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cannot import name 'old_positionals' from 'scanpy._compat #3390

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fbx233 opened this issue Dec 2, 2024 · 1 comment
Open
2 of 3 tasks

cannot import name 'old_positionals' from 'scanpy._compat #3390

fbx233 opened this issue Dec 2, 2024 · 1 comment

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@fbx233
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fbx233 commented Dec 2, 2024

Please make sure these conditions are met

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

{
"name": "ImportError",
"message": "cannot import name 'old_positionals' from 'scanpy._compat' (/datapool/home/fengbx/mambaforge/envs/omicverse/lib/python3.10/site-packages/scanpy/_compat.py)",
"stack": "---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[26], line 4
2 import numpy as np
3 import pandas as pd
----> 4 import scanpy as sc
5 import matplotlib.pyplot as plt
6 from matplotlib import patheffects

File ~/mambaforge/envs/omicverse/lib/python3.10/site-packages/scanpy/init.py:45
30 set_figure_params = settings.set_figure_params
32 from anndata import (
33 AnnData,
34 concat,
(...)
42 read_umi_tools,
43 )
---> 45 from . import datasets, experimental, external, get, logging, metrics, queries
46 from . import plotting as pl
47 from . import preprocessing as pp

File ~/mambaforge/envs/omicverse/lib/python3.10/site-packages/scanpy/datasets/init.py:5
1 """Builtin Datasets."""
3 from future import annotations
----> 5 from ._datasets import (
6 blobs,
7 burczynski06,
8 krumsiek11,
9 moignard15,
10 paul15,
11 pbmc3k,
12 pbmc3k_processed,
13 pbmc68k_reduced,
14 toggleswitch,
15 visium_sge,
16 )
17 from ._ebi_expression_atlas import ebi_expression_atlas
19 all = [
20 "blobs",
21 "burczynski06",
(...)
30 "ebi_expression_atlas",
31 ]

File ~/mambaforge/envs/omicverse/lib/python3.10/site-packages/scanpy/datasets/_datasets.py:13
11 from .. import _utils
12 from .. import logging as logg
---> 13 from .._compat import old_positionals
14 from .._settings import settings
15 from ..readwrite import read, read_visium

ImportError: cannot import name 'old_positionals' from 'scanpy._compat' (/datapool/home/fengbx/mambaforge/envs/omicverse/lib/python3.10/site-packages/scanpy/_compat.py)"
}

Minimal code sample

import os
import numpy as np
import pandas as pd
import scanpy as sc

Error output

Versions


@fbx233 fbx233 added Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer labels Dec 2, 2024
@ilan-gold
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I cannot reproduce this locally, and you didn't provide any details on version or platform. Can you post your environment details as the issue template requested?

@ilan-gold ilan-gold removed the Triage 🩺 This issue needs to be triaged by a maintainer label Dec 3, 2024
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