xarray bump

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11.8"]
+        python-version: ["3.10", "3.11.8"]
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python

pyproject.toml

@@ -22,9 +22,9 @@ classifiers = [
 sopa = "sopa.main:app"
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
-spatialdata = ">=0.2.0"
-spatialdata-io = ">=0.1.3"
+python = ">=3.10,<3.13"
+spatialdata = ">=0.2.6"
+spatialdata-io = ">=0.1.6"
 scanpy = ">=1.9.8"
 botocore = "1.34.19"
 typer = ">=0.9.0"

sopa/_sdata.py

@@ -7,11 +7,10 @@
 import geopandas as gpd
 import pandas as pd
 from anndata import AnnData
-from datatree import DataTree
 from spatialdata import SpatialData
 from spatialdata.models import SpatialElement
 from spatialdata.transformations import Identity, get_transformation, set_transformation
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from ._constants import SopaAttrs, SopaFiles, SopaKeys
 

sopa/io/explorer/images.py

@@ -6,12 +6,11 @@
 
 import numpy as np
 import tifffile as tf
-from datatree import DataTree
 from multiscale_spatial_image import to_multiscale
 from spatialdata import SpatialData
 from spatialdata.transformations import Affine, set_transformation
 from tqdm import tqdm
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from ..._sdata import get_intrinsic_cs, get_spatial_image
 from ...utils.image import resize_numpy, scale_dtype

sopa/io/reader/wsi.py

@@ -4,11 +4,10 @@
 from typing import Any
 
 import xarray
-from datatree import DataTree
 from spatialdata import SpatialData
 from spatialdata.models import Image2DModel
 from spatialdata.transformations import Identity, Scale
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 
 def wsi(

sopa/patches/infer.py

@@ -12,11 +12,10 @@
 
 import numpy as np
 import tqdm
-from datatree import DataTree
 from spatialdata import SpatialData
 from spatialdata.models import Image2DModel
 from spatialdata.transformations import Scale
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from .._constants import SopaKeys
 from .._sdata import get_intrinsic_cs, get_spatial_image

sopa/patches/patches.py

@@ -10,12 +10,11 @@
 import numpy as np
 import pandas as pd
 from dask.diagnostics import ProgressBar
-from datatree import DataTree
 from shapely.geometry import GeometryCollection, MultiPolygon, Polygon, box
 from spatialdata import SpatialData
 from spatialdata.models import ShapesModel
 from spatialdata.transformations import get_transformation
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from .._constants import EPS, ROI, SopaFiles, SopaKeys
 from .._sdata import (

sopa/segmentation/tissue.py

@@ -6,11 +6,10 @@
 import geopandas as gpd
 import numpy as np
 import spatialdata
-from datatree import DataTree
 from shapely.geometry import Polygon
 from spatialdata import SpatialData
 from spatialdata.models import ShapesModel
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 from .._constants import ROI, SopaAttrs
 from .._sdata import get_intrinsic_cs, get_spatial_element

sopa/utils/image.py

@@ -3,9 +3,8 @@
 import dask.array as da
 import dask_image.ndinterp
 import numpy as np
-from datatree import DataTree
 from spatialdata import SpatialData
-from xarray import DataArray
+from xarray import DataArray, DataTree
 
 
 def resize(xarr: DataArray, scale_factor: float) -> da.Array: