Fixes #1050 (closed)
TODO
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Make all the linters happy ( pylintis the most difficult but has good suggestions) -
Make sure the scripts are still working (some changes are at least somewhat non-trivial) -
bin/testing(can be decently tested by running CI with some fake change) -
bin/postprocessing-> manual testing (partially tested) -
extract_module-> manual testing -
create_docker-> manual testing (partially tested)
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