Skip to content

[BUG] src/resources/ contents already provided by ctxcore #630

@dlaehnemann

Description

@dlaehnemann

Describe the bug
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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions