Check for the presence of the Relion lock directory before accessing default_pipeline.star

[d-j-hatton]

Use a context manager to check for the presence of the .relion_lock directory before accessing the default_pipeline.star file. If it doesn't exist create it and remove it once the file has been read. If it does exist wait and try again; timeout after 20 attempts and store the information that there was a failure in the context manager. The method that reads the star file may then check for this failure and return an empty Document object instead of attempting to read the file. In the case of a failure the lock directory will not be removed on exit. Some restructuring has been done so that this lock is only applied when the file is actually being read and to allow the necessary information on which files to lock for to be passed from the Project class to the RelionPipeline class where the star file reading is done.

[codecov-commenter]

Codecov Report

Merging #87 (8b24bdd) into main (b92bb44) will increase coverage by 0.52%.
The diff coverage is 75.00%.

@@            Coverage Diff             @@
##             main      #87      +/-   ##
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+ Coverage   37.38%   37.90%   +0.52%     
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  Files          22       22              
  Lines        2798     2844      +46     
  Branches      428      433       +5     
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+ Hits         1046     1078      +32     
- Misses       1701     1711      +10     
- Partials       51       55       +4