Command line interface for
This module provides the command line interface for
consisting of the
showyourwork command and various subcommands.
All commands and subcommands are executed within an isolated conda environment
running the version of
showyourwork specified by the article’s
setting. This allows users running any version of
showyourwork to build any
Modify the call from showyourwork … to showyourwork build… if the user didn’t explicitly provide a valid subcommand or option.
Click can in principle handle this (the @click.group decorator accepts an invoke_without_command option) but if we do that I don’t _think_ we can simultaneously set ignore_unknown_options. We need to be able to forward unknown options directly to snakemake.
This hack allows users to call, e.g.,
showyourwork build –rerun-incomplete
(the invocation they had to use previously). We allow this by injecting the build subcommand into sys.argv prior to click taking control.