Refactor subcommand calls in rotary repair.py

rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements

BSD 3-Clause "New" or "Revised" License

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Refactor subcommand calls in rotary repair.py #66

Closed LeeBergstrand closed 10 months ago

LeeBergstrand commented 10 months ago

Addresses: https://github.com/jmtsuji/rotary/pull/63#discussion_r1368078767

Move subcommand.run to a function
Move logger.debug() call before subcommand.run into the function so it can be edited in one place.
Make check=True to be the fault behaviour when calling a subcommand by moving it into the function. Now it be left out.
Move std.stdout into the function so one can pass the output from the prior command directly into the subcommand call.

LeeBergstrand commented 10 months ago

@jmtsuji See: https://github.com/jmtsuji/rotary/pull/63#discussion_r1369418086

LeeBergstrand commented 10 months ago

@jmtsuji I could only use Pycharm's automated refactoring tools (https://www.jetbrains.com/help/pycharm/refactoring-source-code.html) to do these edits. If you could go through this code in review to make sure I mapped all the commands properly that would be great. Also, once the conflicts are resolved, I would re-run your test to ensure nothing breaks.