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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
786 stars 273 forks source link

Python version survey #1230

Open jmarshall opened 1 year ago

jmarshall commented 1 year ago

At present, we build pysam wheels for Python 3.6 though 3.12.

Python versions 3.6 and 3.7 have reached end of life. While cibuildwheel continues to support them, we will likely continue building wheels for them; but note that supporting 3.6 is already holding pysam back somewhat (see e.g. fcb4c2deaddbc73c1e5e1c5081e32a05b714a3b0).

To inform our decision-making, it would be useful to get some idea of what Python versions pysam users are using. Please vote with a :+1: on the comments below corresponding to versions that you are using pysam with.

jmarshall commented 1 year ago

Python 3.6

jmarshall commented 1 year ago

Python 3.7

jmarshall commented 1 year ago

Python 3.8

jmarshall commented 1 year ago

Python 3.9

jmarshall commented 1 year ago

Python 3.10

jmarshall commented 1 year ago

Python 3.11

jmarshall commented 1 year ago

Python 3.12

nhansen commented 1 year ago

python >=3.7

dpoznik commented 1 month ago

Do you happen to have a timeline for adding Python 3.13 support?

jmarshall commented 1 month ago

When the next release occurs, which is imminent.

jmarshall commented 4 weeks ago

As the release/infra branch shows, there are no new changes needed to support Python 3.13. So I would expect that pip3.13 install pysam will work fine in the meantime with the existing release, if you have the build requirements installed. The next release will merely make this easier, by having prebuilt 3.13 wheels too.

dpoznik commented 4 weeks ago

Ah, yes. Sorry, I should have been more specific. I did find that pysam builds well under Python 3.13; I was mostly curious about the availability of prebuilt wheels, to speed up CI pipelines, etc. I searched through the issues and PRs but should have thought to check whether there was a working branch on the topic. Thanks so much for your work on the package!