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:

CuBIDS/cubids/cubids.py

Lines 392 to 393 in b8f5d47

	if "run" in list(entities.keys()) and "run-0" in filepath:
	entities["run"] = "0" + str(entities["run"])

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

[tsalo]

One workaround might be to use BIDSLayout's build_path method. That way we might not need to figure out how to parse these entities.