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4dn-dcic / tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
MIT License
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Support for Python 3.12 #406

Closed dmichaels-harvard closed 3 months ago

alexander-veit commented 3 months ago

I am getting SyntaxWarnings at various places when using Python 3.12, e.g., 

/home/ubuntu/GitHub/tibanna/tibanna/awsem.py:396: SyntaxWarning: invalid escape sequence '\.'
  filename = re.match('(.+)\.{0}$'.format(unzip), filename).group(1)

This is exptected with Python 3.12: https://docs.python.org/dev/whatsnew/3.12.html#other-language-changes I think we need to use raw strings instead.