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Refactoring 2021.1 -> 2021.2

Pierre Paleo requested to merge refactoring_2021.1 into master

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This MR is a refactoring of the codebase (close #225 (closed) ).
This is a required step for implementing a well-defined XRD-CT pipeline. But the first deliverable of XRD-CT pipeline can be a set of scripts based on nabu <= 2021.1.0.

It also brings the cuda backend for GroupedPipeline.

To do

  • Refactor the configuration file ingestion according to this scheme
  • Move resources.cli to app
  • Create nabu.pipeline with fullfield and xrdct
  • Rename/move the pipeline classes with more understandable names
  • Move preproc.sinogram to reconstruction.sinogram
  • Get rid of unnecessary inheritance schemes (CCDProcessing, SinoProcessing, etc)
  • Set FlatField class default behavior
  • Remove occurrences of __have_scipy__
  • Move/rename phase retrieval classes
  • Ensure backward compatibility with <= 2021.1.0
  • Populate some __init__.py files for shortcuts
  • Ensure all unit tests pass
  • (Bonus) Cuda backend for GroupedPipeline (close #251 (closed) )
  • (Bonus) Integrate multi-angle auto-CoR
  • Start to lift limitation "even number of angles for half tomography"
  • End-to-end reconstruction test
Edited by Pierre Paleo

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