Reset calibration_metadata.yml before saving the initial calibration metadata

There was a reported issue for multiple dark processing that the second dark request for AGIPD fails.

I faced the same issue last days while testing for our next deployment for LPD, DSSC and AGIPD.

Description

When there is a dark request we create a new calibration_metadata.yml file. At the end of DSSC, LPD and AGIPD dark processing a key for modules-mapping is added by Overallmodules_darks_summary notebook.

After reprocessing again the same run using the same out-folder the calibration_metadata.yml file is not created properly.

https://git.xfel.eu/detectors/pycalibration/-/blob/master/src/xfel_calibrate/calibrate.py#L659

I don't really understand why this issue happening even though we are using "w" while create the yml file.

https://git.xfel.eu/detectors/pycalibration/-/blob/master/src/cal_tools/tools.py#L794

This is just a fix to reset the file and save the empty initialized dict before saving the metadata from calibrate.py. Until I understand more why this happens.

How Has This Been Tested?

Relevant Documents (optional)

I have added the malformed yml files. Line 84 is the line with the issue.

calibration_metadata_dssc.yml

calibration_metadata_lpd.yml

Types of changes

Checklist:

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Reviewers

@kluyvert @schmidtp