From a0017353f177d3f1fe5a4d3ba95f0e724ed8908d Mon Sep 17 00:00:00 2001 From: ArneDefauw Date: Fri, 29 Nov 2024 08:41:02 +0100 Subject: [PATCH 1/3] xarray bump --- sopa/_sdata.py | 3 +-- sopa/io/explorer/images.py | 3 +-- sopa/io/reader/wsi.py | 3 +-- sopa/patches/infer.py | 3 +-- sopa/patches/patches.py | 3 +-- sopa/segmentation/tissue.py | 3 +-- sopa/utils/image.py | 3 +-- 7 files changed, 7 insertions(+), 14 deletions(-) diff --git a/sopa/_sdata.py b/sopa/_sdata.py index 8ec923d..1f9dc3c 100644 --- a/sopa/_sdata.py +++ b/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 diff --git a/sopa/io/explorer/images.py b/sopa/io/explorer/images.py index 7de0676..ff41623 100644 --- a/sopa/io/explorer/images.py +++ b/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 diff --git a/sopa/io/reader/wsi.py b/sopa/io/reader/wsi.py index e3723d0..d309695 100644 --- a/sopa/io/reader/wsi.py +++ b/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( diff --git a/sopa/patches/infer.py b/sopa/patches/infer.py index e2e46b8..be0bc41 100644 --- a/sopa/patches/infer.py +++ b/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 diff --git a/sopa/patches/patches.py b/sopa/patches/patches.py index 3e28501..2fcc914 100644 --- a/sopa/patches/patches.py +++ b/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 ( diff --git a/sopa/segmentation/tissue.py b/sopa/segmentation/tissue.py index 6043c97..8cd2fd8 100644 --- a/sopa/segmentation/tissue.py +++ b/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 diff --git a/sopa/utils/image.py b/sopa/utils/image.py index da98593..a0d487b 100644 --- a/sopa/utils/image.py +++ b/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: From cccded231c247408d36c90007820efc05d4c1748 Mon Sep 17 00:00:00 2001 From: Blampey Quentin Date: Fri, 29 Nov 2024 15:12:17 +0100 Subject: [PATCH 2/3] update spatialdata/io version + lock file --- .github/workflows/ci.yml | 2 +- poetry.lock | 4953 ++++++++++++++++++++------------------ pyproject.toml | 6 +- 3 files changed, 2611 insertions(+), 2350 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 462607a..e2d85be 100644 --- a/.github/workflows/ci.yml +++ b/.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", "3.12"] steps: #---------------------------------------------- # check-out repo and set-up python diff --git a/poetry.lock b/poetry.lock 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