napari-spatialdata 0.4.0__tar.gz → 0.4.1__tar.gz

napari-spatialdata-0.4.1/.github/workflows/release.yml

@@ -0,0 +1,30 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release:
+    # requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python -m build .
+          twine upload dist/*

napari-spatialdata-0.4.0/.github/workflows/test_and_deploy.yml → napari-spatialdata-0.4.1/.github/workflows/test.yml

@@ -62,29 +62,3 @@ jobs:
 
       - name: Coverage
         uses: codecov/codecov-action@v3
-
-  deploy:
-    # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your
-    # github secrets (see readme for details)
-    needs: [test]
-    runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine build
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
-        run: |
-          git tag
-          python -m build .
-          twine upload dist/*

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.3.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.4.0
+Version: 0.4.1
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla

napari-spatialdata-0.4.1/src/napari_spatialdata/_constants/config.py

@@ -0,0 +1,4 @@
+POLYGON_THRESHOLD = 100
+POINT_THRESHOLD = 100000
+N_CIRCLES_WARNING_THRESHOLD = 250000
+N_SHAPES_WARNING_THRESHOLD = 10000

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata/_sdata_widgets.py

@@ -1,12 +1,15 @@
 from __future__ import annotations
 
+from pathlib import Path
 from typing import TYPE_CHECKING, Iterable
 
 import shapely
 from napari.utils.events import EventedList
+from qtpy.QtGui import QIcon
 from qtpy.QtWidgets import QLabel, QListWidget, QListWidgetItem, QVBoxLayout, QWidget
 from spatialdata import SpatialData
 
+from napari_spatialdata._constants.config import N_CIRCLES_WARNING_THRESHOLD, N_SHAPES_WARNING_THRESHOLD
 from napari_spatialdata._viewer import SpatialDataViewer
 from napari_spatialdata.utils._utils import _get_sdata_key, get_duplicate_element_names, get_elements_meta_mapping
 
@@ -14,10 +17,13 @@ if TYPE_CHECKING:
     from napari import Viewer
     from napari.utils.events.event import Event
 
+icon_path = Path(__file__).parent / "resources/exclamation.png"
+
 
 class ElementWidget(QListWidget):
     def __init__(self, sdata: EventedList):
         super().__init__()
+        self._icon = QIcon(str(icon_path))
         self._sdata = sdata
         self._duplicate_element_names, _ = get_duplicate_element_names(self._sdata)
         self._elements: None | dict[str, dict[str, str | int]] = None
@@ -25,9 +31,38 @@ class ElementWidget(QListWidget):
     def _onItemChange(self, selected_coordinate_system: QListWidgetItem | int | Iterable[str]) -> None:
         self.clear()
         elements, _ = get_elements_meta_mapping(self._sdata, selected_coordinate_system, self._duplicate_element_names)
-        self.addItems(elements.keys())
+        self._set_element_widget_items(elements)
         self._elements = elements
 
+    def _set_element_widget_items(self, elements: dict[str, dict[str, str | int]]) -> None:
+        for key, dict_val in elements.items():
+            sdata = self._sdata[dict_val["sdata_index"]]
+            element_type = dict_val["element_type"]
+            element_name = dict_val["original_name"]
+            item = QListWidgetItem(key)
+            if element_type == "shapes":
+                if (
+                    type((element := sdata.shapes[element_name]).iloc[0].geometry) == shapely.Point
+                    and len(element) > N_CIRCLES_WARNING_THRESHOLD
+                ):
+                    item.setIcon(self._icon)
+                    item.setToolTip(
+                        "Visualizing this many circles is currently slow in napari. Consider whether you want to "
+                        "visualize."
+                    )
+                    self.addItem(item)
+                elif (
+                    type((element := sdata.shapes[element_name]).iloc[0].geometry)
+                    in [shapely.Polygon, shapely.MultiPolygon]
+                    and len(element) > N_SHAPES_WARNING_THRESHOLD
+                ):
+                    item.setIcon(self._icon)
+                    item.setToolTip(
+                        "Visualizing this many shapes is currently slow in napari. Consider whether you want to "
+                        "visualize."
+                    )
+            self.addItem(item)
+
 
 class CoordinateSystemWidget(QListWidget):
     def __init__(self, sdata: EventedList):

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.4.0'
-__version_tuple__ = version_tuple = (0, 4, 0)
+__version__ = version = '0.4.1'
+__version_tuple__ = version_tuple = (0, 4, 1)

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata/_view.py

@@ -2,8 +2,6 @@ from typing import Any, FrozenSet, Optional, Sequence
 
 import napari
 from anndata import AnnData
-from dask.dataframe.core import DataFrame as DaskDataFrame
-from geopandas.geodataframe import GeoDataFrame
 from loguru import logger
 from napari._qt.qt_resources import get_stylesheet
 from napari._qt.utils import QImg2array
@@ -18,7 +16,7 @@ from qtpy.QtWidgets import (
     QVBoxLayout,
     QWidget,
 )
-from spatialdata import join_sdata_spatialelement_table
+from spatialdata import join_spatialelement_table
 
 from napari_spatialdata._model import DataModel
 from napari_spatialdata._scatterwidgets import AxisWidgets, MatplotlibWidget
@@ -119,7 +117,9 @@ class QtAdataScatterWidget(QWidget):
 
         if sdata := layer.metadata.get("sdata"):
             element_name = layer.metadata.get("name")
-            _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left")
+            _, table = join_spatialelement_table(
+                sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left"
+            )
             layer.metadata["adata"] = table
 
         if layer is not None and "adata" in layer.metadata:
@@ -315,11 +315,7 @@ class QtAdataViewWidget(QWidget):
                 self.var_widget.clear()
                 self.obsm_widget.clear()
                 self.color_by.clear()
-                if (
-                    isinstance(layer, (Points, Shapes))
-                    and isinstance(layer.metadata["sdata"][layer.metadata["name"]], (DaskDataFrame, GeoDataFrame))
-                    and (cols_df := layer.metadata["_columns_df"]) is not None
-                ):
+                if isinstance(layer, (Points, Shapes)) and (cols_df := layer.metadata.get("_columns_df")) is not None:
                     self.dataframe_columns_widget.addItems(map(str, cols_df.columns))
                     self.model.system_name = layer.metadata.get("name", None)
             return
@@ -351,7 +347,9 @@ class QtAdataViewWidget(QWidget):
         if sdata := layer.metadata.get("sdata"):
             element_name = layer.metadata.get("name")
             how = "left" if isinstance(layer, Labels) else "inner"
-            _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, how)
+            _, table = join_spatialelement_table(
+                sdata=sdata, spatial_element_names=element_name, table_name=table_name, how=how
+            )
             layer.metadata["adata"] = table
 
         if layer is not None and "adata" in layer.metadata:

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata/_viewer.py

@@ -18,7 +18,7 @@ from spatialdata._core.query.relational_query import (
     _get_unique_label_values_as_index,
     _left_join_spatialelement_table,
 )
-from spatialdata.models import PointsModel, ShapesModel
+from spatialdata.models import PointsModel, ShapesModel, force_2d
 from spatialdata.transformations import Affine, Identity
 from spatialdata.transformations._utils import scale_radii
 
@@ -35,7 +35,6 @@ from napari_spatialdata.utils._viewer_utils import _get_polygons_properties
 
 if TYPE_CHECKING:
     import numpy.typing as npt
-    from dask.dataframe.core import DataFrame as DaskDataFrame
     from napari.layers import Layer
     from napari.utils.events import Event, EventedList
     from spatialdata import SpatialData
@@ -49,8 +48,8 @@ class SpatialDataViewer(QObject):
         self.viewer = viewer
         self.sdata = sdata
         self._layer_event_caches: dict[str, list[dict[str, Any]]] = {}
-        self.viewer.bind_key("Shift-L", self._inherit_metadata, overwrite=False)
-        self.viewer.bind_key("Shift-E", self._save_to_sdata, overwrite=False)
+        self.viewer.bind_key("Shift-L", self._inherit_metadata, overwrite=True)
+        self.viewer.bind_key("Shift-E", self._save_to_sdata, overwrite=True)
         self.viewer.layers.events.inserted.connect(self._on_layer_insert)
         self._active_layer_table_names = None
         self.viewer.layers.events.removed.connect(self._on_layer_removed)
@@ -182,8 +181,11 @@ class SpatialDataViewer(QObject):
                     raise ValueError("Cannot export a points element with no points")
                 transformed_data = np.array([selected.data_to_world(xy) for xy in selected.data])
                 swap_data = np.fliplr(transformed_data)
-                model = PointsModel.parse(swap_data, transformations=transformation)
-                sdata.points[selected.name] = model
+                # ignore z axis if present
+                if swap_data.shape[1] == 3:
+                    swap_data = swap_data[:, :2]
+                parsed = PointsModel.parse(swap_data, transformations=transformation)
+                sdata.points[selected.name] = parsed
             if type(selected) == Shapes:
                 if len(selected.data) == 0:
                     raise ValueError("Cannot export a shapes element with no shapes")
@@ -191,15 +193,16 @@ class SpatialDataViewer(QObject):
                     Polygon(i) for i in _transform_coordinates(selected.data, f=lambda x: x[::-1])
                 ]
                 gdf = GeoDataFrame({"geometry": polygons})
-                model = ShapesModel.parse(gdf, transformations=transformation)
-                sdata.shapes[selected.name] = model
+                force_2d(gdf)
+                parsed = ShapesModel.parse(gdf, transformations=transformation)
+                sdata.shapes[selected.name] = parsed
                 swap_data = None
             if type(selected) == Image or type(selected) == Labels:
                 raise NotImplementedError
 
             self.layer_names.add(selected.name)
             self._layer_event_caches[selected.name] = []
-            self._update_metadata(selected, model, swap_data)
+            self._update_metadata(selected, parsed, swap_data)
             selected.events.data.connect(self._update_cache_indices)
             selected.events.name.connect(self._validate_name)
             self.layer_saved.emit(coordinate_system)

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata/utils/_utils.py

@@ -27,7 +27,7 @@ from pandas.core.dtypes.common import (
 from scipy.sparse import issparse, spmatrix
 from scipy.spatial import KDTree
 from spatial_image import SpatialImage
-from spatialdata import SpatialData, get_extent, join_sdata_spatialelement_table
+from spatialdata import SpatialData, get_extent, join_spatialelement_table
 from spatialdata.models import SpatialElement, get_axes_names
 from spatialdata.transformations import get_transformation
 
@@ -383,7 +383,9 @@ def _get_init_metadata_adata(sdata: SpatialData, table_name: str, element_name:
     """
     if not table_name:
         return None
-    _, adata = join_sdata_spatialelement_table(sdata, element_name, table_name, how="left", match_rows="left")
+    _, adata = join_spatialelement_table(
+        sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
+    )
 
     if adata.shape[0] == 0:
         return None

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.4.0
+Version: 0.4.1
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla

{napari-spatialdata-0.4.0 → napari-spatialdata-0.4.1}/src/napari_spatialdata.egg-info/SOURCES.txt

@@ -9,7 +9,8 @@ README.md
 pyproject.toml
 setup.cfg
 tox.ini
-.github/workflows/test_and_deploy.yml
+.github/workflows/release.yml
+.github/workflows/test.yml
 .napari/DESCRIPTION.md
 docs/Makefile
 docs/api.md
@@ -54,6 +55,7 @@ src/napari_spatialdata/_constants/_constants.py
 src/napari_spatialdata/_constants/_pkg_constants.py
 src/napari_spatialdata/_constants/_utils.py
 src/napari_spatialdata/_constants/config.py
+src/napari_spatialdata/resources/exclamation.png
 src/napari_spatialdata/utils/__init__.py
 src/napari_spatialdata/utils/_categoricals_utils.py
 src/napari_spatialdata/utils/_test_utils.py

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

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