TypeError: SpatialData.__init__() got an unexpected keyword argument 'table' #344
Description
---Hello, I am currently encountering the following issue: a problem with reading Cosmx. It was installed through the following method:
conda create -n spatial-data python=3.11 # python >= 3.11
pip install git+https://github.com/scverse/spatialdata-io.git@main
pip install git+https://github.com/scverse/spatialdata-plot.git@main
conda install ipykernel --yes----
sdata = cosmx(path="../data/CosMx/Lung5_Rep1/Lung5_Rep1-Flat_files_and_images/", dataset_id="Lung5_Rep1")
TypeError Traceback (most recent call last)
Cell In[9], line 1
----> 1 sdata = cosmx(path="../data/CosMx/Lung5_Rep1/Lung5_Rep1-Flat_files_and_images/", dataset_id="Lung5_Rep1")
File ~/miniconda3/envs/spatial-data/lib/python3.11/site-packages/spatialdata_io/readers/cosmx.py:294, in cosmx(path, dataset_id, transcripts, imread_kwargs, image_models_kwargs)
272 points[f"{fov}_points"] = PointsModel.parse(
273 sub_table,
274 coordinates={"x": CosmxKeys.X_LOCAL_TRANSCRIPT, "y": CosmxKeys.Y_LOCAL_TRANSCRIPT},
(...) 281 },
282 )
284 # TODO: what to do with fov file?
285 # if fov_file is not None:
286 # fov_positions = pd.read_csv(path / fov_file, header=0, index_col=CosmxKeys.FOV)
(...) 291 # logg.warning(f"FOV {str(fov)} does not exist, skipping it.")
292 # continue
--> 294 return SpatialData(images=images, labels=labels, points=points, table=table)
TypeError: SpatialData.init() got an unexpected keyword argument 'table'