fixes #493
See Issue, and also improved the init function of Run as well as read_run.
Now
Changes
disk_operator.py: Added two methods, one for determining the validity of an existing file and another to delete all non-valid files. Also added logging via the protzilla logger.
Run class: fixed a confusing init function and improved the run_read, now it doesnt immediately write the run after reading it, and also fixed a bug regarding the df_mode not persisting and defaulting to "disk"
standard.yaml: removed the disk mode from the workflow file, which would cause issues
Testing
Now every file io operation is logged, so you can start a workflow with both df_modes and see what happens. I recommend also going back a couple steps and recalculating to see the deletion of now invalid files, and also recalculating the current method and changing instance identifiers and such.
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
[x] The code has been formatted with black
Code review
[x] I have self-reviewed my code.
[ ] At least one other developer reviewed and approved the changes
Description
fixes #493 See Issue, and also improved the init function of Run as well as read_run. Now
Changes
disk_operator.py: Added two methods, one for determining the validity of an existing file and another to delete all non-valid files. Also added logging via the protzilla logger. Run class: fixed a confusing init function and improved the run_read, now it doesnt immediately write the run after reading it, and also fixed a bug regarding the df_mode not persisting and defaulting to "disk" standard.yaml: removed the disk mode from the workflow file, which would cause issues
Testing
Now every file io operation is logged, so you can start a workflow with both df_modes and see what happens. I recommend also going back a couple steps and recalculating to see the deletion of now invalid files, and also recalculating the current method and changing instance identifiers and such.
PR checklist
Development
Mergeability
blackCode review