Improve error handling to only handle specific errors, also print sta…

Description

fixes #505 Basically, improved the read_run function and the ErrorHandler wrapper. Now the stacktrace is printed if in debug mode, and also if a step cannot be read, a logging warning is produced, but the rest of the steps are read, preventing the yellow screen of death.

Changes

only in disk_operator.py

Testing

Change the step_type of a valid run, or whatever you want to make the reading of that step fail, and see how that step does not appear in the run anymore, but the rest of the run is read correctly.

PR checklist

Development

[x] If necessary, I have updated the documentation (README, docstrings, etc.)
[x] If necessary, I have created / updated tests.

Mergeability

[x] main-branch has been merged into local branch to resolve conflicts
[x] The tests and linter have passed AFTER local merge
[ ] The code has been formatted with black

Code review

[ ] I have self-reviewed my code.
[ ] At least one other developer reviewed and approved the changes

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
disk_operator.py					20-21, 35, 114-116
protzilla/data_preprocessing
filter_proteins.py
outlier_detection.py
peptide_filter.py
transformation.py
protzilla/importing
peptide_import.py
protzilla/methods
data_preprocessing.py
importing.py					142
Project Total

cschlaffner / PROTzilla2