Doppio live processing requirements

[stephen-riggs]

Various changes are needed for doppio-live to work.

These are primarily connected to the job number assigned, as we need to be able to vary these if the default pipeline file is being changed by a user. For eBIC operations, the behaviour should be as before, but for doppio-live the jobs are assigned properly using ccpem-pipeliner.

Changes are also needed for the output motion corrected mrc file. The output path for doppio uses the pipeline star file to find a suitable job number. It currently does not include the GridSquare folder so may need changing again in future. The behaviour at eBIC should be unchanged.

Other bits:

• Removes the picker_murfey_id from the database tables
• Standardise to import murfey.server and not the _transport_object directly
• Typing hints

[codecov]

Codecov Report

❌ Patch coverage is 40.29851% with 200 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.83%. Comparing base (94ea29d) to head (a1ed499).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #790      +/-   ##
==========================================
- Coverage   54.89%   53.83%   -1.07%     
==========================================
  Files         104      104              
  Lines       11259    11673     +414     
  Branches     1490     1617     +127     
==========================================
+ Hits         6181     6284     +103     
- Misses       4753     5039     +286     
- Partials      325      350      +25     

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[Koldstream]

I've had a good look over and I feel pretty happy with it! I had forgotten how many changes had been made overall.

As discussed on Friday the logic for the paths in processing_params.py will need looking at, and further testing for the job reservation system... I'll have another look at this soon.

[tieneupin]

Looks good to me now. Nice work! 👍