Add progress bar for bagel bids

[alyssadai]

The bids command is currently very slow even for a few hundred subjects, primarily due to pybids (specifically the steps initializing the BIDS dataset). To make this more user-friendly we should add a progress bar for sub-processes of this command where possible.

Since the BIDSLayout step does not have an easily accessible iterative process from which to track progress, we should instead consider implementing this for the for loops we use to merge subject-level BIDS and phenotypic info.

https://typer.tiangolo.com/tutorial/progressbar/

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[github-actions]

We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
We have applied the _flag:stale label to indicate that this issue should be reviewed again.
When you review, please reread the spec and then apply one of these three options:

• prioritize: apply the flag:schedule label to suggest moving this issue into the backlog now
• close: if the issue is no longer relevant, explain why (give others a chance to reply) and then close.
• archive: sometimes an issue has important information or ideas but we won't work on it soon. In this case
  apply the someday label to show that this won't be prioritized. The stalebot will ignore issues with this
  label in the future. Use sparingly!