normalize_per_cell raises numpy.core._exceptions.UFuncTypeError

[scottgigante-immunai]

• 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 master branch of scanpy.

---

Minimal code sample (that we can copy&paste without having any data)

import numpy as np
import anndata as ad
import scanpy as sc

adata = ad.AnnData(np.random.poisson(0.2, (100, 200)))
sc.pp.normalize_per_cell(adata, 1e6)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/scottgigante/envs/immunaISR/lib/python3.8/site-packages/scanpy/preprocessing/_simple.py", line 527, in normalize_per_cell
    normalize_per_cell(adata.X, counts_per_cell_after, counts_per_cell)
  File "/Users/scottgigante/envs/immunaISR/lib/python3.8/site-packages/scanpy/preprocessing/_simple.py", line 562, in normalize_per_cell
    counts_per_cell /= counts_per_cell_after
numpy.core._exceptions.UFuncTypeError: Cannot cast ufunc 'divide' output from dtype('float64') to dtype('int64') with casting rule 'same_kind'

Versions

-----
anndata     0.9.1
scanpy      1.9.3
-----
PIL                 9.5.0
cffi                1.15.1
cloudpickle         2.2.1
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.2
defusedxml          0.7.1
dill                0.3.6
google              NA
h5py                3.8.0
importlib_resources NA
joblib              1.3.0.dev0
kiwisolver          1.4.4
llvmlite            0.40.0
matplotlib          3.7.1
mpl_toolkits        NA
mpmath              1.3.0
natsort             8.3.1
numba               0.57.0
numpy               1.24.3
packaging           23.1
pandas              2.0.2
psutil              5.9.5
pyarrow             12.0.0
pyparsing           3.0.9
pytz                2023.3
scipy               1.10.1
session_info        1.0.0
six                 1.16.0
sklearn             1.2.2
sympy               1.11.1
threadpoolctl       3.1.0
torch               2.0.0
tqdm                4.65.0
typing_extensions   NA
yaml                6.0
zipp                NA
-----
Python 3.8.10 (v3.8.10:3d8993a744, May  3 2021, 08:55:58) [Clang 6.0 (clang-600.0.57)]
macOS-10.16-x86_64-i386-64bit
-----
Session information updated at 2023-06-05 12:34

[scottgigante-immunai]

Workaround:

adata.X = adata.X.astype(np.float64)
sc.pp.normalize_per_cell(adata, 1e6)

[flying-sheep]

please use normalize_total instead

[scottgigante-immunai]

Given the old function now raises an error, could you at least add a FutureWarning (or np.exceptions.VisibleDeprecationWarning) indicating the new function to be used? Thanks!

…

On Wed, 7 June 2023, 05:35 Philipp A., ***@***.***> wrote: Closed #2500 <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/scverse/scanpy/issues/2500&g=ZWVjM2FjODk0ZjdmMTI1Nw==&h=N2Y4NmFmODU2ZTBlYjI1NzEzZDVlY2M3ZDQxMmVkMGVkZjY2OGMxZjEzMjZiMjNlODhmMGFhMTkwYjFmNGVjOQ==&p=YzJlOmltbXVuYWk6YzpnOjlhYTRmOGNmMDU2NDdjZTQ1ZTI0NjFjZmQ1OTY3NjljOnYxOmg6VA==> as not planned. — Reply to this email directly, view it on GitHub <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/scverse/scanpy/issues/2500%23event-9456493371&g=ZGJmZGZhMzNmOTM5ZTgzYQ==&h=Y2JmZjM5MDc2MjMzNjM3MGQwMzk1MDYxZmE3MDZlYzBiNWEzYzdjMTMwNWY5MjgxNTU5YmQ3NDI0ZDBjNWRhZg==&p=YzJlOmltbXVuYWk6YzpnOjlhYTRmOGNmMDU2NDdjZTQ1ZTI0NjFjZmQ1OTY3NjljOnYxOmg6VA==>, or unsubscribe <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/notifications/unsubscribe-auth/AUHCMAWZ7ISUHUBPHQDLLCDXKBDOHANCNFSM6AAAAAAY3HAO3E&g=NDU3YTZlZTA4ZDE0MzNhZQ==&h=OWQzOWMxNDgxMjZkZGM3ZWUxMmQ1ZTFlN2UwNjI5ZDI4YjFmMDA3OGVmYjc5MTljZDVkMDlhMTE1YjRiODBmNg==&p=YzJlOmltbXVuYWk6YzpnOjlhYTRmOGNmMDU2NDdjZTQ1ZTI0NjFjZmQ1OTY3NjljOnYxOmg6VA==> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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[flying-sheep]

I had the same thought and opened #2505 to track that!

[scottgigante-immunai]

Thanks!

…

On Wed, Jun 7, 2023 at 9:34 AM Philipp A. ***@***.***> wrote: I had the same thought and opened #2505 <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/scverse/scanpy/issues/2505&g=NmVkM2RiMWY2M2U4YzZhYw==&h=YTlmZWU5MDlhNTJlOWJjMTkxZDczZTg2MGE2ODdiNzU2NmIwYjE2OTMzZTczY2M1ZjNlNzEyM2Q0Mjc1OWM5Yg==&p=YzJlOmltbXVuYWk6YzpnOjBhNjA3ZDgxZmY2OGQ1YTVjYWY3YWUzM2MzZGM0MDU3OnYxOmg6VA==> to track that! — Reply to this email directly, view it on GitHub <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/scverse/scanpy/issues/2500%23issuecomment-1580835422&g=YWNlMjU3YjI5ODM4NTJkYQ==&h=ZTJiNzVlYzQ0NzM5YmY0ZTdiMWEzMDQ2MmQ0MGMwOWZmZTVlOGRhN2JmYjZiYTcxYjg1Nzg3OTRjMzEwZDY3OA==&p=YzJlOmltbXVuYWk6YzpnOjBhNjA3ZDgxZmY2OGQ1YTVjYWY3YWUzM2MzZGM0MDU3OnYxOmg6VA==>, or unsubscribe <https://checkpoint.url-protection.com/v1/url?o=https%3A//github.com/notifications/unsubscribe-auth/AUHCMAR6XJXLYMBK224NMETXKB7MDANCNFSM6AAAAAAY3HAO3E&g=OGRhMDE2YzcyZWIwNGMxNg==&h=M2I1NTIwM2JlNTIwNjA4MGViYjE3YTRmYjQ0MWM3NzNhYzNkNjBlNzVjYjg1NDUwMGVkMjJhNWFkYmZlZTIxYQ==&p=YzJlOmltbXVuYWk6YzpnOjBhNjA3ZDgxZmY2OGQ1YTVjYWY3YWUzM2MzZGM0MDU3OnYxOmg6VA==> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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