napari-spatialdata 0.5.3__tar.gz → 0.5.4__tar.gz

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/.github/workflows/test.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest] # [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.10", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -86,6 +86,11 @@ jobs:
           python-version: 3.11
           cache-dependency-path: pyproject.toml
 
+      - name: Install dependencies with 'pre' extras (since the above doesn't check pre-releases)
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[pre]
+
       - uses: tlambert03/setup-qt-libs@v1
 
       - uses: octokit/request-action@v2.x

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/.mypy.ini

@@ -1,6 +1,6 @@
 [mypy]
 mypy_path = napari-spatialdata
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/.pre-commit-config.yaml

@@ -2,12 +2,12 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.8
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/CHANGELOG.md

@@ -8,6 +8,24 @@ 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
 
+## [0.5.4] - 2024-11-26
+
+### Changed
+
+- Support for `xarray.DataTree` (which moved from `datatree.DataTree`)
+
+### Added
+
+- CLI interface from spatialdata branch
+- New function to get layer by name #315 @minhtien-trinh
+- New annotation function to display text near polygons #315 @minhtien-trinh
+
+### Fixed
+
+- Bug wrong radii transformed circles (e.g. with Visium lowres) #318
+- Bugs: instance id shifted by 1; obsm visualization; background color for labels #320
+- Bug adjusting contrast limit for RGB data #276
+
 ## [0.5.3] - 2024-09-25
 
 ### Fixed

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: napari-spatialdata
-Version: 0.5.3
+Version: 0.5.4
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -16,11 +16,12 @@ Classifier: Framework :: napari
 Classifier: Topic :: Software Development :: Testing
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.9.2
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: anndata
@@ -88,7 +89,7 @@ Requires-Dist: napari[pyqt5]; extra == "all"
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
 
-This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [documentation](https://spatialdata.scverse.org/).
+This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
 
 ## Installation
 

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/README.md

@@ -11,7 +11,7 @@
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spatialdata)](https://napari-hub.org/plugins/napari-spatialdata)
 [![DOI](https://zenodo.org/badge/477021400.svg)](https://zenodo.org/badge/latestdoi/477021400)
 
-This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [documentation](https://spatialdata.scverse.org/).
+This repository contains a napari plugin for interactively exploring and annotating SpatialData objects. Here you can find the [napari-spatialdata documentation](https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html). `napari-spatialdata` is part of the `SpatialData` ecosystem. To learn more about SpatialData, please see the [spatialdata documentation](https://spatialdata.scverse.org/).
 
 ## Installation
 

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/benchmarks/benchmark_qt_widget.py

@@ -2,6 +2,7 @@ import numpy as np
 from napari import Viewer
 from napari.layers import Image
 from napari.utils.events import EventedList
+
 from napari_spatialdata._sdata_widgets import SdataWidget
 
 
@@ -17,3 +18,6 @@ class SdataWidgetSuite:
 
     def time_layer_added(self) -> None:
         self.viewer.add_layer(self.image)
+
+    def teardown(self) -> None:
+        self.viewer.close()

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/docs/index.md

@@ -9,6 +9,7 @@
 api.md
 cli.md
 contributing.md
+limitations.md
 references.md
 ```
 

napari_spatialdata-0.5.4/docs/limitations.md

@@ -0,0 +1,8 @@
+# Limitations
+
+Contributions are welcomed!
+
+- On macOS, the maximum point size is constrained ([details in the Vispy issue tracker](https://github.com/vispy/vispy/issues/2078));
+  it is important to keep this in mind when zooming in on points to [explore the points property on mouse hover](https://github.com/scverse/napari-spatialdata/issues/35#issuecomment-2383792431).
+- 3D data representation is supported in `spatialdata`; 3D data visualization is supported in `napari`.
+  Still, in `napari-spatialdata` we currently don't support 3D data visualization.

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/docs/notebooks/mibitof_analysis.ipynb

@@ -46,12 +46,11 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
     "from spatialdata import SpatialData\n",
-    "import squidpy as sq\n",
-    "import scanpy as sc\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)"
+    "from napari_spatialdata import Interactive\n",
+    "\n",
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)"
    ]
   },
   {
@@ -205,7 +204,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -254,7 +253,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -295,7 +294,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -347,7 +346,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -398,7 +397,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -439,7 +438,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -480,7 +479,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/docs/notebooks/nanostring_analysis.ipynb

@@ -46,12 +46,12 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
-    "from spatialdata import SpatialData\n",
-    "import squidpy as sq\n",
     "import scanpy as sc\n",
+    "from spatialdata import SpatialData\n",
+    "\n",
+    "from napari_spatialdata import Interactive\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)"
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)"
    ]
   },
   {
@@ -278,7 +278,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -327,7 +327,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -390,7 +390,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -431,7 +431,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -483,7 +483,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -572,7 +572,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -613,7 +613,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/docs/notebooks/scatterwidget.ipynb

@@ -41,12 +41,13 @@
    "cell_type": "code",
    "execution_count": 10,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "from napari_spatialdata import QtAdataScatterWidget\n",
+    "import matplotlib.pyplot as plt\n",
     "import squidpy as sq\n",
-    "import matplotlib.pyplot as plt"
-   ],
-   "outputs": []
+    "\n",
+    "from napari_spatialdata import QtAdataScatterWidget"
+   ]
   },
   {
    "attachments": {},
@@ -60,10 +61,10 @@
    "cell_type": "code",
    "execution_count": 11,
    "metadata": {},
+   "outputs": [],
    "source": [
     "adata = sq.datasets.visium_hne_adata()"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -77,10 +78,10 @@
    "cell_type": "code",
    "execution_count": 13,
    "metadata": {},
+   "outputs": [],
    "source": [
     "%gui qt5"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -94,11 +95,11 @@
    "cell_type": "code",
    "execution_count": 14,
    "metadata": {},
+   "outputs": [],
    "source": [
     "widget = QtAdataScatterWidget(adata)\n",
     "widget.show()"
-   ],
-   "outputs": []
+   ]
   },
   {
    "attachments": {},
@@ -112,11 +113,11 @@
    "cell_type": "code",
    "execution_count": 15,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   },
   {
    "attachments": {},
@@ -130,21 +131,21 @@
    "cell_type": "code",
    "execution_count": 19,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 21,
    "metadata": {},
+   "outputs": [],
    "source": [
     "plt.imshow(widget.screenshot())\n",
-    "plt.axis('off')"
-   ],
-   "outputs": []
+    "plt.axis(\"off\")"
+   ]
   }
  ],
  "metadata": {

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/docs/notebooks/spatialdata.ipynb

@@ -66,10 +66,11 @@
    "source": [
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
-    "from napari_spatialdata import Interactive\n",
     "from spatialdata import SpatialData\n",
     "\n",
-    "plt.rcParams['figure.figsize'] = (20, 20)\n",
+    "from napari_spatialdata import Interactive\n",
+    "\n",
+    "plt.rcParams[\"figure.figsize\"] = (20, 20)\n",
     "\n",
     "FILE_PATH = \"../../../data/cosmx/data.zarr\" # Change this\n",
     "sdata = SpatialData.read(FILE_PATH)"
@@ -156,7 +157,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -246,7 +247,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -299,7 +300,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -358,7 +359,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -401,7 +402,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -459,7 +460,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -502,7 +503,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -543,7 +544,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   },
   {
@@ -584,7 +585,7 @@
    ],
    "source": [
     "plt.imshow(interactive.screenshot())\n",
-    "plt.axis('off')"
+    "plt.axis(\"off\")"
    ]
   }
  ],

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/examples/spatialdata_visium.py

@@ -3,9 +3,10 @@
 
 # The dataset can be downloaded from https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html
 
-from napari_spatialdata import Interactive
 from spatialdata import SpatialData
 
+from napari_spatialdata import Interactive
+
 if __name__ == "__main__":
     sdata = SpatialData.read("../data/visium/data.zarr")  # Change this path!
     i = Interactive(sdata)

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/pyproject.toml

@@ -7,7 +7,7 @@ write_to = "src/napari_spatialdata/_version.py"
 
 [tool.black]
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 (
@@ -38,7 +38,7 @@ exclude = [
     "setup.py",
 ]
 line-length = 120
-target-version = "py39"
+target-version = "py310"
 [tool.ruff.lint]
 ignore = [
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/setup.cfg

@@ -19,15 +19,16 @@ classifiers =
 	Topic :: Software Development :: Testing
 	Programming Language :: Python
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
 	Operating System :: OS Independent
 	License :: OSI Approved :: BSD License
 
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.9.2
+python_requires = >=3.10
 setup_requires = setuptools_scm
 install_requires = 
 	anndata

{napari_spatialdata-0.5.3 → napari_spatialdata-0.5.4}/src/napari_spatialdata/_interactive.py

@@ -3,11 +3,12 @@ from __future__ import annotations
 from typing import TYPE_CHECKING, Any
 
 import napari
+from napari.layers import Image, Labels, Points, Shapes
 from napari.utils.events import EventedList
+from spatialdata._types import ArrayLike
 
 from napari_spatialdata._sdata_widgets import SdataWidget
 from napari_spatialdata.utils._utils import (
-    NDArrayA,
     get_duplicate_element_names,
     get_elements_meta_mapping,
     get_itemindex_by_text,
@@ -97,6 +98,30 @@ class Interactive:
         """Run the napari application."""
         napari.run()
 
-    def screenshot(self) -> NDArrayA | Any:
+    def screenshot(self) -> ArrayLike | Any:
         """Take a screenshot of the viewer in its current state."""
         return self._viewer.screenshot(canvas_only=False)
+
+    def get_layer(self, layer_name: str) -> Image | Labels | Points | Shapes | None:
+        """Get a layer by name."""
+        try:
+            return self._viewer.layers[layer_name]
+        except KeyError:
+            return None
+
+    def add_text_to_polygons(self, layer_name: str, text_annotations: list[str]) -> None:
+        """Add text annotations to a polygon layer."""
+        polygon_layer = self.get_layer(layer_name)
+        if not polygon_layer:
+            raise ValueError(f"Polygon layer '{layer_name}' not found.")
+        if len(text_annotations) != len(polygon_layer.data):
+            raise ValueError(
+                f"The number of text annotations must match the number of polygons. "
+                f"Polygons: {len(polygon_layer.data)}, Text: {len(text_annotations)}."
+            )
+        polygon_layer.text = {
+            "string": text_annotations,
+            "size": 10,
+            "color": "red",
+            "anchor": "center",
+        }