[pre-commit.ci] pre-commit autoupdate (#300)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](pre-commit/mirrors-mypy@v1.11.1...v1.11.2) - [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.8](astral-sh/ruff-pre-commit@v0.5.7...v0.6.8) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
scverse · Oct 2, 2024 · 9b8bb4a · 9b8bb4a
1 parent f84b79b
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Showing 16 changed files with 82 additions and 71 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/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
 
 

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": {

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

diff --git a/examples/spatialdata_visium.py b/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)