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I just fixed the bioconda recipe for pyscenic, including adding upstream packages to conda-forge and fixing the ctxcore recipe as well. It now installs and at least properly imports and runs the CLI help message.
But during the conda environment installation (micromamba create -n pyscenic pyscenic with the channels configured according to bioconda recommendations), it now still throws this warning:
Linking pyscenic-0.12.1-pyhdfd78af_1
warning libmamba [pyscenic-0.12.1-pyhdfd78af_1] The following files were already present in the environment:
- lib/python3.10/site-packages/resources/__init__.py
- lib/python3.10/site-packages/resources/delineations/__init__.py
- lib/python3.10/site-packages/resources/tests/__init__.py
- lib/python3.10/site-packages/resources/tests/c6.all.v6.1.symbols.gmt
I'm assuming this is because ctxcore also contains exactly those files. So I think something in the separation of ctxcore and pyscenic functionality is not quite right, and pyscenic might be using the wrong versions of something here. I don't have time to investigate further, but wanted to at least document this potential bug.
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