Job name normalization causing issues

[niklassiemer]

another thought: could be some inconsistency in the name normalization. For hdf5 file '-' seems replaced by m, in the job table, the '-' is still there. In the working directory, it becomes E20Vnmmtest_hdf/E20Vnm-test/ = some mixture.
I got confused by this at some point, that's why I had changed from minus to underscore. Yet, for me, minus is more convenient to type, so high chances I do this again.
Also, when I remove the job via pr.remove_job, the _hdf5 directory stays in place.

Originally posted by @freyso in pyiron/pyiron_atomistics#1422 (comment)

Looks like we have remaining troubles due to automatic job renaming if it comes to removal/restart of jobs!

[freyso]

while working on solving this, I STRONGLY recommend to fix up the error reporting in the present scenario. The file name of the h5 file being parsed should be reported with the exception. If this had been done, we might have found the cause earlier.

Better messages could be done by exception chaining:
https://realpython.com/python-raise-exception/#chaining-exceptions-with-the-from-clause

[samwaseda]

@freyso’s suggestion is pretty nice, but in my opinion we have a fundamental problem with the communication with files. Maybe it’s time to define something like FileObject that was recently moved to pyiron_snippets, that would take care of the file name conversion, so there is a clear layer and place where it takes place and we don’t have to worry about this kind of stuff in general.