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I tried installing pyliger on a fresh conda env with different versions of Python and consistently failed to load the library. Steps to reproduce the problem:
> mamba create -n test python=3.10
> mamba activate test
> pip install pyliger
> python
>>> import pyliger
I got the following error:
/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/umap/plot.py:20: UserWarning: The umap.plot package requires extra plotting libraries to be installed.
You can install these via pip using
pip install umap-learn[plot]
or via conda using
conda install pandas matplotlib datashader bokeh holoviews colorcet scikit-image
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/pyliger/__init__.py", line 5, in <module>
from .plotting import plot_by_dataset_and_cluster, plot_gene, plot_gene_loadings, plot_spatial
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/pyliger/plotting/__init__.py", line 3, in <module>
from ._gene_loadings import plot_gene_loadings
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/pyliger/plotting/_gene_loadings.py", line 7, in <module>
from ..tools import calc_dataset_specificity, get_factor_markers
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/pyliger/tools/__init__.py", line 2, in <module>
from ._umap import run_umap
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/pyliger/tools/_umap.py", line 2, in <module>
import umap.plot
File "/Users/myusername/mambaforge/envs/test/lib/python3.10/site-packages/umap/plot.py", line 31, in <module>
raise ImportError(
ImportError: umap.plot requires pandas matplotlib datashader bokeh holoviews scikit-image and colorcet to be installed
By going to the mamba installation directory and removing the offending line I was able to circumvent the issue. Maybe a forgotten import statement that could be removed?
I tried installing pyliger on a fresh conda env with different versions of Python and consistently failed to load the library. Steps to reproduce the problem:
I got the following error:
By going to the mamba installation directory and removing the offending line I was able to circumvent the issue. Maybe a forgotten import statement that could be removed?
pyliger/src/pyliger/tools/_umap.py
Line 2 in 2ae9add
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