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Static plotting for spatialdata
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TypeError: unhashable type: 'list' #170

Open ZhengTiger opened 1 year ago

ZhengTiger commented 1 year ago

Hello, thank you for developing such a good tool.

When I followed this tutorial, I have error:

import math

import matplotlib.pyplot as plt
import spatialdata_plot
from spatialdata.datasets import raccoon
from spatialdata.transformations import (
    Affine,
    Identity,
    MapAxis,
    Scale,
    Sequence,
    Translation,
    get_transformation,
    get_transformation_between_coordinate_systems,
    set_transformation,
)
sdata = raccoon()

print(sdata)

sdata.pl.render_images().pl.show()

INFO Transposing data of type: <class 'dask.array.core.Array'> to ('c', 'y', 'x').
SpatialData object with: ├── Images │ └── 'raccoon': SpatialImage[cyx] (3, 768, 1024) ├── Labels │ └── 'segmentation': SpatialImage[yx] (768, 1024) └── Shapes └── 'circles': GeoDataFrame shape: (4, 2) (2D shapes) with coordinate systems: ▸ 'global', with elements: raccoon (Images), segmentation (Labels), circles (Shapes)

TypeError Traceback (most recent call last) Cell In[14], line 5 1 sdata = raccoon() 3 print(sdata) ----> 5 sdata.pl.render_images().pl.show()

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\spatialdata_plot\pl\basic.py:654, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save) 652 for cmd, params in render_cmds.items(): 653 if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: --> 654 _render_images( 655 sdata=sdata, 656 render_params=params, 657 coordinate_system=cs, 658 ax=ax, 659 fig_params=fig_params, 660 scalebar_params=scalebar_params, 661 legend_params=legend_params, 662 # extent=extent[cs], 663 ) 664 elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: 665 _render_shapes( 666 sdata=sdata, 667 render_params=params, (...) 672 legend_params=legend_params, 673 )

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\spatialdata_plot\pl\render.py:348, in _render_images(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params) 346 # 2A) Image has 3 channels, no palette/cmap info -> use RGB 347 if n_channels == 3 and render_params.palette is None and not got_multiple_cmaps: --> 348 ax.imshow(np.stack([layers[c] for c in channels], axis=-1), alpha=render_params.alpha) 350 # 2B) Image has n channels, no palette/cmap info -> sample n categorical colors 351 elif render_params.palette is None and not got_multiple_cmaps: 352 # overwrite if n_channels == 2 for intuitive result

File <__array_function__ internals>:180, in stack(*args, **kwargs)

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\numpy\core\shape_base.py:420, in stack(arrays, axis, out) 416 if not overrides.ARRAY_FUNCTION_ENABLED: 417 # raise warning if necessary 418 _arrays_for_stack_dispatcher(arrays, stacklevel=2) --> 420 arrays = [asanyarray(arr) for arr in arrays] 421 if not arrays: 422 raise ValueError('need at least one array to stack')

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\numpy\core\shape_base.py:420, in (.0) 416 if not overrides.ARRAY_FUNCTION_ENABLED: 417 # raise warning if necessary 418 _arrays_for_stack_dispatcher(arrays, stacklevel=2) --> 420 arrays = [asanyarray(arr) for arr in arrays] 421 if not arrays: 422 raise ValueError('need at least one array to stack')

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\xarray\core\common.py:165, in AbstractArray.array(self, dtype) 164 def array(self: Any, dtype: DTypeLike = None) -> np.ndarray: --> 165 return np.asarray(self.values, dtype=dtype)

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\xarray\core\dataarray.py:729, in DataArray.values(self) 720 @property 721 def values(self) -> np.ndarray: 722 """ 723 The array's data as a numpy.ndarray. 724 (...) 727 type does not support coercion like this (e.g. cupy). 728 """ --> 729 return self.variable.values

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\xarray\core\variable.py:608, in Variable.values(self) 605 @property 606 def values(self): 607 """The variable's data as a numpy.ndarray""" --> 608 return _as_array_or_item(self._data)

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\xarray\core\variable.py:314, in _as_array_or_item(data) 300 def _as_array_or_item(data): 301 """Return the given values as a numpy array, or as an individual item if 302 it's a 0d datetime64 or timedelta64 array. 303 (...) 312 TODO: remove this (replace with np.asarray) once these issues are fixed 313 """ --> 314 data = np.asarray(data) 315 if data.ndim == 0: 316 if data.dtype.kind == "M":

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\dask\array\core.py:1700, in Array.array(self, dtype, kwargs) 1699 def array(self, dtype=None, kwargs): -> 1700 x = self.compute() 1701 if dtype and x.dtype != dtype: 1702 x = x.astype(dtype)

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\dask\base.py:342, in DaskMethodsMixin.compute(self, kwargs) 318 def compute(self, kwargs): 319 """Compute this dask collection 320 321 This turns a lazy Dask collection into its in-memory equivalent. (...) 340 dask.compute 341 """ --> 342 (result,) = compute(self, traverse=False, **kwargs) 343 return result

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\dask\base.py:615, in compute(traverse, optimize_graph, scheduler, get, *args, kwargs) 612 if not collections: 613 return args --> 615 schedule = get_scheduler( 616 scheduler=scheduler, 617 collections=collections, 618 get=get, 619 ) 621 dsk = collections_to_dsk(collections, optimize_graph, kwargs) 622 keys, postcomputes = [], []

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\dask\base.py:1440, in get_scheduler(get, scheduler, collections, cls) 1437 raise ValueError(get_err_msg) 1439 try: -> 1440 from distributed import get_client 1442 return get_client().get 1443 except (ImportError, ValueError):

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\distributed__init__.py:23 20 from dask.config import config # type: ignore 22 from distributed._version import get_versions ---> 23 from distributed.actor import Actor, ActorFuture, BaseActorFuture 24 from distributed.client import ( 25 Client, 26 CompatibleExecutor, (...) 35 wait, 36 ) 37 from distributed.core import Status, connect, rpc

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\distributed\actor.py:13 9 from typing import Generic, Literal, NoReturn, TypeVar 11 from tornado.ioloop import IOLoop ---> 13 from distributed.client import Future 14 from distributed.protocol import to_serialize 15 from distributed.utils import LateLoopEvent, iscoroutinefunction, sync, thread_state

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\distributed\client.py:116 94 from distributed.utils import ( 95 CancelledError, 96 LoopRunner, (...) 106 thread_state, 107 ) 108 from distributed.utils_comm import ( 109 WrappedKey, 110 gather_from_workers, (...) 114 unpack_remotedata, 115 ) --> 116 from distributed.worker import get_client, get_worker, secede 118 logger = logging.getLogger(name) 120 _global_clients: weakref.WeakValueDictionary[ 121 int, Client 122 ] = weakref.WeakValueDictionary()

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\distributed\worker.py:119 117 from distributed.utils_perf import disable_gc_diagnosis, enable_gc_diagnosis 118 from distributed.versions import get_versions --> 119 from distributed.worker_memory import ( 120 DeprecatedMemoryManagerAttribute, 121 DeprecatedMemoryMonitor, 122 WorkerDataParameter, 123 WorkerMemoryManager, 124 ) 125 from distributed.worker_state_machine import ( 126 AcquireReplicasEvent, 127 BaseWorker, (...) 151 WorkerState, 152 ) 154 if TYPE_CHECKING: 155 # FIXME import from typing (needs Python >=3.10)

File D:\1.study\miniconda3\envs\scverse\lib\site-packages\distributed\worker_memory.py:55 52 from distributed.nanny import Nanny 53 from distributed.worker import Worker ---> 55 WorkerDataParameter: TypeAlias = Union[ 56 # pre-initialized 57 MutableMapping[str, object], 58 # constructor 59 Callable[[], MutableMapping[str, object]], 60 # constructor, passed worker.local_directory 61 Callable[[str], MutableMapping[str, object]], 62 # (constructor, kwargs to constructor) 63 tuple[Callable[..., MutableMapping[str, object]], dict[str, Any]], 64 # initialize internally 65 None, 66 ] 68 worker_logger = logging.getLogger("distributed.worker.memory") 69 worker_logger.addFilter(RateLimiterFilter(r"Unmanaged memory use is high"))

File D:\1.study\miniconda3\envs\scverse\lib\typing.py:243, in _tp_cache..inner(*args, *kwds) 241 except TypeError: 242 pass # All real errors (not unhashable args) are raised below. --> 243 return func(args, **kwds)

File D:\1.study\miniconda3\envs\scverse\lib\typing.py:316, in _SpecialForm.getitem(self, parameters) 314 @_tp_cache 315 def getitem(self, parameters): --> 316 return self._getitem(self, parameters)

File D:\1.study\miniconda3\envs\scverse\lib\typing.py:421, in Union(self, parameters) 419 msg = "Union[arg, ...]: each arg must be a type." 420 parameters = tuple(_type_check(p, msg) for p in parameters) --> 421 parameters = _remove_dups_flatten(parameters) 422 if len(parameters) == 1: 423 return parameters[0]

File D:\1.study\miniconda3\envs\scverse\lib\typing.py:215, in _remove_dups_flatten(parameters) 213 params.append(p) 214 # Weed out strict duplicates, preserving the first of each occurrence. --> 215 all_params = set(params) 216 if len(all_params) < len(params): 217 new_params = []

TypeError: unhashable type: 'list'

Thank you for your help！

timtreis commented 2 months ago

Hey @zhenghu159, terribly sorry for only responding to this now. I think we've solved that issue by now, but still thanks for reporting back then!

lisch7 commented 1 month ago

@timtreis Same issue when I processed HD data. How to deal with this problem, please? Here is my SpatialData object and code:

SpatialData object
├── Images
│     ├── '_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│     ├── '_hires_image': DataArray[cyx] (3, 5164, 6000)
│     └── '_lowres_image': DataArray[cyx] (3, 517, 600)
├── Shapes
│     └── '_square_008um': GeoDataFrame shape: (275237, 1) (2D shapes)
└── Tables
      └── 'square_008um': AnnData (275237, 18085)
with coordinate systems:
    ▸ 'downscaled_hires', with elements:
        _hires_image (Images), _square_008um (Shapes)
    ▸ 'downscaled_lowres', with elements:
        _lowres_image (Images), _square_008um (Shapes)
    ▸ 'global', with elements:
        _cytassist_image (Images), _square_008um (Shapes)

And when I run 

import matplotlib.pyplot as plt
import spatialdata_plot
sdata.pl.render_images("_cytassist_image").pl.show()

Error information is as follows:

INFO     Dropping coordinate system 'downscaled_hires' since it doesn't have relevant elements.                    
INFO     Dropping coordinate system 'downscaled_lowres' since it doesn't have relevant elements.                   
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[43], line 1
----> 1 sdata.pl.render_images("_cytassist_image").pl.show()

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata_plot/pl/basic.py:862, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
    856     if wanted_images_on_this_cs:
    857         rasterize = (params_copy.scale is None) or (
    858             isinstance(params_copy.scale, str)
    859             and params_copy.scale != "full"
    860             and (dpi is not None or figsize is not None)
    861         )
--> 862         _render_images(
    863             sdata=sdata,
    864             render_params=params_copy,
    865             coordinate_system=cs,
    866             ax=ax,
    867             fig_params=fig_params,
    868             scalebar_params=scalebar_params,
    869             legend_params=legend_params,
    870             rasterize=rasterize,
    871         )
    873 elif cmd == "render_shapes" and has_shapes:
    874     wanted_elements, wanted_shapes_on_this_cs, wants_shapes = _get_wanted_render_elements(
    875         sdata, wanted_elements, params_copy, cs, "shapes"
    876     )

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata_plot/pl/render.py:559, in _render_images(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params, rasterize)
    557 palette = render_params.palette
    558 img = sdata_filt[render_params.element]
--> 559 extent = get_extent(img, coordinate_system=coordinate_system)
    560 scale = render_params.scale
    562 # get best scale out of multiscale image

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/functools.py:877, in singledispatch.<locals>.wrapper(*args, **kw)
    873 if not args:
    874     raise TypeError(f'{funcname} requires at least '
    875                     '1 positional argument')
--> 877 return dispatch(args[0].__class__)(*args, **kw)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata/_core/data_extent.py:305, in _(e, coordinate_system)
    303 @get_extent.register
    304 def _(e: DataArray, coordinate_system: str = "global") -> BoundingBoxDescription:
--> 305     return _get_extent_of_data_array(e, coordinate_system=coordinate_system)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata/_core/data_extent.py:95, in _get_extent_of_data_array(e, coordinate_system)
     93         i = data_axes.index(ax)
     94         extent[ax] = (0, e.shape[i])
---> 95 return _compute_extent_in_coordinate_system(
     96     element=e,
     97     coordinate_system=coordinate_system,
     98     extent=extent,
     99 )

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata/_core/data_extent.py:360, in _compute_extent_in_coordinate_system(element, coordinate_system, extent)
    358 d = get_transformation(element, get_all=True)
    359 points = PointsModel.parse(df, coordinates={k: k for k in axes}, transformations=d)
--> 360 transformed_corners = pd.DataFrame(transform(points, to_coordinate_system=coordinate_system).compute())
    361 # Make sure min and max values are in the same order as axes
    362 extent = {}

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/functools.py:877, in singledispatch.<locals>.wrapper(*args, **kw)
    873 if not args:
    874     raise TypeError(f'{funcname} requires at least '
    875                     '1 positional argument')
--> 877 return dispatch(args[0].__class__)(*args, **kw)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/spatialdata/_core/operations/transform.py:436, in _(data, transformation, maintain_positioning, to_coordinate_system)
    434 arrays = []
    435 for ax in axes:
--> 436     arrays.append(data[ax].to_dask_array(lengths=True).reshape(-1, 1))
    437 xdata = DataArray(da.concatenate(arrays, axis=1), coords={"points": range(len(data)), "dim": list(axes)})
    438 xtransformed = transformation._transform_coordinates(xdata)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/dask/dataframe/core.py:2010, in _Frame.to_dask_array(self, lengths, meta)
   1987 """Convert a dask DataFrame to a dask array.
   1988 
   1989 Parameters
   (...)
   2007 -------
   2008 """
   2009 if lengths is True:
-> 2010     lengths = tuple(self.map_partitions(len, enforce_metadata=False).compute())
   2012 arr = self.values
   2014 chunks = self._validate_chunks(arr, lengths)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/dask/base.py:376, in DaskMethodsMixin.compute(self, **kwargs)
    352 def compute(self, **kwargs):
    353     """Compute this dask collection
    354 
    355     This turns a lazy Dask collection into its in-memory equivalent.
   (...)
    374     dask.compute
    375     """
--> 376     (result,) = compute(self, traverse=False, **kwargs)
    377     return result

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/dask/base.py:649, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
    646 if not collections:
    647     return args
--> 649 schedule = get_scheduler(
    650     scheduler=scheduler,
    651     collections=collections,
    652     get=get,
    653 )
    655 dsk = collections_to_dsk(collections, optimize_graph, **kwargs)
    656 keys, postcomputes = [], []

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/dask/base.py:1524, in get_scheduler(get, scheduler, collections, cls)
   1521     raise ValueError(get_err_msg)
   1523 try:
-> 1524     from distributed import get_client
   1526     return get_client().get
   1527 except (ImportError, ValueError):

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/distributed/__init__.py:23
     20 from dask.config import config  # type: ignore
     22 from distributed._version import get_versions
---> 23 from distributed.actor import Actor, ActorFuture, BaseActorFuture
     24 from distributed.client import (
     25     Client,
     26     CompatibleExecutor,
   (...)
     35     wait,
     36 )
     37 from distributed.core import Status, connect, rpc

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/distributed/actor.py:13
      9 from typing import Generic, Literal, NoReturn, TypeVar
     11 from tornado.ioloop import IOLoop
---> 13 from distributed.client import Future
     14 from distributed.protocol import to_serialize
     15 from distributed.utils import LateLoopEvent, iscoroutinefunction, sync, thread_state

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/distributed/client.py:132
    110 from distributed.utils import (
    111     CancelledError,
    112     LoopRunner,
   (...)
    122     thread_state,
    123 )
    124 from distributed.utils_comm import (
    125     WrappedKey,
    126     gather_from_workers,
   (...)
    130     unpack_remotedata,
    131 )
--> 132 from distributed.worker import get_client, get_worker, secede
    134 logger = logging.getLogger(__name__)
    136 _global_clients: weakref.WeakValueDictionary[
    137     int, Client
    138 ] = weakref.WeakValueDictionary()

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/distributed/worker.py:119
    117 from distributed.utils_comm import gather_from_workers, pack_data, retry_operation
    118 from distributed.versions import get_versions
--> 119 from distributed.worker_memory import (
    120     DeprecatedMemoryManagerAttribute,
    121     DeprecatedMemoryMonitor,
    122     WorkerDataParameter,
    123     WorkerMemoryManager,
    124 )
    125 from distributed.worker_state_machine import (
    126     AcquireReplicasEvent,
    127     BaseWorker,
   (...)
    151     WorkerState,
    152 )
    154 if TYPE_CHECKING:
    155     # FIXME import from typing (needs Python >=3.10)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/site-packages/distributed/worker_memory.py:56
     53     from distributed.nanny import Nanny
     54     from distributed.worker import Worker
---> 56 WorkerDataParameter: TypeAlias = Union[
     57     # pre-initialized
     58     MutableMapping[Key, object],
     59     # constructor
     60     Callable[[], MutableMapping[Key, object]],
     61     # constructor, passed worker.local_directory
     62     Callable[[str], MutableMapping[Key, object]],
     63     # (constructor, kwargs to constructor)
     64     tuple[Callable[..., MutableMapping[Key, object]], dict[str, Any]],
     65     # initialize internally
     66     None,
     67 ]
     69 worker_logger = logging.getLogger("distributed.worker.memory")
     70 worker_logger.addFilter(RateLimiterFilter(r"Unmanaged memory use is high"))

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/typing.py:243, in _tp_cache.<locals>.inner(*args, **kwds)
    241 except TypeError:
    242     pass  # All real errors (not unhashable args) are raised below.
--> 243 return func(*args, **kwds)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/typing.py:316, in _SpecialForm.__getitem__(self, parameters)
    314 @_tp_cache
    315 def __getitem__(self, parameters):
--> 316     return self._getitem(self, parameters)

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/typing.py:421, in Union(self, parameters)
    419 msg = "Union[arg, ...]: each arg must be a type."
    420 parameters = tuple(_type_check(p, msg) for p in parameters)
--> 421 parameters = _remove_dups_flatten(parameters)
    422 if len(parameters) == 1:
    423     return parameters[0]

File ~/biosoft/miniconda3/envs/squidpy/lib/python3.9/typing.py:215, in _remove_dups_flatten(parameters)
    213         params.append(p)
    214 # Weed out strict duplicates, preserving the first of each occurrence.
--> 215 all_params = set(params)
    216 if len(all_params) < len(params):
    217     new_params = []

TypeError: unhashable type: 'list'

Here is my environment:

conda list
# packages in environment at /data2/data2_mailab003/biosoft/miniconda3/envs/squidpy:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
aiobotocore               2.5.4                    pypi_0    pypi
aiohappyeyeballs          2.4.3                    pypi_0    pypi
aiohttp                   3.10.10                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
anndata                   0.10.9                   pypi_0    pypi
array-api-compat          1.9                      pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     24.2.0                   pypi_0    pypi
botocore                  1.31.17                  pypi_0    pypi
ca-certificates           2024.8.30            hbcca054_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
certifi                   2024.8.30                pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorcet                  3.1.0                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.8.0                 pypi_0    pypi
dask-expr                 1.1.10                   pypi_0    pypi
dask-image                2024.5.3                 pypi_0    pypi
datashader                0.16.3                   pypi_0    pypi
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distributed               2024.8.0                 pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fcsparser                 0.2.8                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
geopandas                 1.0.1                    pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h5py                      3.12.1                   pypi_0    pypi
idna                      3.10                     pypi_0    pypi
igraph                    0.11.6                   pypi_0    pypi
imagecodecs               2024.9.22                pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
importlib-metadata        8.5.0                    pypi_0    pypi
importlib-resources       6.4.5                    pypi_0    pypi
inflect                   7.4.0                    pypi_0    pypi
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.18.1                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
lamin-utils               0.13.6                   pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.43                 h712a8e2_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libffi                    3.3                  h58526e2_2    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgcc                    14.1.0               h77fa898_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgcc-ng                 14.1.0               h69a702a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgomp                   14.1.0               h77fa898_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libsqlite                 3.46.0               hde9e2c9_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libstdcxx                 14.1.0               hc0a3c3a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libstdcxx-ng              14.1.0               h4852527_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libzlib                   1.2.13               h4ab18f5_6    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
llvmlite                  0.43.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
louvain                   0.8.2                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                3.0.1                    pypi_0    pypi
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
matplotlib-scalebar       0.8.1                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
more-itertools            10.5.0                   pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
multiscale-spatial-image  1.0.1                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.5                  he02047a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
ome-zarr                  0.9.0                    pypi_0    pypi
omnipath                  1.0.8                    pypi_0    pypi
openssl                   1.1.1w               hd590300_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.3                    pypi_0    pypi
param                     2.1.1                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
partd                     1.4.2                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    10.4.0                   pypi_0    pypi
pims                      0.7                      pypi_0    pypi
pip                       24.2               pyh8b19718_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
platformdirs              4.3.6                    pypi_0    pypi
pooch                     1.8.2                    pypi_0    pypi
prompt-toolkit            3.0.48                   pypi_0    pypi
propcache                 0.2.0                    pypi_0    pypi
psutil                    6.0.0                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    pypi_0    pypi
pyarrow                   17.0.0                   pypi_0    pypi
pyct                      0.5.0                    pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pynndescent               0.5.13                   pypi_0    pypi
pyogrio                   0.10.0                   pypi_0    pypi
pyparsing                 3.2.0                    pypi_0    pypi
pyproj                    3.6.1                    pypi_0    pypi
python                    3.9.0           hffdb5ce_5_cpython    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
readfcs                   1.1.8                    pypi_0    pypi
readline                  8.2                  h8228510_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
requests                  2.32.3                   pypi_0    pypi
rich                      13.9.2                   pypi_0    pypi
s3fs                      2023.6.0                 pypi_0    pypi
scanpy                    1.10.3                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scikit-learn              1.5.2                    pypi_0    pypi
scipy                     1.13.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                75.1.0             pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
shapely                   2.0.6                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
slicerator                1.1.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
spatial-image             1.1.0                    pypi_0    pypi
spatialdata               0.2.3                    pypi_0    pypi
spatialdata-io            0.1.5                    pypi_0    pypi
spatialdata-plot          0.2.6                    pypi_0    pypi
sqlite                    3.46.0               h6d4b2fc_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
squidpy                   1.6.1                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
statsmodels               0.14.4                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
tblib                     3.0.0                    pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2024.8.30                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
toolz                     1.0.0                    pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.5                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typeguard                 4.3.0                    pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
urllib3                   1.26.20                  pypi_0    pypi
validators                0.34.0                   pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xarray                    2024.7.0                 pypi_0    pypi
xarray-dataclasses        1.8.0                    pypi_0    pypi
xarray-datatree           0.0.14                   pypi_0    pypi
xarray-schema             0.0.3                    pypi_0    pypi
xarray-spatial            0.4.0                    pypi_0    pypi
xz                        5.2.6                h166bdaf_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
yarl                      1.15.2                   pypi_0    pypi
zarr                      2.18.2                   pypi_0    pypi
zict                      3.0.0                    pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi
zlib                      1.2.13               h4ab18f5_6    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
$ pip list
Package                 Version
----------------------- --------------------
adjustText              0.8
aiohappyeyeballs        2.4.3
aiohttp                 3.10.10
aiosignal               1.3.1
anndata                 0.9.2
annoy                   1.17.3
appdirs                 1.4.4
apturl                  0.5.2
asciitree               0.3.3
astor                   0.8.1
asttokens               2.4.0
async-timeout           4.0.3
attrs                   24.2.0
autograd                1.6.2
autograd-gamma          0.5.0
backcall                0.2.0
bcrypt                  3.1.7
beautifulsoup4          4.12.2
biopython               1.81
bioservices             1.11.2
blinker                 1.4
boltons                 23.0.0
Brlapi                  0.7.0
cachetools              5.3.1
cattrs                  23.1.2
certifi                 2019.11.28
cfgv                    3.4.0
chardet                 3.0.4
charset-normalizer      3.4.0
click                   8.1.7
cloudpickle             2.2.1
colorama                0.4.3
colorcet                3.0.1
colorlog                6.7.0
comm                    0.1.4
command-not-found       0.3
contourpy               1.1.1
cryptography            2.8
ctxcore                 0.2.0
cupshelpers             1.0
cycler                  0.12.1
cytoolz                 0.12.2
dask                    2023.5.0
dask-image              2023.3.0
datashader              0.15.2
datashape               0.5.2
DateTime                5.2
dbus-python             1.2.16
debugpy                 1.8.0
decorator               5.1.1
defer                   1.0.6
dill                    0.3.7
distlib                 0.3.8
distro                  1.4.0
distro-info             0.23+ubuntu1.1
docrep                  0.3.2
dunamai                 1.19.2
duplicity               0.8.12.0
dynamo-release          1.4.0
easydev                 0.12.1
einops                  0.7.0
entrypoints             0.3
ERgene                  1.2.8
et-xmlfile              1.1.0
exceptiongroup          1.1.3
executing               2.0.0
fasteners               0.14.1
fbpca                   1.0
filelock                3.13.1
fonttools               4.49.0
formulaic               0.6.6
frozendict              2.3.8
frozenlist              1.4.1
fsspec                  2024.9.0
future                  0.18.2
gdown                   4.7.1
geosketch               1.2
get-annotations         0.1.2
get_version             3.5.4
gevent                  23.9.1
google-auth             2.23.2
google-auth-oauthlib    1.0.0
graphlib-backport       1.0.3
greenlet                3.0.0
grequests               0.7.0
grpcio                  1.59.0
gseapy                  0.10.8
h5py                    3.10.0
harmonypy               0.0.9
hnswlib                 0.7.0
httplib2                0.14.0
identify                2.5.35
idna                    2.8
igraph                  0.10.4
imageio                 2.31.1
importlib-metadata      7.0.1
importlib-resources     6.1.1
inflect                 7.4.0
interface-meta          1.3.0
intervaltree            2.1.0
ipykernel               6.29.5
ipython                 8.12.3
ipywidgets              8.1.1
jedi                    0.19.1
joblib                  1.3.2
jupyter_client          8.6.3
jupyter_core            5.4.0
jupyterlab-widgets      3.0.9
keyring                 18.0.1
kiwisolver              1.4.5
ktplotspy               0.2.0
language-selector       0.1
launchpadlib            1.10.13
lazr.restfulclient      0.14.2
lazr.uri                1.0.3
lazy_loader             0.3
leidenalg               0.10.2
lifelines               0.27.8
llvmlite                0.38.1
locket                  1.0.0
lockfile                0.12.2
loompy                  3.0.7
louis                   3.12.0
louvain                 0.8.0
lxml                    4.9.3
macaroonbakery          1.3.1
Mako                    1.1.0
Markdown                3.5
MarkupSafe              1.1.0
matplotlib              3.7.5
matplotlib-inline       0.1.6
matplotlib-scalebar     0.8.1
metatime                1.3.0
mizani                  0.9.3
mofax                   0.3.6
monotonic               1.5
more-itertools          10.5.0
multidict               6.1.0
multiprocess            0.70.15
natsort                 8.4.0
nest-asyncio            1.6.0
netifaces               0.10.4
networkx                3.1
nodeenv                 1.8.0
numba                   0.55.2
numcodecs               0.12.1
numdifftools            0.9.41
numpy                   1.22.4
numpy-groupies          0.9.22
oauthlib                3.1.0
olefile                 0.46
omnipath                1.0.8
openpyxl                3.1.2
packaging               23.2
pandas                  2.0.3
param                   1.13.0
paramiko                2.6.0
parso                   0.8.3
partd                   1.4.1
patsy                   0.5.6
pexpect                 4.6.0
pickleshare             0.7.5
pillow                  10.4.0
PIMS                    0.7
pip                     24.2
platformdirs            3.11.0
plotnine                0.12.3
pre-commit              3.5.0
progressbar2            4.2.0
prompt-toolkit          3.0.39
propcache               0.2.0
protobuf                4.24.4
psutil                  6.0.0
pure-eval               0.2.2
pyarrow                 13.0.0
pyasn1                  0.5.0
pyasn1-modules          0.3.0
pybedtools              0.9.1
pybind11                2.11.1
pycairo                 1.16.2
pyct                    0.5.0
pycups                  1.9.73
pydeseq2                0.4.1
pygam                   0.8.0
Pygments                2.18.0
PyGObject               3.36.0
PyJWT                   1.7.1
pymacaroons             0.13.0
PyNaCl                  1.3.0
pynndescent             0.5.11
pyparsing               3.1.1
pyRFC3339               1.1
pysam                   0.22.0
python-apt              2.0.1+ubuntu0.20.4.1
python-circos           0.3.0
python-dateutil         2.8.2
python-debian           0.1.36+ubuntu1.1
python-dotplot          0.0.1
python-igraph           0.10.4
python-utils            3.8.1
pytz                    2024.1
PyWavelets              1.4.1
pyxdg                   0.26
PyYAML                  5.3.1
pyzmq                   25.1.1
reportlab               3.5.34
requests                2.32.3
requests-cache          1.1.0
requests-oauthlib       1.3.1
requests-unixsocket     0.2.0
rsa                     4.9
scanoramaCT             1.2.0
scanpy                  1.9.8
scikit-image            0.21.0
scikit-learn            1.3.2
scikit-misc             0.2.0
scrublet                0.2.3
scvelo                  0.3.2
seaborn                 0.13.2
SecretStorage           2.3.1
session-info            1.0.0
setuptools              75.1.0
simplejson              3.16.0
six                     1.14.0
slicerator              1.1.0
sortedcontainers        2.4.0
soupsieve               2.5
spatial_image           1.1.0
spatialdata             0.0.1
squidpy                 1.2.3
ssh-import-id           5.10
stack-data              0.6.3
statsmodels             0.14.1
stdlib-list             0.10.0
suds-community          1.1.2
systemd-python          234
tbb                     2021.10.0
tensorboard             2.14.0
tensorboard-data-server 0.7.1
termcolor               2.3.0
texttable               1.6.7
threadpoolctl           3.3.0
tifffile                2023.7.10
toolz                   1.0.0
tornado                 6.3.3
tqdm                    4.66.2
traitlets               5.11.2
typeguard               4.3.0
typing_extensions       4.12.2
tzdata                  2023.3
ubuntu-advantage-tools  8001
ubuntu-drivers-common   0.0.0
ufw                     0.36
umap-learn              0.5.5
unattended-upgrades     0.1
UpSetPlot               0.8.0
url-normalize           1.4.3
urllib3                 2.2.3
usb-creator             0.3.7
validators              0.34.0
virtualenv              20.25.0
wadllib                 1.3.3
wcwidth                 0.2.8
Werkzeug                3.0.0
wheel                   0.34.2
widgetsnbextension      4.0.9
wrapt                   1.16.0
xarray                  2023.1.0
xarray-dataclasses      1.8.0
xkit                    0.0.0
xmltodict               0.13.0
yarl                    1.15.2
zarr                    2.16.1
zipp                    3.17.0
zope.event              5.0
zope.interface          6.1
timtreis commented 1 month ago

Image It seems that you have spatialdata installed both using conda (0.2.3) and pip (0.0.1). Could you remove both and reinstall the latest version? Never seen an error like yours before, so I'm trying to exclude the easy options first :)

lisch7 commented 1 month ago

Hi, thanks for your reply. I reinstalled spatialdata. But it still reporting the same error message. And now my environment is as follows:

pip list
Package                 Version
----------------------- --------------------
adjustText              0.8
aiohappyeyeballs        2.4.3
aiohttp                 3.10.10
aiosignal               1.3.1
anndata                 0.9.2
annoy                   1.17.3
appdirs                 1.4.4
apturl                  0.5.2
asciitree               0.3.3
astor                   0.8.1
asttokens               2.4.0
async-timeout           4.0.3
attrs                   24.2.0
autograd                1.6.2
autograd-gamma          0.5.0
backcall                0.2.0
bcrypt                  3.1.7
beautifulsoup4          4.12.2
biopython               1.81
bioservices             1.11.2
blinker                 1.4
boltons                 23.0.0
Brlapi                  0.7.0
cachetools              5.3.1
cattrs                  23.1.2
certifi                 2019.11.28
cfgv                    3.4.0
chardet                 3.0.4
charset-normalizer      3.4.0
click                   8.1.7
cloudpickle             2.2.1
colorama                0.4.3
colorcet                3.0.1
colorlog                6.7.0
comm                    0.1.4
command-not-found       0.3
contourpy               1.1.1
cryptography            2.8
ctxcore                 0.2.0
cupshelpers             1.0
cycler                  0.12.1
cytoolz                 0.12.2
dask                    2023.5.0
dask-image              2023.3.0
datashader              0.15.2
datashape               0.5.2
DateTime                5.2
dbus-python             1.2.16
debugpy                 1.8.0
decorator               5.1.1
defer                   1.0.6
dill                    0.3.7
distlib                 0.3.8
distro                  1.4.0
distro-info             0.23+ubuntu1.1
docrep                  0.3.2
dunamai                 1.19.2
duplicity               0.8.12.0
dynamo-release          1.4.0
easydev                 0.12.1
einops                  0.7.0
entrypoints             0.3
ERgene                  1.2.8
et-xmlfile              1.1.0
exceptiongroup          1.1.3
executing               2.0.0
fasteners               0.14.1
fbpca                   1.0
filelock                3.13.1
fonttools               4.49.0
formulaic               0.6.6
frozendict              2.3.8
frozenlist              1.4.1
fsspec                  2024.9.0
future                  0.18.2
gdown                   4.7.1
geosketch               1.2
get-annotations         0.1.2
get_version             3.5.4
gevent                  23.9.1
google-auth             2.23.2
google-auth-oauthlib    1.0.0
graphlib-backport       1.0.3
greenlet                3.0.0
grequests               0.7.0
grpcio                  1.59.0
gseapy                  0.10.8
h5py                    3.10.0
harmonypy               0.0.9
hnswlib                 0.7.0
httplib2                0.14.0
identify                2.5.35
idna                    2.8
igraph                  0.10.4
imageio                 2.31.1
importlib-metadata      7.0.1
importlib-resources     6.1.1
inflect                 7.4.0
interface-meta          1.3.0
intervaltree            2.1.0
ipykernel               6.29.5
ipython                 8.12.3
ipywidgets              8.1.1
jedi                    0.19.1
joblib                  1.3.2
jupyter_client          8.6.3
jupyter_core            5.4.0
jupyterlab-widgets      3.0.9
keyring                 18.0.1
kiwisolver              1.4.5
ktplotspy               0.2.0
language-selector       0.1
launchpadlib            1.10.13
lazr.restfulclient      0.14.2
lazr.uri                1.0.3
lazy_loader             0.3
leidenalg               0.10.2
lifelines               0.27.8
llvmlite                0.38.1
locket                  1.0.0
lockfile                0.12.2
loompy                  3.0.7
louis                   3.12.0
louvain                 0.8.0
lxml                    4.9.3
macaroonbakery          1.3.1
Mako                    1.1.0
Markdown                3.5
MarkupSafe              1.1.0
matplotlib              3.7.5
matplotlib-inline       0.1.6
matplotlib-scalebar     0.8.1
metatime                1.3.0
mizani                  0.9.3
mofax                   0.3.6
monotonic               1.5
more-itertools          10.5.0
multidict               6.1.0
multiprocess            0.70.15
natsort                 8.4.0
nest-asyncio            1.6.0
netifaces               0.10.4
networkx                3.1
nodeenv                 1.8.0
numba                   0.55.2
numcodecs               0.12.1
numdifftools            0.9.41
numpy                   1.22.4
numpy-groupies          0.9.22
oauthlib                3.1.0
olefile                 0.46
omnipath                1.0.8
openpyxl                3.1.2
packaging               23.2
pandas                  2.0.3
param                   1.13.0
paramiko                2.6.0
parso                   0.8.3
partd                   1.4.1
patsy                   0.5.6
pexpect                 4.6.0
pickleshare             0.7.5
pillow                  10.4.0
PIMS                    0.7
pip                     24.2
platformdirs            3.11.0
plotnine                0.12.3
pre-commit              3.5.0
progressbar2            4.2.0
prompt-toolkit          3.0.39
propcache               0.2.0
protobuf                4.24.4
psutil                  6.0.0
pure-eval               0.2.2
pyarrow                 13.0.0
pyasn1                  0.5.0
pyasn1-modules          0.3.0
pybedtools              0.9.1
pybind11                2.11.1
pycairo                 1.16.2
pyct                    0.5.0
pycups                  1.9.73
pydeseq2                0.4.1
pygam                   0.8.0
Pygments                2.18.0
PyGObject               3.36.0
PyJWT                   1.7.1
pymacaroons             0.13.0
PyNaCl                  1.3.0
pynndescent             0.5.11
pyparsing               3.1.1
pyRFC3339               1.1
pysam                   0.22.0
python-apt              2.0.1+ubuntu0.20.4.1
python-circos           0.3.0
python-dateutil         2.8.2
python-debian           0.1.36+ubuntu1.1
python-dotplot          0.0.1
python-igraph           0.10.4
python-utils            3.8.1
pytz                    2024.1
PyWavelets              1.4.1
pyxdg                   0.26
PyYAML                  5.3.1
pyzmq                   25.1.1
reportlab               3.5.34
requests                2.32.3
requests-cache          1.1.0
requests-oauthlib       1.3.1
requests-unixsocket     0.2.0
rsa                     4.9
scanoramaCT             1.2.0
scanpy                  1.9.8
scikit-image            0.21.0
scikit-learn            1.3.2
scikit-misc             0.2.0
scrublet                0.2.3
scvelo                  0.3.2
seaborn                 0.13.2
SecretStorage           2.3.1
session-info            1.0.0
setuptools              75.1.0
simplejson              3.16.0
six                     1.14.0
slicerator              1.1.0
sortedcontainers        2.4.0
soupsieve               2.5
spatial_image           1.1.0
squidpy                 1.2.3
ssh-import-id           5.10
stack-data              0.6.3
statsmodels             0.14.1
stdlib-list             0.10.0
suds-community          1.1.2
systemd-python          234
tbb                     2021.10.0
tensorboard             2.14.0
tensorboard-data-server 0.7.1
termcolor               2.3.0
texttable               1.6.7
threadpoolctl           3.3.0
tifffile                2023.7.10
toolz                   1.0.0
tornado                 6.3.3
tqdm                    4.66.2
traitlets               5.11.2
typeguard               4.3.0
typing_extensions       4.12.2
tzdata                  2023.3
ubuntu-advantage-tools  8001
ubuntu-drivers-common   0.0.0
ufw                     0.36
umap-learn              0.5.5
unattended-upgrades     0.1
UpSetPlot               0.8.0
url-normalize           1.4.3
urllib3                 2.2.3
usb-creator             0.3.7
validators              0.34.0
virtualenv              20.25.0
wadllib                 1.3.3
wcwidth                 0.2.8
Werkzeug                3.0.0
wheel                   0.34.2
widgetsnbextension      4.0.9
wrapt                   1.16.0
xarray                  2023.1.0
xarray-dataclasses      1.8.0
xkit                    0.0.0
xmltodict               0.13.0
yarl                    1.15.2
zarr                    2.16.1
zipp                    3.17.0
zope.event              5.0
zope.interface          6.1
conda list
# packages in environment at /data2/data2_mailab003/biosoft/miniconda3/envs/squidpy:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
aiobotocore               2.5.4                    pypi_0    pypi
aiohappyeyeballs          2.4.3                    pypi_0    pypi
aiohttp                   3.10.10                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
anndata                   0.10.9                   pypi_0    pypi
array-api-compat          1.9                      pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     24.2.0                   pypi_0    pypi
botocore                  1.31.17                  pypi_0    pypi
ca-certificates           2024.8.30            hbcca054_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
certifi                   2024.8.30                pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorcet                  3.1.0                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.8.0                 pypi_0    pypi
dask-expr                 1.1.10                   pypi_0    pypi
dask-image                2024.5.3                 pypi_0    pypi
datashader                0.16.3                   pypi_0    pypi
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distributed               2024.8.0                 pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fcsparser                 0.2.8                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
geopandas                 1.0.1                    pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h5py                      3.12.1                   pypi_0    pypi
idna                      3.10                     pypi_0    pypi
igraph                    0.11.6                   pypi_0    pypi
imagecodecs               2024.9.22                pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
importlib-metadata        8.5.0                    pypi_0    pypi
importlib-resources       6.4.5                    pypi_0    pypi
inflect                   7.4.0                    pypi_0    pypi
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.18.1                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
lamin-utils               0.13.6                   pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.43                 h712a8e2_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libffi                    3.3                  h58526e2_2    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgcc                    14.1.0               h77fa898_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgcc-ng                 14.1.0               h69a702a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libgomp                   14.1.0               h77fa898_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libsqlite                 3.46.0               hde9e2c9_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libstdcxx                 14.1.0               hc0a3c3a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libstdcxx-ng              14.1.0               h4852527_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
libzlib                   1.2.13               h4ab18f5_6    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
llvmlite                  0.43.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
louvain                   0.8.2                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                3.0.1                    pypi_0    pypi
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
matplotlib-scalebar       0.8.1                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
more-itertools            10.5.0                   pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
multiscale-spatial-image  1.0.1                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.5                  he02047a_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
ome-zarr                  0.9.0                    pypi_0    pypi
omnipath                  1.0.8                    pypi_0    pypi
openssl                   1.1.1w               hd590300_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.3                    pypi_0    pypi
param                     2.1.1                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
partd                     1.4.2                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    10.4.0                   pypi_0    pypi
pims                      0.7                      pypi_0    pypi
pip                       24.2               pyh8b19718_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
platformdirs              4.3.6                    pypi_0    pypi
pooch                     1.8.2                    pypi_0    pypi
prompt-toolkit            3.0.48                   pypi_0    pypi
propcache                 0.2.0                    pypi_0    pypi
psutil                    6.0.0                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    pypi_0    pypi
pyarrow                   17.0.0                   pypi_0    pypi
pyct                      0.5.0                    pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pynndescent               0.5.13                   pypi_0    pypi
pyogrio                   0.10.0                   pypi_0    pypi
pyparsing                 3.2.0                    pypi_0    pypi
pyproj                    3.6.1                    pypi_0    pypi
python                    3.9.0           hffdb5ce_5_cpython    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
readfcs                   1.1.8                    pypi_0    pypi
readline                  8.2                  h8228510_1    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
requests                  2.32.3                   pypi_0    pypi
rich                      13.9.2                   pypi_0    pypi
s3fs                      2023.6.0                 pypi_0    pypi
scanpy                    1.10.3                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scikit-learn              1.5.2                    pypi_0    pypi
scipy                     1.13.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                75.1.0             pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
shapely                   2.0.6                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
slicerator                1.1.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
spatial-image             1.1.0                    pypi_0    pypi
spatialdata               0.2.3                    pypi_0    pypi
spatialdata-io            0.1.5                    pypi_0    pypi
spatialdata-plot          0.2.6                    pypi_0    pypi
sqlite                    3.46.0               h6d4b2fc_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
squidpy                   1.6.1                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
statsmodels               0.14.4                   pypi_0    pypi
stdlib-list               0.10.0                   pypi_0    pypi
tblib                     3.0.0                    pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2024.8.30                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
toolz                     1.0.0                    pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.5                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typeguard                 4.3.0                    pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
urllib3                   1.26.20                  pypi_0    pypi
validators                0.34.0                   pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xarray                    2024.7.0                 pypi_0    pypi
xarray-dataclasses        1.8.0                    pypi_0    pypi
xarray-datatree           0.0.14                   pypi_0    pypi
xarray-schema             0.0.3                    pypi_0    pypi
xarray-spatial            0.4.0                    pypi_0    pypi
xz                        5.2.6                h166bdaf_0    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
yarl                      1.15.2                   pypi_0    pypi
zarr                      2.18.2                   pypi_0    pypi
zict                      3.0.0                    pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi
zlib                      1.2.13               h4ab18f5_6    https://mirrors.bfsu.edu.cn./anaconda/cloud/conda-forge
lisch7 commented 1 month ago

Well, I reinstalled the conda env using the following code: 

python -m pip install "spatialdata[extra]"
python -m pip install squidpy

And it works fine now. But I don't know what is wrong. Here is my new environment information:

conda list
# packages in environment at /data2/data2_mailab003/biosoft/miniconda3/envs/spatialdata:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
_openmp_mutex             5.1                       1_gnu    defaults
aiobotocore               2.5.4                    pypi_0    pypi
aiohappyeyeballs          2.4.3                    pypi_0    pypi
aiohttp                   3.10.10                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
alabaster                 0.7.16                   pypi_0    pypi
anndata                   0.10.9                   pypi_0    pypi
annotated-types           0.7.0                    pypi_0    pypi
app-model                 0.3.0                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
array-api-compat          1.9                      pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 2.4.1                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     24.2.0                   pypi_0    pypi
babel                     2.16.0                   pypi_0    pypi
botocore                  1.31.17                  pypi_0    pypi
build                     1.2.2.post1              pypi_0    pypi
ca-certificates           2024.9.24            h06a4308_0    defaults
cachey                    0.2.1                    pypi_0    pypi
certifi                   2024.8.30                pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorcet                  3.1.0                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.8.0                 pypi_0    pypi
dask-expr                 1.1.10                   pypi_0    pypi
dask-image                2024.5.3                 pypi_0    pypi
datashader                0.16.3                   pypi_0    pypi
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distributed               2024.8.0                 pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
docstring-parser          0.16                     pypi_0    pypi
docutils                  0.21.2                   pypi_0    pypi
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fcsparser                 0.2.8                    pypi_0    pypi
flexcache                 0.3                      pypi_0    pypi
flexparser                0.3.1                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
freetype-py               2.5.1                    pypi_0    pypi
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
geopandas                 1.0.1                    pypi_0    pypi
get-annotations           0.1.2                    pypi_0    pypi
h5py                      3.12.1                   pypi_0    pypi
heapdict                  1.0.1                    pypi_0    pypi
hsluv                     5.0.4                    pypi_0    pypi
idna                      3.10                     pypi_0    pypi
igraph                    0.11.6                   pypi_0    pypi
imagecodecs               2024.9.22                pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        8.5.0                    pypi_0    pypi
importlib-resources       6.4.5                    pypi_0    pypi
in-n-out                  0.2.1                    pypi_0    pypi
inflect                   7.4.0                    pypi_0    pypi
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.18.1                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
jsonschema                4.23.0                   pypi_0    pypi
jsonschema-specifications 2024.10.1                pypi_0    pypi
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
lamin-utils               0.13.7                   pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.40                 h12ee557_0    defaults
legacy-api-wrap           1.4                      pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
libffi                    3.4.4                h6a678d5_1    defaults
libgcc-ng                 11.2.0               h1234567_1    defaults
libgomp                   11.2.0               h1234567_1    defaults
libstdcxx-ng              11.2.0               h1234567_1    defaults
llvmlite                  0.43.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
loguru                    0.7.2                    pypi_0    pypi
magicgui                  0.9.1                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                3.0.1                    pypi_0    pypi
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
matplotlib-scalebar       0.8.1                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
more-itertools            10.5.0                   pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
multiscale-spatial-image  1.0.1                    pypi_0    pypi
napari                    0.5.4                    pypi_0    pypi
napari-console            0.1.0                    pypi_0    pypi
napari-matplotlib         2.0.1                    pypi_0    pypi
napari-plugin-engine      0.2.0                    pypi_0    pypi
napari-spatialdata        0.5.3                    pypi_0    pypi
napari-svg                0.2.0                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0    defaults
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.2.1                    pypi_0    pypi
npe2                      0.7.7                    pypi_0    pypi
numba                     0.60.0                   pypi_0    pypi
numcodecs                 0.12.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
numpydoc                  1.8.0                    pypi_0    pypi
ome-zarr                  0.9.0                    pypi_0    pypi
omnipath                  1.0.8                    pypi_0    pypi
openssl                   3.0.15               h5eee18b_0    defaults
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.3                    pypi_0    pypi
param                     2.1.1                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
partd                     1.4.2                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    11.0.0                   pypi_0    pypi
pims                      0.7                      pypi_0    pypi
pint                      0.24.3                   pypi_0    pypi
pip                       24.2             py39h06a4308_0    defaults
platformdirs              4.3.6                    pypi_0    pypi
pooch                     1.8.2                    pypi_0    pypi
prompt-toolkit            3.0.48                   pypi_0    pypi
propcache                 0.2.0                    pypi_0    pypi
psutil                    6.0.0                    pypi_0    pypi
psygnal                   0.11.1                   pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    pypi_0    pypi
pyarrow                   17.0.0                   pypi_0    pypi
pyconify                  0.1.6                    pypi_0    pypi
pyct                      0.5.0                    pypi_0    pypi
pydantic                  2.9.2                    pypi_0    pypi
pydantic-compat           0.1.2                    pypi_0    pypi
pydantic-core             2.23.4                   pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pynndescent               0.5.13                   pypi_0    pypi
pyogrio                   0.10.0                   pypi_0    pypi
pyopengl                  3.1.7                    pypi_0    pypi
pyparsing                 3.2.0                    pypi_0    pypi
pyproj                    3.6.1                    pypi_0    pypi
pyproject-hooks           1.2.0                    pypi_0    pypi
pyqt5                     5.15.11                  pypi_0    pypi
pyqt5-qt5                 5.15.15                  pypi_0    pypi
pyqt5-sip                 12.15.0                  pypi_0    pypi
python                    3.9.20               he870216_1    defaults
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
qtconsole                 5.6.0                    pypi_0    pypi
qtpy                      2.4.1                    pypi_0    pypi
readfcs                   1.1.8                    pypi_0    pypi
readline                  8.2                  h5eee18b_0    defaults
referencing               0.35.1                   pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rich                      13.9.2                   pypi_0    pypi
rpds-py                   0.20.0                   pypi_0    pypi
s3fs                      2023.6.0                 pypi_0    pypi
scanpy                    1.10.3                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scikit-learn              1.5.2                    pypi_0    pypi
scipy                     1.13.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                75.1.0           py39h06a4308_0    defaults
shapely                   2.0.6                    pypi_0    pypi
shellingham               1.5.4                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
slicerator                1.1.0                    pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
spatial-image             1.1.0                    pypi_0    pypi
spatialdata               0.2.3                    pypi_0    pypi
spatialdata-io            0.1.5                    pypi_0    pypi
spatialdata-plot          0.2.6                    pypi_0    pypi
sphinx                    7.4.7                    pypi_0    pypi
sphinxcontrib-applehelp   2.0.0                    pypi_0    pypi
sphinxcontrib-devhelp     2.0.0                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.1.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      2.0.0                    pypi_0    pypi
sphinxcontrib-serializinghtml 2.0.0                    pypi_0    pypi
sqlite                    3.45.3               h5eee18b_0    defaults
squidpy                   1.6.1                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
statsmodels               0.14.4                   pypi_0    pypi
stdlib-list               0.11.0                   pypi_0    pypi
superqt                   0.6.7                    pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tblib                     3.0.0                    pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2024.8.30                pypi_0    pypi
tinycss2                  1.3.0                    pypi_0    pypi
tk                        8.6.14               h39e8969_0    defaults
tomli                     2.0.2                    pypi_0    pypi
tomli-w                   1.1.0                    pypi_0    pypi
toolz                     1.0.0                    pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.5                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typeguard                 4.3.0                    pypi_0    pypi
typer                     0.12.5                   pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
umap-learn                0.5.6                    pypi_0    pypi
urllib3                   1.26.20                  pypi_0    pypi
validators                0.34.0                   pypi_0    pypi
vispy                     0.14.3                   pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.44.0           py39h06a4308_0    defaults
wrapt                     1.16.0                   pypi_0    pypi
xarray                    2024.7.0                 pypi_0    pypi
xarray-dataclasses        1.8.0                    pypi_0    pypi
xarray-datatree           0.0.14                   pypi_0    pypi
xarray-schema             0.0.3                    pypi_0    pypi
xarray-spatial            0.4.0                    pypi_0    pypi
xz                        5.4.6                h5eee18b_1    defaults
yarl                      1.15.3                   pypi_0    pypi
zarr                      2.18.2                   pypi_0    pypi
zict                      3.0.0                    pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_1    defaults

Perhaps because I installed squidpy using pip install 'squidpy[interactive]' before ?