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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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pip check reports cython as a requirement #898

Closed Midnighter closed 1 year ago

Midnighter commented 1 year ago

I have a bioconda package that depends on biom-format. Among its tests is a pip check which reports cython as missing.

I see two possible solution:

  1. Add cython to the conda-forge biom-format feedstock as a run dependency. I think, this is the worse solution.
  2. Remove cython from the install_requires. You already list it in pyproject.toml and cython is imported by setup.py itself. So at that point it's too late to install the requirement anyway. I consider this the better option. Unless, of course, cython is truly needed at runtime but I don't see why that would be the case.
wasade commented 1 year ago

Thanks, @Midnighter! This is a historical carryover from very early in the project where managing Cython code was a bit different. I agree that (2) is a much better way to go about it.

How urgent is this?

Midnighter commented 1 year ago

I've disabled the pip check for now in order to proceed with the recipe.

Since it's a pretty small change, I can also create a PR for it if you like.

wasade commented 1 year ago

Oh, that would be really helpful, thank you!