Scipion-em-reliontomo

Users:
- After having performed a refine or classification of particles, fields _rlnLogLikeliContribution,
_rlnMaxValueProbDistribution and _rlnNrOfSignificantSamples are registered, so they can be plotted versus the
no. particles using the data viewer and used as quality control metrics.
- Add extra params to some more protocols apart from refine subtomograms.
- Fix some initial MPI/Threads combinations (Thanks to Bram Koster).
- Rename the protocols the same as in native Relion.
- Enhancing the helps and use of RelionTomo4 (Thanks to J. L. Vilas).
- Validation conditions have been release and checked (Thanks to J. L. Vilas).
Developers:
- Tests rewritten using the test dataset relion40_sta_tutorial_data, using the Test Centralization Layer (TCL), and
decoupled in independent tests.
- Remove BETA status

Users:
- Hotfix: the protocol visualization on the left panel was fixed.
- Call the tlt file generation method considering the excluded views.
- Fix the 3d classification Scipion Classes objects generation (previous bad particle assignment).
Developers:
- Fix: the coordinates generated in the convert input step of the prepare data protocol are now float instead of
integer.

- Installation requirements better managed.
- Fix: Relion output now copies the acquisition.
- Fix: The sampling rate displayed for the initial volume was incorrect.
- Fix: FSC object stored unused data for the FSC viewer. That data was removed.
- Tests updated.

- Wizard to apply operation in relion particles
- 3D Classification defines its possible outputs
- An initio fixed (not using optimization set)
- Other FSCs are plotted in the refine and postprocess protocols

- 3D Classification more completed/standard
- 3D classes can be fed to mapback or others
- Refine and 3D classification use and register optimisation_set.star files

- Prepare more robust and optimized to subsets of coordinates and Tilt series. Still ctf could be added to the ecuation.