Future warning in \preprocessing\_highly_variable_genes.py:226

[dorzhey]

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?

Python compiler of Pandas is giving Future Warning that in line:
disp_grouped = df.groupby("mean_bin")["dispersions"]
at \preprocessing_highly_variable_genes.py:226
Gives this warning:
"The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning."

Minimal code sample

disp_grouped = df.groupby("mean_bin", observed=False)["dispersions"]

Error output

\scanpy\preprocessing\_highly_variable_genes.py:226: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.

Versions

-----
anndata     0.10.5.post1
scanpy      1.9.8
-----
PIL                 10.2.0
beta_ufunc          NA
binom_ufunc         NA
colorama            0.4.6
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.2
google              NA
h5py                3.9.0
hypergeom_ufunc     NA
igraph              0.11.4
invgauss_ufunc      NA
joblib              1.2.0
kiwisolver          1.4.4
leidenalg           0.10.2
llvmlite            0.42.0
matplotlib          3.8.0
mkl                 2.4.0
mpl_toolkits        NA
natsort             7.1.1
nbinom_ufunc        NA
ncf_ufunc           NA
nct_ufunc           NA
ncx2_ufunc          NA
nt                  NA
numba               0.59.0
numpy               1.26.4
packaging           23.1
pandas              2.2.1
psutil              5.9.8
pyparsing           3.0.9
pythoncom           NA
pytz                2023.3.post1
pywin32_system32    NA
pywintypes          NA
scipy               1.11.4
session_info        1.0.0
setuptools          68.2.2
six                 1.16.0
skewnorm_ufunc      NA
sklearn             1.2.2
texttable           1.7.0
threadpoolctl       2.2.0
torch               2.2.1
torchgen            NA
tqdm                4.65.0
typing_extensions   NA
wcwidth             0.2.13
win32api            NA
win32com            NA
yaml                6.0.1
zoneinfo            NA
-----
Python 3.11.7 | packaged by Anaconda, Inc. | (main, Dec 15 2023, 18:05:47) [MSC v.1916 64 bit (AMD64)]
Windows-10-10.0.22621-SP0
-----
Session information updated at 2024-03-26 18:50

[ivirshup]

@dorzhey can you reproduce this with the latest scanpy release? I believe it should be fixed there.

[dorzhey]

@ivirshup Yes it still there

[ivirshup]

In scanpy 1.10, the line referenced is:

• scanpy/scanpy/preprocessing/_highly_variable_genes.py

  Line 226 in 214e05b

  self,

But in 1.9.8 the line is:

• scanpy/scanpy/preprocessing/_highly_variable_genes.py

  Line 226 in 6da39f1

  disp_grouped = df.groupby("mean_bin")["dispersions"]

So, to me it seems like the warning would require running an older version of the code.

Can you demonstrate that in a session where sc.__version__ == "1.10.0" you get this warning and show that here? Something like:

import scanpy as sc
sc.pp.highly_variable_genes(sc.pp.pbmc3k_processed())
sc.logging.print_versions()