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Edinburgh-Genome-Foundry / DnaWeaver

A route planner for DNA assembly
https://dnaweaver.genomefoundry.org
MIT License
29 stars 9 forks source link

Update GoldenGateAssemblyMethod.py #11

Closed jlerman44 closed 3 years ago

jlerman44 commented 3 years ago

This was hardcoded to 4 bp, but I realized it should be self.overhang_size

jlerman44 commented 3 years ago

@Zulko @veghp - follow up to the previous release. I found 1 more spot where 4bp overhang was hard-coded. This should resolve that.

jlerman44 commented 3 years ago

@alexsongrj - FYI

veghp commented 3 years ago

Thanks, I merged into dev and also migrated to Travis com so it will run the CI properly now (Travis org is retired). PDF Reports adds a bit of an overhead to testing, but perhaps it's good to include anyways. The test fails on a certain pango_context_set_round_glyph_positions. Based on this conversation there may not be an easy solution.

I'll try and address it together with another issue, but any comments are welcome.

jlerman44 commented 3 years ago

@veghp - will the Debian stable (11, Bullseye) release with updated Pango solve the issue? It is referenced in the conversation you linked. I believe it comes out tomorrow. Building a lot of tools from source to try to solve the issue failed miserably in my hands.

veghp commented 3 years ago

Thanks -- I believe Travis uses Ubuntu. I specified a WeasyPrint version as recommended in their documentation, in the PDF Reports dependency. It passes build now. I'll have a look at another issue, then I will make a release.

jlerman44 commented 3 years ago

@veghp - awesome. We did a test in our wet lab, and this code definitely does a thing!

jlerman44 commented 3 years ago

@veghp - any chance you can push this to master & pypi sometime soon?

veghp commented 3 years ago

Fixing the other issue got delayed so I released v0.3.7 here and on PyPI now. Thanks for the patience