Please make sure these conditions are met
What happened?
Hi, I'd appreciate any ideas about an issue with violins being squished and points not lining up. This started after a recent update of my mamba/conda environment but worked fine before. I tried searching for similar issues here and also on Seaborn's page but don't have any leads and can't say I'm well-versed with plotting in Python yet.
Thanks!
Minimal code sample
# /// script
# requires-python = ">=3.12"
# dependencies = [
# "scanpy@git+https://github.com/scverse/scanpy.git@main",
# "anndata==0.12.6"
# ]
# ///
#
# This script automatically imports the development branch of scanpy to check for issues
import scanpy as sc
import anndata as ad
adata = sc.datasets.pbmc68k_reduced()
sc.pl.violin(adata, ["n_genes", "n_counts", "percent_mito", "S_score"], groupby="bulk_labels", rotation=90)
Error output
Versions
Details
scanpy 1.12
anndata 0.12.6
---- ----
ipykernel 6.29.5
cloudpickle 3.1.2
natsort 8.4.0
matplotlib 3.10.8
session-info2 0.4
colorama 0.4.6
PyQtWebEngine 5.15.7
psutil 7.2.2
ipywidgets 8.1.8
sphinxcontrib-applehelp 2.0.0
executing 2.2.1
pyzmq 27.1.0
beautifulsoup4 4.14.3
stack_data 0.6.3
scikit-learn 1.8.0
PyYAML 6.0.3
sphinxcontrib-serializinghtml 1.1.10
six 1.17.0
prompt_toolkit 3.0.52
joblib 1.5.3
platformdirs 4.9.2
numba 0.63.1
debugpy 1.8.20
seaborn 0.13.2
sphinxcontrib-qthelp 2.0.0
typing_extensions 4.15.0
packaging 26.0
pyxdg 0.28
spyder-kernels 3.1.3
jupyter_client 7.4.9
setuptools 82.0.0
donfig 0.8.1.post1
scipy 1.17.0
decorator 5.2.1
jedi 0.19.2
matplotlib-inline 0.2.1
numcodecs 0.16.5
legacy-api-wrap 1.5
PyQt5_sip 12.17.0
entrypoints 0.4
comm 0.2.3
asttokens 3.0.1
zarr 3.1.5
threadpoolctl 3.6.0
pillow 12.1.1
parso 0.8.6
statsmodels 0.14.6
ipython 9.10.0
google-crc32c 1.8.0
numpy 2.3.5
pytz 2025.2
defusedxml 0.7.1
pandas 3.0.1
sphinxcontrib-devhelp 2.0.0
kiwisolver 1.4.9
PyQt5 5.15.11
h5py 3.13.0
patsy 1.0.2
msgpack 1.1.2
traitlets 5.14.3
jupyter_core 5.9.1
tornado 6.5.4
charset-normalizer 3.4.4
sphinxcontrib-jsmath 1.0.1
astroid 4.0.4
pyparsing 3.3.2
python-dateutil 2.9.0.post0
lxml 6.0.2
Pygments 2.19.2
pure_eval 0.2.3
llvmlite 0.46.0
cycler 0.12.1
soupsieve 2.8.3
wcwidth 0.6.0
fast-array-utils 1.3.1
sphinxcontrib-htmlhelp 2.1.0
chardet 5.2.0
---- ----
Python 3.12.12 | packaged by conda-forge | (main, Jan 26 2026, 23:51:32) [GCC 14.3.0]
OS Linux-6.12.74-1-lts-x86_64-with-glibc2.43
CPU 32 logical CPU cores
GPU ID: 0, NVIDIA GeForce RTX 4070 Laptop GPU, Driver: 590.48.01, Memory: 8188 MiB
Updated 2026-02-26 19:08
Please make sure these conditions are met
What happened?
Hi, I'd appreciate any ideas about an issue with violins being squished and points not lining up. This started after a recent update of my mamba/conda environment but worked fine before. I tried searching for similar issues here and also on Seaborn's page but don't have any leads and can't say I'm well-versed with plotting in Python yet.
Thanks!
Minimal code sample
Error output
Versions
Details