apply and copy-exemplars functions can't parse command-line input correctly

[gabridele]

Summary

Following the Example Walkthrough, when I tried to run the apply function, by putting the filenames as positional arguments instead of their paths, the terminal raised an issue claiming that those paths didn't exist. As far as I understood, the reason behind this is the type of parsing being carried out: in the cli.py script, the parser makes use of _is_file function defined in line 26, that calls _path_exists function at line 19 that checked for the existence of the path. I ran into the same issue when I was trying to run the copy-exemplars command.

Additional details

• CuBIDS version: 1.1.1 (git cloned latest version as of November 25th)
• Datalad version: 1.1.4

What were you trying to do?

I was trying to run the apply and copy-exemplars functions

What did you expect to happen?

I expected the apply function to apply the changes I suggested. Likewise, I expected copy-exemplars command to produce an exemplar dataset.

What actually happened?

Program couldn't find these files just from their filename (as it's explained in the documentation). Also, in apply when I provided the name of the directory of the exemplar dataset (directory to be created), it raised an error telling me that the path doesn't exist. To my understanding of the tutorial, the user should be able to provide the name of the directory and the cubids library would take care of creating it and turning it into a datalad dataset.

Reproducing the bug