[Bug]: Warnings are being omitted if pynxtools is re-imported

[rettigl]

Contact Details

No response

What happened?

If pynxtools is imported twice (e.g. because of auto-reload), many warnings are not being printed. This is probably an issue with the logger setup.

Relevant log output

Import pynxtools using 
%load_ext autoreload
%autoreload 2

First conversion:
convert(input_file=("NXmpes_config_v1.json", "Scan1496.yaml"), reader="mpes", nxdl="NXmpes_arpes", objects=(res_xarray,), output="test.nxs")

Using mpes reader to convert the given files:  
• NXmpes_config_v1.json
• Scan1496.yaml
Main element /ENTRY[entry]/notes/description not provided. Removing the parent group /ENTRY[entry]/notes.
Main element /ENTRY[entry]/experiment_documentation/description not provided. Removing the parent group /ENTRY[entry]/experiment_documentation.
Could not find value for key /ENTRY[entry]/experiment_description with value ['@eln:/ENTRY/identifier', '@attrs:metadata/entry_identifier', '@attrs:metadata/elabFTW/project/title'].
Tried prefixes: [('@eln', '/ENTRY/identifier'), ('@attrs', 'metadata/entry_identifier'), ('@attrs', 'metadata/elabFTW/project/title')].
Could not find value for key /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay with value @attrs:metadata/scan_info/delay.
Tried prefixes: [('@attrs', 'metadata/scan_info/delay')].
WARNING: The value at /ENTRY[entry]/INSTRUMENT[instrument]/MANIPULATOR[manipulator]/sample_bias_voltmeter/measurement should be one of the following: ['voltage']
WARNING: The data entry corresponding to /ENTRY[entry]/data/temperature is required and hasn't been supplied by the reader.
WARNING: The data entry corresponding to /ENTRY[entry]/data/delay is required and hasn't been supplied by the reader.
WARNING: The data entry corresponding to /ENTRY[entry]/core_levels is required and hasn't been supplied by the reader.
WARNING: Field /ENTRY[entry]/energy_axis_calibration/program written without documentation.
WARNING: Field /ENTRY[entry]/energy_axis_calibration/version written without documentation.
WARNING: There were attributes set for the field /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay, but the field does not exist.
WARNING: The attribute /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay/@units will not be written.
WARNING: There were attributes set for the field /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay, but the field does not exist.
WARNING: The attribute /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay/@reference_beam will not be written.
The output file generated: test.nxs.

Now change something in the pynxtools source (e.g. adding a blank line, I did in the helpers.py file). This is auto-reloaded.

Now convert again:

Using mpes reader to convert the given files:  
• NXmpes_config_v1.json
• Scan1496.yaml
Main element /ENTRY[entry]/notes/description not provided. Removing the parent group /ENTRY[entry]/notes.
Main element /ENTRY[entry]/experiment_documentation/description not provided. Removing the parent group /ENTRY[entry]/experiment_documentation.
Could not find value for key /ENTRY[entry]/experiment_description with value ['@eln:/ENTRY/identifier', '@attrs:metadata/entry_identifier', '@attrs:metadata/elabFTW/project/title'].
Tried prefixes: [('@eln', '/ENTRY/identifier'), ('@attrs', 'metadata/entry_identifier'), ('@attrs', 'metadata/elabFTW/project/title')].
Could not find value for key /ENTRY[entry]/INSTRUMENT[instrument]/beamTYPE[beam_pump]/pulse_delay with value @attrs:metadata/scan_info/delay.
Tried prefixes: [('@attrs', 'metadata/scan_info/delay')].
The output file generated: test.nxs.