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

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Oct 2, 2024
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[pre-commit.ci] pre-commit autoupdate #300

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70e49b0
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Sep 30, 2024
633adf6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 30, 2024
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -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]
Expand Down Expand Up @@ -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]
1 change: 1 addition & 0 deletions benchmarks/benchmark_qt_widget.py
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Expand Up @@ -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


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21 changes: 10 additions & 11 deletions docs/notebooks/mibitof_analysis.ipynb
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Expand Up @@ -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)"
]
},
{
Expand Down Expand Up @@ -205,7 +204,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -254,7 +253,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -295,7 +294,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -347,7 +346,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -398,7 +397,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -439,7 +438,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -480,7 +479,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
}
],
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22 changes: 11 additions & 11 deletions docs/notebooks/nanostring_analysis.ipynb
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Expand Up @@ -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)"
]
},
{
Expand Down Expand Up @@ -278,7 +278,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -327,7 +327,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -390,7 +390,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -431,7 +431,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -483,7 +483,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -572,7 +572,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -613,7 +613,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
}
],
Expand Down
39 changes: 20 additions & 19 deletions docs/notebooks/scatterwidget.ipynb
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Expand Up @@ -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": {},
Expand All @@ -60,10 +61,10 @@
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"adata = sq.datasets.visium_hne_adata()"
],
"outputs": []
]
},
{
"attachments": {},
Expand All @@ -77,10 +78,10 @@
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"%gui qt5"
],
"outputs": []
]
},
{
"attachments": {},
Expand All @@ -94,11 +95,11 @@
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"widget = QtAdataScatterWidget(adata)\n",
"widget.show()"
],
"outputs": []
]
},
{
"attachments": {},
Expand All @@ -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": {},
Expand All @@ -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": {
Expand Down
23 changes: 12 additions & 11 deletions docs/notebooks/spatialdata.ipynb
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Expand Up @@ -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)"
Expand Down Expand Up @@ -156,7 +157,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -246,7 +247,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -299,7 +300,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -358,7 +359,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -401,7 +402,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -459,7 +460,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -502,7 +503,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -543,7 +544,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
},
{
Expand Down Expand Up @@ -584,7 +585,7 @@
],
"source": [
"plt.imshow(interactive.screenshot())\n",
"plt.axis('off')"
"plt.axis(\"off\")"
]
}
],
Expand Down
3 changes: 2 additions & 1 deletion examples/spatialdata_visium.py
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Expand Up @@ -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)
Expand Down
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