`cubids-apply` adds extra leading zero to run entity

[tsalo]

In my case, it tried to rename sub-03_ses-1_task-rest_acq-multiecho_run-02_echo-1_part-mag_bold.nii.gz to sub-03_ses-1_task-rest_acq-multiechoVARIANTNumVolumes_run-002_bold.nii.gz. Note the shift from one leading zero to two.

This seems to be due to this section of CuBIDS.change_filename:

https://github.com/PennLINC/CuBIDS/blob/b8f5d47d64ba86506880a58249929ab13000c54a/cubids/cubids.py#L392-L393

EDIT: This only happens if the run entity includes leading zeroes. Also, it doesn't account for multiple leading zeroes.

[mattcieslak]

I think we don't want this to happen