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blab / pathogen-embed

Create reduced dimension embeddings for pathogen sequences
https://pypi.org/project/pathogen-embed/
MIT License
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Why is bioconda recipe more constrained than setup.py? #27

Open corneliusroemer opened 1 month ago

corneliusroemer commented 1 month ago

I noticed that the bioconda pins are much more restrictive than the pins in setup.py

What's the reason for this? Can I relax the bioconda pins so that pathogen-embed doesn't constrain all the environments it's installed in, most notably nextstrain conda-base?

See setup.py constraints:

https://github.com/blab/pathogen-embed/blob/617a5619493c085136ff12639b82c25ea79f7348/setup.py#L26-L37

vs. bioconda recipe constraints:

    - python >=3.8
    - numpy >=1.24.4,<2
    - pandas >=1.2.0,<2
    - biopython >=1.83,<2
    - scikit-learn >=1.3,<1.5
    - umap-learn >=0.5.0,<0.6.0
    - numba <0.59.0
    - matplotlib-base >=3,<4
    - hdbscan >=0.8.36,<0.9.0

https://github.com/bioconda/bioconda-recipes/blob/127cf1a35701ee0a808af57380d515d4865a5ef5/recipes/pathogen-embed/meta.yaml#L27-L35

huddlej commented 1 month ago

@corneliusroemer It's an oversight on my part that setup.py isn't as constrained as the Bioconda recipe. I'd plan to eventually follow Augur's lead in that respect.

Are there specific packages in the Bioconda recipe that are causing issues in the Nextstrain conda recipe?