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Since progress indication is not part of the parsing, this commit
extracts the progress indication into functions with well defined
input arguments that hide the progress indication logic from the
parsing function.
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Use the new code that collects the errors in the CLI client.
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- Use a way faster way of parsing the strains file
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While the application is developed with GNU Guix, the end user might
not be using it, and therefore, this commit provides a way for the
user to install the application with the usual python package
management systems.
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