The latest pypi version is 0.1.5, while on github release it is 0.1.4.
$ pixi list -x
Environment: th
Package Version Build Size Kind Source
cell2location 0.1.5 440.1 KiB pypi cell2location-0.1.5-py3-none-any.whl
cuda-toolkit 12.9.1 ha804496_0 20 KiB conda https://conda.anaconda.org/conda-forge/
cuda-version 12.9 h4f385c5_3 21.1 KiB conda https://conda.anaconda.org/conda-forge/
ipykernel 7.0.1 pyha191276_0 128.9 KiB conda https://conda.anaconda.org/conda-forge/
ipywidgets 8.1.7 pyhd8ed1ab_0 111.9 KiB conda https://conda.anaconda.org/conda-forge/
jax 0.7.2 pyhd8ed1ab_0 1.8 MiB conda https://conda.anaconda.org/conda-forge/
jaxlib 0.7.2 cuda129_py311h6669c4c_200 165.6 MiB conda https://conda.anaconda.org/conda-forge/
jupyterlab 4.4.9 pyhd8ed1ab_0 8.1 MiB conda https://conda.anaconda.org/conda-forge/
leidenalg 0.10.2 py311h1ddb823_1 86 KiB conda https://conda.anaconda.org/conda-forge/
marimo 0.16.5 py311hf8ae3fa_0 28.6 MiB conda https://conda.anaconda.org/conda-forge/
pip 25.2 pyh8b19718_0 1.1 MiB conda https://conda.anaconda.org/conda-forge/
pixi-kernel 0.6.7 pyhbbac1ac_0 39.1 KiB conda https://conda.anaconda.org/conda-forge/
py-opencv 4.12.0 qt6_py311h44848da_604 1.1 MiB conda https://conda.anaconda.org/conda-forge/
pyro-ppl 1.9.1 pyhd8ed1ab_1 452.9 KiB conda https://conda.anaconda.org/conda-forge/
python 3.11.14 hfe2f287_1_cpython 29.4 MiB conda https://conda.anaconda.org/conda-forge/
python-igraph 0.11.9 py311hc282e73_1 1.5 MiB conda https://conda.anaconda.org/conda-forge/
pytorch-gpu 2.8.0 cuda129_mkl_h43a4b0b_301 46.2 KiB conda https://conda.anaconda.org/conda-forge/
scanpy 1.11.5 pyhd8ed1ab_0 1.9 MiB conda https://conda.anaconda.org/conda-forge/
scikit-misc 0.5.1 py311h262f814_3 163.4 KiB conda https://conda.anaconda.org/conda-forge/
scvi-tools 1.4.0.post1 pyhd8ed1ab_0 340 KiB conda https://conda.anaconda.org/conda-forge/
squidpy 1.6.5 pyhd8ed1ab_0 120.2 KiB conda https://conda.anaconda.org/conda-forge/
Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.
Minimal code sample (that we can run without your data, using public data)
https://github.com/BayraktarLab/cell2location/blob/master/docs/notebooks/cell2location_tutorial.ipynb
# list cell types and genes for plotting
ctypes = ['T_CD4+_TfH_GC', 'T_CD4+_naive', 'B_GC_LZ']
genes = ['CD3D', 'CR2']
with mpl.rc_context({'axes.facecolor': 'black'}):
# select one slide
slide = select_slide(adata_vis, 'V1_Human_Lymph_Node')
from tutorial_utils import plot_genes_per_cell_type
plot_genes_per_cell_type(slide, genes, ctypes);---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
[/tmp/ipykernel_64763/2598101914.py](http://127.0.0.1:8000/tmp/ipykernel_64763/2598101914.py) in ?()
6 # select one slide
7 slide = select_slide(adata_vis, 'V1_Human_Lymph_Node')
8
9 from tutorial_utils import plot_genes_per_cell_type
---> 10 plot_genes_per_cell_type(slide, genes, ctypes);
[~/git/pixi-envs/cell2loc/tutorial_utils.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/tutorial_utils.py) in ?(slide, genes, ctypes)
14 # plots of every gene
15 for j in range(n_genes):
16 # limit color scale at 99.2% quantile of gene expression (computed across cell types)
17 quantile_across_ct = np.array(
---> 18 [
19 np.quantile(slide.layers[n][:, slide.var["SYMBOL"] == genes[j]].toarray(), 0.992)
20 for n in slide.uns["mod"]["factor_names"]
21 ]
[~/git/pixi-envs/cell2loc/tutorial_utils.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/tutorial_utils.py) in ?(.0)
18 def plot_genes_per_cell_type(slide, genes, ctypes):
---> 19 n_genes = len(genes)
20 n_ctypes = len(ctypes)
21 fig, axs = plt.subplots(
22 nrows=n_genes, ncols=n_ctypes + 1, figsize=(4.5 * (n_ctypes + 1) + 2, 5 * n_genes + 1), squeeze=False
[~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py) in ?(self, key)
29 def __getitem__(self, key):
---> 30 index, new_shape = self._validate_indices(key)
31
32 # 1D array
33 if len(index) == 1:
[~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py) in ?(self, key)
279 if ix.shape != mid_shape:
280 raise IndexError(
281 f"bool index {i} has shape {mid_shape} instead of {ix.shape}"
282 )
--> 283 index.extend(ix.nonzero())
284 array_indices.extend(range(index_ndim, tmp_ndim))
285 index_ndim = tmp_ndim
286 else: # dense array
[~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/pandas/core/generic.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/pandas/core/generic.py) in ?(self, name)
6317 and name not in self._accessors
6318 and self._info_axis._can_hold_identifiers_and_holds_name(name)
6319 ):
6320 return self[name]
-> 6321 return object.__getattribute__(self, name)
AttributeError: 'Series' object has no attribute 'nonzero' 
The latest pypi version is 0.1.5, while on github release it is 0.1.4.
Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.
Minimal code sample (that we can run without your data, using public data)
https://github.com/BayraktarLab/cell2location/blob/master/docs/notebooks/cell2location_tutorial.ipynb
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) [/tmp/ipykernel_64763/2598101914.py](http://127.0.0.1:8000/tmp/ipykernel_64763/2598101914.py) in ?() 6 # select one slide 7 slide = select_slide(adata_vis, 'V1_Human_Lymph_Node') 8 9 from tutorial_utils import plot_genes_per_cell_type ---> 10 plot_genes_per_cell_type(slide, genes, ctypes); [~/git/pixi-envs/cell2loc/tutorial_utils.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/tutorial_utils.py) in ?(slide, genes, ctypes) 14 # plots of every gene 15 for j in range(n_genes): 16 # limit color scale at 99.2% quantile of gene expression (computed across cell types) 17 quantile_across_ct = np.array( ---> 18 [ 19 np.quantile(slide.layers[n][:, slide.var["SYMBOL"] == genes[j]].toarray(), 0.992) 20 for n in slide.uns["mod"]["factor_names"] 21 ] [~/git/pixi-envs/cell2loc/tutorial_utils.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/tutorial_utils.py) in ?(.0) 18 def plot_genes_per_cell_type(slide, genes, ctypes): ---> 19 n_genes = len(genes) 20 n_ctypes = len(ctypes) 21 fig, axs = plt.subplots( 22 nrows=n_genes, ncols=n_ctypes + 1, figsize=(4.5 * (n_ctypes + 1) + 2, 5 * n_genes + 1), squeeze=False [~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py) in ?(self, key) 29 def __getitem__(self, key): ---> 30 index, new_shape = self._validate_indices(key) 31 32 # 1D array 33 if len(index) == 1: [~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/scipy/sparse/_index.py) in ?(self, key) 279 if ix.shape != mid_shape: 280 raise IndexError( 281 f"bool index {i} has shape {mid_shape} instead of {ix.shape}" 282 ) --> 283 index.extend(ix.nonzero()) 284 array_indices.extend(range(index_ndim, tmp_ndim)) 285 index_ndim = tmp_ndim 286 else: # dense array [~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/pandas/core/generic.py](http://127.0.0.1:8000/lab/tree/~/git/pixi-envs/cell2loc/.pixi/envs/th/lib/python3.11/site-packages/pandas/core/generic.py) in ?(self, name) 6317 and name not in self._accessors 6318 and self._info_axis._can_hold_identifiers_and_holds_name(name) 6319 ): 6320 return self[name] -> 6321 return object.__getattribute__(self, name) AttributeError: 'Series' object has no attribute 'nonzero'