Use pathlib #31
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Use pathlib #31
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…Path objects as input or log files.
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Convert all input, outputs, and log statements to use pathlib instead of working with paths as strings.
A few minor annoyances, however; Snakemake support for pathlib is currently not complete, most promimently, expand statements and log file declarations cannot use pathlib objects at the moment, so they are explicitly converted to strings in the rule files. I plan to change this when Snakemake becomes fully compatible further on.
I also introduce the develop branch in this PR, intending that the master branch of the repo should be considered stable and will only receive commits when enough new features have been added to the develop branch.