zero padded run numbers in output files

[jmumford]

Likely not the most elegant solution, but it works. Michael will test on some other data sets and then I'll let you know if it works without errors on those data.

I've encountered an issue with pybids where graph.layout.entities['run'].files does not consistently include the derivative entities, which may be used in an attempt to retrieve the padded run number. I have a workaround that seems stable.

Note, it seems older fmriprep may produce output files where run numbers are not zero padded while the BIDS data did have zero padded run numbers. In this case it is a bit random whether or not the fitlins output files will have zero padded run numbers, depending on whether or not the derivative entities were included in graph.layout.entities['run'].files.keys(). Probably not a big deal.

black changed a lot, my addition starts on line 284.