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Written by victorjavierlo on 2024-11-09 at 21:29

Do you recommend any good resources or code examples on how to upload a package to conda-forge? #conda #bioinformatics

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Written by Peter Cock on 2024-11-09 at 22:51

@victorjavierlo no, but I’ve done a few. I would start by looking at packages in the same language with similar dependencies/build systems.

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Written by victorjavierlo on 2024-11-10 at 08:50

@pjacock It is a Python package.

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Written by Peter Cock on 2024-11-10 at 09:51

@victorjavierlo pure Python, nothing you need to compile? That should be easy 🤞

Next question, general (conda-forge) or bioinformatics/biology specific (bioconda)? Example of latter is https://github.com/bioconda/bioconda-recipes/tree/master/recipes/thapbi-pict with just a metadata file.

The details of how to submit and maintain the recipe differ, but the metadata yaml is practical the same.

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Written by Peter Cock on 2024-11-10 at 09:52

@victorjavierlo Now, are all your dependencies in conda? BioConda packages can depend on either BioConda or conda-forge, but conda-forge ones should only depend only on others from conda-forge

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Written by victorjavierlo on 2024-11-10 at 14:11

@pjacock I was thinking in conda-forge.

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Written by victorjavierlo on 2024-11-10 at 14:13

@pjacock This is the package https://github.com/victorsanchezarevalo/pymportx/

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Written by Peter Cock on 2024-11-10 at 17:44

@victorjavierlo That looks like an excellent fit to BioConda to me, but a stretch from conda-forge.

Either way, it looks the the first hurdle is there is no Python package defined for people to install. Nowadays that means a pyproject.toml file, until recent done with a setup.py

Next you’d typically be releasing the code on PyPI so that “pip install pymportx” works. You don’t have to release on PyPI, but it would be best practice.

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