] = field(init=False, default=None, repr=True)
-    _points_var: Optional[pd.Series] = field(init=False, default=None, repr=True)
-    _scale: Optional[float] = field(init=False, default=None)
+    _region_key: Optional[str] = field(default=None, repr=True)
+    _instance_key: Optional[str] = field(default=None, repr=True)
+    _color_by: str = field(default="", repr=True, init=False)
     _system_name: Optional[str] = field(default=None, repr=True)
 
-    _spot_diameter: Union[NDArrayA, float] = field(init=False, default=1)
-    _point_diameter: Union[NDArrayA, float] = field(init=False, default=1)
     _scale_key: Optional[str] = field(init=False, default="tissue_hires_scalef")  # TODO(giovp): use constants for these
 
     _palette: Optional[str] = field(init=False, default=None, repr=False)
     _cmap: str = field(init=False, default="viridis", repr=False)
     _symbol: str = field(init=False, default=Symbol.DISC, repr=False)
 
-    VALID_ATTRIBUTES = ("obs", "var", "obsm", "points")
+    VALID_ATTRIBUTES = ("obs", "var", "obsm", "columns_df")
 
     def __post_init__(self) -> None:
         self.events = EmitterGroup(
             source=self,
             layer=Event,
             adata=Event,
+            color_by=Event,
         )
 
-    def get_items(self, attr: str) -> Tuple[str, ...]:
+    def get_items(self, attr: str) -> Optional[Tuple[str, ...]]:
         """
         Return valid keys for an attribute.
 
         Parameters
         ----------
         attr
-            Attribute of :mod:`anndata.AnnData` to access.
+            Attribute of :mod:`anndata.AnnData` to access or if columns_df indicates
+            the column is part of the SpatialElement dataframe and this will be retrieved.
 
         Returns
         -------
-        The available items.
+        The available items coerced to a tuple of strings.
         """
         if attr in ("obs", "obsm"):
             return tuple(map(str, getattr(self.adata, attr).keys()))
-        if attr == "points":
-            if self.points_var is not None:
-                return tuple(map(str, self.points_var.unique()))
-            return tuple(["No points found."])  # noqa: C409
-        return tuple(map(str, getattr(self.adata, attr).index))
+        if attr == "columns_df" and self.layer is not None and (df_cols := self.layer.metadata.get("_columns_df")):
+            return tuple(map(str, df_cols.columns))
+        if attr == "var":
+            return tuple(map(str, getattr(self.adata, attr).index))
+        return None
 
     @_ensure_dense_vector
     def get_obs(
@@ -86,12 +84,35 @@ class ImageModel:
         """
         if name not in self.adata.obs.columns:
             raise KeyError(f"Key `{name}` not found in `adata.obs`.")
-        return self.adata.obs[name], self._format_key(name)
+        if name != self.instance_key:
+            adata_obs = self.adata.obs[[self.instance_key, name]]
+            adata_obs.set_index(self.instance_key, inplace=True)
+        else:
+            adata_obs = self.adata.obs
+        return adata_obs[name], self._format_key(name)
+
+    @_ensure_dense_vector
+    def get_columns_df(self, name: Union[str, int], **_: Any) -> Tuple[Optional[NDArrayA], str]:
+        """
+        Return a column of the dataframe of the SpatialElement.
+
+        Parameters
+        ----------
+        name
+            Name of the column in the dataframe to retrieve.
+
+        Returns
+        -------
+        The dataframe column of interest and the formatted name of the column.
+        """
+        if self.layer is None:
+            raise ValueError("Layer must be present")
+        return self.layer.metadata["_columns_df"][name], self._format_key(name)
 
     @_ensure_dense_vector
     def get_var(self, name: Union[str, int], **_: Any) -> Tuple[Optional[NDArrayA], str]:  # TODO(giovp): fix docstring
         """
-        Return a gene.
+        Return a column in anndata.var_names.
 
         Parameters
         ----------
@@ -151,25 +172,6 @@ class ImageModel:
 
         return (res if res.ndim == 1 else res[:, index]), pretty_name
 
-    def get_points(self, name: str, **_: Any) -> Tuple[Optional[NDArrayA], str]:  # TODO(giovp): fix docstring
-        """
-        Return a gene in spatial coordinates.
-
-        Parameters
-        ----------
-        name
-            Gene name.
-
-        Returns
-        -------
-        The values and the formatted ``name``.
-        """
-        if name not in self.points_var.unique():
-            raise KeyError(f"Key `{name}` not found in `adata.uns['points']['gene']`.")
-        coords = self.points_coordinates
-        coords = coords[self.points_var == name]
-        return np.insert(coords[:, ::-1][:, :2] * self.scale, 0, values=0, axis=1), self._format_key(name)
-
     def _format_key(
         self, key: Union[str, int], index: Optional[Union[int, str]] = None, adata_layer: bool = False
     ) -> str:
@@ -180,8 +182,28 @@ class ImageModel:
 
         return str(key) + (f":{self.layer}" if self.layer is not None else ":X")
 
+    @property
+    def color_by(self) -> str:
+        """The name by which the layer is currently colored."""
+        return self._color_by
+
+    @color_by.setter
+    def color_by(self, color_column: str) -> None:
+        self._color_by = color_column
+        self.events.color_by()
+
+    @property
+    def table_names(self) -> Sequence[Optional[str]]:
+        """The table names annotating the current active napari layer, if any."""
+        return self._table_names
+
+    @table_names.setter
+    def table_names(self, table_names: Sequence[Optional[str]]) -> None:
+        self._table_names = table_names
+
     @property
     def layer(self) -> Optional[Layer]:  # noqa: D102
+        """The current active napari layer."""
         return self._layer
 
     @layer.setter
@@ -189,8 +211,18 @@ class ImageModel:
         self._layer = layer
         self.events.layer()
 
+    @property
+    def active_table_name(self) -> Optional[str]:
+        """The table name currently active in the widget."""
+        return self._active_table_name
+
+    @active_table_name.setter
+    def active_table_name(self, active_table_name: Optional[str]) -> None:
+        self._active_table_name = active_table_name
+
     @property
     def adata(self) -> AnnData:  # noqa: D102
+        """The anndata object corresponding to the current active table name."""
         return self._adata
 
     @adata.setter
@@ -198,16 +230,9 @@ class ImageModel:
         self._adata = adata
         self.events.adata()
 
-    @property
-    def spatial_key(self) -> str:  # noqa: D102
-        return self._spatial_key
-
-    @spatial_key.setter
-    def spatial_key(self, key: str) -> None:
-        self._spatial_key = key
-
     @property
     def adata_layer(self) -> Optional[str]:  # noqa: D102
+        """The current anndata layer."""
         return self._adata_layer
 
     @adata_layer.setter
@@ -215,65 +240,26 @@ class ImageModel:
         self._adata_layer = adata_layer
 
     @property
-    def coordinates(self) -> NDArrayA:  # noqa: D102
-        return self._coordinates  # type: ignore[return-value]
-
-    @coordinates.setter
-    def coordinates(self, coordinates: NDArrayA) -> None:
-        self._coordinates = coordinates
-
-    @property
-    def points_coordinates(self) -> NDArrayA:  # noqa: D102
-        if TYPE_CHECKING:
-            assert self._points_coordinates is not None
-        return self._points_coordinates
-
-    @points_coordinates.setter
-    def points_coordinates(self, points_coordinates: NDArrayA) -> None:
-        self._points_coordinates = points_coordinates
-
-    @property
-    def points_var(self) -> pd.Series:  # noqa: D102
-        return self._points_var
-
-    @points_var.setter
-    def points_var(self, points_var: pd.Series) -> None:
-        self._points_var = points_var
-
-    @property
-    def scale(self) -> Optional[float]:  # noqa: D102
-        return self._scale
-
-    @scale.setter
-    def scale(self, scale: float) -> None:
-        self._scale = scale
-
-    @property
-    def spot_diameter(self) -> Union[NDArrayA, float]:  # noqa: D102
-        return self._spot_diameter
-
-    @spot_diameter.setter
-    def spot_diameter(self, spot_diameter: Union[NDArrayA, float]) -> None:
-        self._spot_diameter = spot_diameter
-
-    @property
-    def point_diameter(self) -> Union[NDArrayA, float]:  # noqa: D102
-        return self._point_diameter
+    def region_key(self) -> Optional[str]:  # noqa: D102
+        """The region key of the currently active table in the widget."""
+        return self._region_key
 
-    @point_diameter.setter
-    def point_diameter(self, point_diameter: Union[NDArrayA, float]) -> None:
-        self._point_diameter = point_diameter
+    @region_key.setter
+    def region_key(self, region_key: str) -> None:
+        self._region_key = region_key
 
     @property
-    def labels_key(self) -> Optional[str]:  # noqa: D102
-        return self._labels_key
+    def instance_key(self) -> Optional[str]:  # noqa: D102
+        """The instance key of the currently active table in the widget."""
+        return self._instance_key
 
-    @labels_key.setter
-    def labels_key(self, region_key: str) -> None:
-        self._labels_key = region_key
+    @instance_key.setter
+    def instance_key(self, instance_key: str) -> None:
+        self._instance_key = instance_key
 
     @property
     def palette(self) -> Optional[str]:  # noqa: D102
+        """The palette from which to draw the colors."""
         return self._palette
 
     @palette.setter
@@ -282,6 +268,7 @@ class ImageModel:
 
     @property
     def cmap(self) -> str:  # noqa: D102
+        """The continuous color map to draw colors from."""
         return self._cmap
 
     @cmap.setter
@@ -306,6 +293,7 @@ class ImageModel:
 
     @property
     def system_name(self) -> Optional[str]:  # noqa: D102
+        """The layer name."""
         return self._system_name
 
     @system_name.setter

{napari-spatialdata-0.3.0 → napari-spatialdata-0.4.0}/src/napari_spatialdata/_reader.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from typing import Callable
 
 from loguru import logger
-from napari_plugin_engine import napari_hook_implementation
 from spatialdata import SpatialData
 
 from napari_spatialdata import Interactive
@@ -11,7 +10,6 @@ from napari_spatialdata import Interactive
 readable_extensions = (".zarr",)
 
 
-@napari_hook_implementation
 def get_reader(path: str) -> Callable[..., list[tuple[None]]] | None:
     """Napari hook specification that start the napari-spatialdata plugin with the given path."""
     # if we know we cannot read the file, we immediately return None.