CalibrationStore integration

[gdetrez]

Integrate the database backed CalibrationStore with Scan-o-matic.

• remove the "old" CalibrationStore from scanomatic.data_processing.calibration and the corresponding unit tests.
• refactor the calibration API to use the new store. That involved moving much of the corresponding tests to the integration suite.
• integrate the new store with the different jobs that use calibrations (mostly to validate the passed ID...) This was the most awkward part as I didn't find an easy way to pass the calibration store through all the factories and models to where it is needed without refactoring way too many things. So I ended-up creating a context manager that creates a store from the environment variables directly. This is not ideal but not worst that the previous situation. And it makes it work without refactoring the whole rpc server.

Tests

I successfully went through the calibration process. I successfully ran comile/analysis/feature extraction.

[codecov-io]

Codecov Report

Merging #325 into master will decrease coverage by 0.13%. The diff coverage is 85.41%.

@@            Coverage Diff             @@
##           master     #325      +/-   ##
==========================================
- Coverage   37.19%   37.05%   -0.14%     
==========================================
  Files         167      167              
  Lines       16592    16421     -171     
  Branches     2922     2894      -28     
==========================================
- Hits         6171     6085      -86     
+ Misses      10003     9931      -72     
+ Partials      418      405      -13

Impacted Files	Coverage Δ
scanomatic/ui_server/ui_server.py	0% <ø> (ø)	:arrow_up:
scanomatic/io/ccc_data.py	100% <ø> (+32.65%)	:arrow_up:
scanomatic/ui_server/data_api.py	0% <0%> (ø)	:arrow_up:
scanomatic/ui_server/calibration_api.py	31.08% <100%> (-0.24%)	:arrow_down:
scanomatic/data_processing/calibration.py	73.11% <100%> (+1.68%)	:arrow_up:
scanomatic/ui_server/database.py	100% <100%> (ø)	:arrow_up:
scanomatic/models/factories/analysis_factories.py	61.8% <100%> (+1.09%)	:arrow_up:
scanomatic/models/factories/scanning_factory.py	56.74% <100%> (+0.74%)	:arrow_up:
...omatic/models/factories/compile_project_factory.py	42.74% <50%> (+0.24%)	:arrow_up:
scanomatic/data/util.py	88% <85.71%> (+88%)	:arrow_up:
... and 5 more

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[gdetrez]

Was the extraction/analysis run with an actual CCC or with the default and do you estimate that it would make a difference?

The default, and as the default calibration is just inserted in the database, it shouldn't make a difference.