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Update tutorial.md to reference pulp version issue

Open jcf2 opened this issue 9 months ago • 2 comments

Tutorial steps did not work on my Python (3.9) as written, so if continuing to write them for "at least version 3.7" maybe this link to a workaround will help.

Proposed changes

After getting an error following the tutorial and searching it up, I located a fix in a snakebids issue. Linking to that might be one option to address this error coming up, without interrupting the current nice flow in the doc?

The error is specifically AttributeError: module 'pulp' has no attribute 'list_solvers' because list_solvers was deprecated in pulp v. 2 and removed in v. 3, and following the tutorial my snakemake install included 3.0.2.

Checklist

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  • [ ] Changes have been tested to ensure that fix is effective or that a feature works.
  • [ ] Changes pass the unit tests
  • [ ] I have included necessary documentation or comments (as necessary)
  • [ ] Any dependent changes have been merged and published

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jcf2 avatar Mar 14 '25 15:03 jcf2

Sorry, just realized I listed my local Python incorrectly as "3.8" when it is 3.9 (fixed above).

jcf2 avatar Mar 14 '25 15:03 jcf2

Thanks for bringing this up! We've known internally about this for a while but haven't noted it anywhere public yet.

I'll merge this for now. My preference will be to fix dependencies so that pulp install properly (doesn't look like we put an upper cap on it right now...).

I'm also going to update the tutorial to say minimum 3.9 as that's currently the lowest supported version.

pvandyken avatar Mar 18 '25 19:03 pvandyken

This is now supplanted by #477

pvandyken avatar Nov 05 '25 18:11 pvandyken