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josiahseaman / FluentDNA

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
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Python 3.7+ issue with `os` import of `errno` #93

Closed aganezov closed 4 years ago

aganezov commented 4 years ago

On python version 3.7, 3.8 on MacOS, errno import from os module raises an ImportError, which happens when running FluentDNA main example with chr19 fasta input.

josiahseaman commented 4 years ago

Thanks for posting this error. Mac testing has been challenging. I'll look into this right away.

"Several undocumented internal imports were removed. One example is that os.errno is no longer available; use import errno directly instead. Note that such undocumented internal imports may be removed any time without notice, even in micro version releases." Docs

Normally I'd expect a deprecation warning, but I guess it's my fault for not having cross-version, cross-platform continuous integration.

josiahseaman commented 4 years ago

@aganezov Would you mind testing the same command now from the python-master branch? We're also testing it on the mac 3.7 environment we have here.

pip install --upgrade git+https://github.com/josiahseaman/DNASkittleUtils pip install --upgrade git+https://github.com/josiahseaman/FluentDNA.git@python-master

./fluentdna --fasta="FluentDNA/example_data/Human selenoproteins.fa"

Thank you so much for pointing this out. Once I'm done testing I'll push the fix to pip and PyPI.

josiahseaman commented 4 years ago

Update: The same error existed on DNASkittleUtils, so I fixed it and pushed the change to PyPI. These commands should resolve the issue.

pip install --upgrade DNASkittleUtils pip install --upgrade git+https://github.com/josiahseaman/FluentDNA.git@python-master

josiahseaman commented 4 years ago

This is now in the latest pip and Release versions.