Merge branch 'scverse:main' into main

scverse · Oct 14, 2024 · dcc6b68 · dcc6b68
2 parents 85e5c61 + a38e286
commit dcc6b68
Show file tree

Hide file tree

Showing 28 changed files with 316 additions and 193 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 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]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,26 @@ 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
+## [0.5.5] - 2024-10-07
+
+### Added
+
+- New function to grab layer by name #315 @minhtien-trinh
+- New annotation function to add text to polygons #315 @minhtien-trinh
+
+## [0.5.4] - 2024-xx-xx
+
+### Fixed
+
+- Bug wrong radii transformed circles (e.g. with Visium lowres)
+
+## [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
 
 ## [0.5.2] - 2024-08-16
 

diff --git a/README.md b/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
 

diff --git a/benchmarks/benchmark_qt_widget.py b/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()
diff --git a/docs/index.md b/docs/index.md
@@ -9,6 +9,7 @@
 api.md
 cli.md
 contributing.md
+limitations.md
 references.md
 ```
 

diff --git a/docs/limitations.md b/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.
diff --git a/docs/notebooks/mibitof_analysis.ipynb b/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\")"
    ]
   }
  ],

diff --git a/docs/notebooks/nanostring_analysis.ipynb b/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\")"
    ]
   }
  ],

diff --git a/docs/notebooks/scatterwidget.ipynb b/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": {