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Replace most print statements with equivalent log calls

Draisma, Arjan requested to merge replace_print_statements into develop

This replaces print statements that do not relate to any sort of progress bar (which are going to be replaced in a different PR)

I have tried my best to check whatever control flow I could, but this may still have some odd cases where debug statements are printed incorrectly. These do not affect log files, only the display in the console when running.

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