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clauswilke / PeptideBuilder

A simple Python library to generate model peptides
MIT License
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Added upper limit to Biopython version #12

Closed George3d6 closed 4 years ago

George3d6 commented 4 years ago

Doesn't work with the latest biopython version (1.76) due to issues importing bio.PDB.Vector, not 100% sure how to fix those without breaking something else, but I think putting and upper limit of the biopython would help for now (1.71.0 is the latest version I found that works).

clauswilke commented 4 years ago

Which version of the code are you using? We merged a fix for this recently, I believe (#11). I don't ever use this code anymore, but I'd rather fix it to work with the latest version of biopython than put a version restriction on it.

George3d6 commented 4 years ago

PeptideBuilder.__version__ says 1.0.4, which seems to be the latest version on pypi. Even if you want to keep it up to date, it might be worth adding "latest version it was tested with" to the README, since it depends on a library with an unstable API.

clauswilke commented 4 years ago

Please try github master. I know I need to do a new release, I just haven't gotten around to it yet.

mtien commented 4 years ago

I forgot about this request.

The newest version of biopython changed the class from Bio.PDB.Vector to from Bio.PDB.vectors. Import statement with the newest biopython version should be from Bio.PDB.vectors import *

clauswilke commented 4 years ago

That has been fixed already: https://github.com/mtien/PeptideBuilder/blob/314611d1f377edfe6b6ea7a48181678b6c025faf/PeptideBuilder/PeptideBuilder.py#L22

I'm going to close this PR because the right way forward is to fix PeptideBuilder so it works with the latest releases of the required dependencies.