Rebuild for python 3.13

[regro-cf-autotick-bot]

This PR has been triggered in an effort to update python313.

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[conda-forge-webservices]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe/meta.yaml:

• No valid build backend found for Python recipe for package biopython using pip. Python recipes using pip need to explicitly specify a build backend in the host section. If your recipe has built with only pip in the host section in the past, you likely should add setuptools to the host section of your recipe.

[peterjc]

ModuleNotFoundError: No module named 'setuptools'

[peterjc]

This is still not finding setuptools.

Note even if it did get further, we have an expected failure in the C code now on Biopython 1.84 with Python 3.13, see biopython/biopython#4706 (comment)

[jakirkham]

Thanks Peter! 🙏

We need to move setuptools to requirements/host. Included suggestions below

More details in issue: conda-forge/conda-forge.github.io#2252

[conda-forge-admin]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

[jakirkham]

Thanks Peter! 🙏

Looks like that helped 😄

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We are now seeing a new error on CI:

import: 'Bio.cpairwise2'
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/biopython_1729769090684/test_tmp/run_test.py", line 152, in <module>
    import Bio.cpairwise2
ImportError: /home/conda/feedstock_root/build_artifacts/biopython_1729769090684/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.13/site-packages/Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so: undefined symbol: PyEval_CallObject

The error is pointing out that PyEval_CallObject was removed in Python 3.13. Here is the relevant release entry:

Remove various functions deprecated in Python 3.9:

• PyEval_CallObject(), PyEval_CallObjectWithKeywords(): Use PyObject_CallNoArgs() or PyObject_Call() instead.

Looks like this may have already been fixed upstream ( biopython/biopython#4706 ). Though it doesn't appear to be in a release yet. Perhaps following up with upstream on a new release would be the next step

[peterjc]

Excellent - that's the expected failure I was alluding to earlier, #49 (comment)

We have started talking about Biopython 1.85 https://lists.open-bio.org/pipermail/biopython/2024-September/017067.html but there are still some other loose ends to settle.

We could backport the fix here in the Biopython 1.84 recipe if there was demand...

[jakirkham]

Thanks Peter! 🙏

Missed that note

If that is the only needed change, it seems reasonable to include

GitHub has a neat trick to create a patch, which is to take a PR URL and add .patch. Then it will generate a patch for it

For example: https://github.com/biopython/biopython/pull/4706.patch

We could include that here with a comment referencing the PR. The next release would generate a conflict, which would be a good reminder to drop the patch (simple to do)

That said, if you would rather have this in a proper release and align support across distributions. Would understand that perspective as well

[peterjc]

I like the patch idea - the Biopython release is at least a week away (based on my availability) without checking with the other maintainers on new potential blockers.