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Refactor progress bars #3470

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Run time

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Job	Run time
hierarchical (3.9)	2m 13s
julia (3.9)	5m 52s
hierarchical (3.11)	2m 5s
base (3.9)	6m 2s
julia (3.11)	5m 35s
docs (3.11)	2m 16s
base (3.11)	6m 2s
mac (3.11)	13m 52s
notebooks1 (3.9)	7m 57s
notebooks2 (3.9)	4m 2s
optimize (3.11)	2m 17s
petab (3.9)	13m 26s
petab (3.11)	13m 27s
quality (3.11)	1m 5s
select (3.9)	1m 46s
windows (3.11)	1m 13s
select (3.11)	1m 54s
	1h 31m 4s