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althonos / pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
https://pyrodigal.readthedocs.org
GNU General Public License v3.0
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Conda availability of 2.2.0 and 2.3.0 restricted to Python 3.11 #41

Closed oschwengers closed 10 months ago

oschwengers commented 11 months ago

Hi Martin, thanks so much for this wonderful Prodigal replacement - we use it a lot!

Due to https://anaconda.org/bioconda/pyrodigal/files, Pyrodigal v2.2.0 and v2.3.0 are only available for Python 3.11.

Since we've included Pyrodigal in Bakta and other 3rd party-deps are not (yet) available for Python 3.11, this is a bit of a show-stopper. It would be very useful if the newer versions were also available for Python 3.8 - 3.10. Would that be possible?

Thanks again and best regards!

althonos commented 11 months ago

Hi @oschwengers !

This is strange because I just pushed an update for PyHMMER which was also updated to use Cython 3.0 now, and there I have Bioconda packages for Python 3.8 to 3.11. Any idea why packages are not being built for Python 3.8 - 3.10?

oschwengers commented 11 months ago

No, unfortunately, I have no clue why this is the case. But, due to https://anaconda.org/bioconda/pyhmmer/files, there is also no PyHMMER for Python 3.11. Maybe somehow related?

althonos commented 11 months ago

This is puzzling, I really don't know how Bioconda chooses the platform to build.

mencian commented 11 months ago

Greetings! I have edit the pyrodigal recipe to build on Python versions 3.8-3.10 and opened a PR over at bioconda-recipes.

althonos commented 11 months ago

Ah thank you @mencian !

oschwengers commented 10 months ago

Thanks to @mencian there are now Pyrodigal versions for both Linux and OSX for 3.8, 3.9, 3.10 and 3.11.