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althonos / pyhmmer

Cython bindings and Python interface to HMMER3.
https://pyhmmer.readthedocs.io
MIT License
129 stars 12 forks source link

Production stable or WIP #45

Open oschwengers opened 1 year ago

oschwengers commented 1 year ago

Hi Martin, thanks a lot for this wonderful Python bindings project (and all others). We're keen to use this to replace HMMER in Bakta and we're quite happy with the results so far. However, I only have one last question regarding your statement in the readme This library is still a work-in-progress, and in an experimental stage, ...

Since this is already published, could you comment on and maybe clarify whether we could/should use this for production purposes in Bakta? We're only using the hmmsearch mode. So if this is stable, we'd be happy to use this.

Again, thanks a lot and best regards, Oliver

althonos commented 1 year ago

HI Oliver! True, this package has been in development for some time and is now published, and I should probably remove this warning message, it's been there since v0.1.0 in 2020 :sweat_smile: There may still be some changes to the API before I actually publish a v1.0, including the Sequence and Alphabet handling. However, I've been using this in production for GECCO and some other private projects so I'd say it's okay to use, in particular if that's for hmmsearch. I'm also happy to help with debugging if you have some issues with downstream users :+1: