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phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
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ImportError: cannot import name 'PathLike' #53

Open zhao-xinlu opened 1 year ago

zhao-xinlu commented 1 year ago

I am installed conga in 29. Oct 2022 following conga readme.md.

conda create -n conga_new_env ipython python=3.6 conda activate conga_new_env # or: "source activate conga_new_env" depending on your conda setup conda install seaborn scikit-learn statsmodels numba pytables conda install -c conda-forge python-igraph leidenalg louvain notebook conda install -c intel tbb # optional pip install scanpy pip install fastcluster # optional conda install pyyaml #optional for using yaml-formatted configuration files for scripts

I activated the conga_new_env, and run code from "Seurat_to_Conga.ipynb". It report an errer : "Seurat_to_Conga.ipynb" when i run the first line "import scanpy as sc"

My python version info is: Python 3.6.15 | packaged by conda-forge | (default, Dec 3 2021, 18:49:41) IPython 7.16.1 -- An enhanced Interactive Python.

Mybe the python version is too old?

Thanks.

sschattgen commented 1 year ago

PathLike was implemented in 3.6 so I'm not sure if that's the issue. https://docs.python.org/3/library/os.html#os.PathLike Nonetheless, you can certainly try moving up in version and see if that helps. I use 3.8 currently, myself.