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 38.67596% with 176 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.67%. Comparing base (e1ae7ee) to head (b821126).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #790      +/-   ##
==========================================
- Coverage   54.71%   54.67%   -0.04%     
==========================================
  Files         104      104              
  Lines       11185    11262      +77     
  Branches     1481     1485       +4     
==========================================
+ Hits         6120     6158      +38     
- Misses       4740     4774      +34     
- Partials      325      330       +5     

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