PyPI release?

[rly]

Is your feature request related to a problem? Please describe. I am using oaklib in a project and import oaklib results in:

tests/unit/test_term_set.py:17: in <module>
    import oaklib  # noqa: F401
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/oaklib/__init__.py:11: in <module>
    from oaklib.selector import get_adapter, get_implementation_from_shorthand  # noqa:F401
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/oaklib/selector.py:16: in <module>
    from oaklib.implementations import GildaImplementation
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/oaklib/implementations/__init__.py:20: in <module>
    from oaklib.implementations.ncbi.ncbi_gene_implementation import NCBIGeneImplementation
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/oaklib/implementations/ncbi/ncbi_gene_implementation.py:14: in <module>
    from oaklib.implementations.ncbi.eutils_implementation import EUtilsImplementation
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/oaklib/implementations/ncbi/eutils_implementation.py:9: in <module>
    from eutils import Client
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/eutils/__init__.py:4: in <module>
    import pkg_resources
../../../miniconda3/envs/temp2/lib/python3.12/site-packages/pkg_resources/__init__.py:98: in <module>
    warnings.warn(
E   DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html

This was fixed in #176 in April but has not yet been released. The last release of eutils, 0.6.0, was in 2019. There have been a few commits to this repo since then such as merging #176. Could you release a new version of eutils soon?

This is not a big deal, but we would like to not raise warnings in our library or its dependencies that may confuse end-users if possible. Thanks!

[jsstevenson]

Hi! I keep forgetting to get this done. I'll do a final check to make sure things are as they should be this week and try to get one out.

(edit: I have stepped back from the biocommons project for a while; please check with another maintainer)

[MarcoAigner]

"pkg_resources is slated for removal as early as 2025-11-30".

For now I am going to suppress the deprecation warning, but think that pypi package should be updated in due time. Thank you! :)

[rly]

Just want to check in here. Let me know if I can help with the release in any way.

[koopmann]

Release would be great, also in pyproject.toml it currently says: [project] name = "biocommons.eutils"

i guess it should be "eutils" right?

[itrujnara]

Is there any progress on this? As of today, the package does not work with Python 3.13 unless setuptools is installed separately, and even in that case, it raises a UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html..

[reece]

Hi All. I'm working on this. Here are known needs:

• #178: Update python-packaging template. For other repos, this is about consistency. In this case, it's also needed because the ci-cd pipelines and build process are so old that they don't work any more.
• #177: Also due to staleness, a number of tests seem to be failing. I need to investigate why.

As of now, that's all that's truly needed to get a release out.

[reece]

I pushed a new release, 0.6.1. It's now available in PyPI at https://pypi.org/project/eutils/0.6.1/.

I've also opened a discussion about archiving this package. IMO, eutils has outlived its utility. Rationale and invitation to comment at https://github.com/biocommons/eutils/discussions/205.