Merge branch 'main' into small_fix/circles_as_points

Author: LucaMarconato

.github/workflows/benchmarks.yml

@@ -80,8 +80,8 @@ jobs:
         id: latest_release
         with:
           route: GET /repos/{owner}/{repo}/releases/latest
-          owner: napari
-          repo: napari
+          owner: scverse
+          repo: napari-spatialdata
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/test.yml

@@ -21,9 +21,10 @@ jobs:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
     strategy:
+      fail-fast: false
       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
@@ -61,7 +62,7 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
 
       - name: Archive figures generated during testing
         if: always()
@@ -86,6 +87,11 @@ 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

.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

.pre-commit-config.yaml

@@ -2,18 +2,18 @@ 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: v1.13.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-merge-conflict
@@ -45,11 +45,11 @@ repos:
       - id: check-toml
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.8.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -8,7 +8,50 @@ 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.x.x] - 2024-xx-xx
+## [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
+
+- Bug table was not reset after an element without table was added #317
+- Bug when changing channel for a multichannel image #301 #302
+- Bug when plotting catgorical annotations on points #304
+
+## [0.5.3] - 2024-08-
+
+### Added
+
+- New Scatter Widget based on PyQtGraph, replacing the previous Matplotlib-based widget.
+  - New Features:
+    - Separate color controls for continuous and discrete data:
+      - Continuous: Histogram of values, LUT adjustment, contrast control.
+      - Discrete: Scrollable legend, class color modification.
+    - Pseudohistogram plot for single-axis data.
+    - Highlight nearby data points under the cursor with dynamic status display.
+    - Expanded ROI annotations (lasso and rectangle tools)
+    - Multiple disjointed ROIs with modifiable options.
+    - Annotation name dialog for saving annotations.
+
+### Updated
+
+Documentation: Notebooks updated with the new Scatter Widget information and screenshots.
 
 ## [0.5.2] - 2024-08-16
 

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
 

benchmarks/benchmark_qt_widget.py

@@ -2,6 +2,7 @@
 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 @@ def time_create_widget(self) -> None:
 
     def time_layer_added(self) -> None:
         self.viewer.add_layer(self.image)
+
+    def teardown(self) -> None:
+        self.viewer.close()

docs/index.md

@@ -9,6 +9,7 @@
 api.md
 cli.md
 contributing.md
+limitations.md
 references.md
 ```
 
@@ -22,4 +23,5 @@ cli.md
 notebooks/nanostring_analysis
 notebooks/mibitof_analysis
 notebooks/scatterwidget
+notebooks/scatterwidget_annotation
 ```

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.