AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet'

[bingy007]

Please make sure these conditions are met

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

What happened?

Hi,

Thanks a lot for helping! I was following this tutorial (https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering.html) and get the error in this step: sc.pp.scrublet(adata, batch_key="sample") AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet'

Can you help with this? Thanks!

Best, B

Minimal code sample

sc.pp.scrublet(adata, batch_key="lib_prep")

Error output

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_54187/3500521297.py in <module>
----> 1 sc.pp.scrublet(adata, batch_key="lib_prep")

AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet'

Versions

-----
anndata     0.10.3
scanpy      1.9.6
-----
PIL                 10.1.0
backcall            0.2.0
cffi                1.14.6
cycler              0.12.1
cython_runtime      NA
dateutil            2.8.2
decorator           5.0.9
defusedxml          0.7.1
exceptiongroup      1.2.0
get_annotations     NA
google              NA
h5py                3.10.0
importlib_resources NA
ipykernel           6.2.0
ipython_genutils    0.2.0
ipywidgets          7.6.3
jedi                0.18.0
joblib              1.3.2
kiwisolver          1.4.5
llvmlite            0.41.1
matplotlib          3.8.2
matplotlib_inline   NA
mpl_toolkits        NA
mudata              0.2.3
muon                0.1.6
natsort             8.4.0
numba               0.58.1
numpy               1.26.2
packaging           21.0
pandas              2.1.3
parso               0.8.2
patsy               0.5.3
pexpect             4.8.0
pickleshare         0.7.5
pkg_resources       NA
prompt_toolkit      3.0.19
ptyprocess          0.7.0
pycparser           2.20
pyexpat             NA
pygments            2.10.0
pynndescent         0.5.11
pyparsing           2.4.7
pytz                2023.3.post1
scipy               1.11.4
scrublet            NA
seaborn             0.12.2
session_info        1.0.0
setuptools          65.5.1
six                 1.16.0
sklearn             1.3.2
statsmodels         0.14.0
storemagic          NA
threadpoolctl       3.2.0
torch               1.12.1+cu102
tornado             6.1
tqdm                4.66.1
traitlets           5.0.5
typing_extensions   NA
umap                0.5.5
wcwidth             0.2.5
yaml                6.0.1
zipp                NA
zmq                 22.2.1
-----
IPython             7.26.0
jupyter_client      6.1.12
jupyter_core        4.7.1
notebook            6.4.3
-----
Python 3.9.0 (default, Oct  6 2020, 11:01:41) [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]
Linux-3.10.0-1160.108.1.el7.x86_64-x86_64-with-glibc2.17
-----
Session information updated at 2024-04-23 14:43

[AlePur]

I think this is not a bug. You have to update to latest version of scanpy

[Zethson]

@bingy007 please report back if you can reproduce this with the latest scanpy versions.

[TuDou-PK]

It works when I update the scanpy version from 1.9.8 to 1.10.1