Scipion-em-imod

Users:
- fix default params (close check default values 281 )
- change several form params from Enum to Boolean and from Float to Int, change default values from wrong str to int/float
- Protocol Import transformation matrix admits {TS} pattern
Developers:
- move constants to a dedicated file
- remove BETA status
- unify runProgram , use params dict
- unify close outputs step
- add possible outputs to all protocols
- reduce number of get() queries
- change several form params from Enum to Boolean and from Float to Int, change default values from wrong str to int/float
- do convert to float and normalize stacks in preXcorr
- fix newstack options: tapering, antialias etc.
- unify failed output set creation
- remove try/except decorator
- refactor tests code
- remove redundant store/write, getDim and other calls
- use indirect pointers
- use copyItems analog for creating outputs and updating their attrs
- implemented parallel steps for many protocols
- add a new batch of tests based TCL.
- some fixes from errors detected with the new tests.
- protocol excluded views: remove the in file option.

- CTF correction: get rid of the decorator. Manage the failed TS in the createOutputStep.
- Fix a bug in the base class for the generation of alignment files when there input TS are not aligned and there
aren't excluded views.
- Fix a bug in the generation of defocus files.

Users:
- Protocols' help added.
- Help of the parameters was enhanced.
- New feature: patch tracking alignment added.
- Trimming options in fiducial model added
- The order of the parameters in the forms was slightly modified according to the user actions.
- Protocol CTF correction:
* Now it can deal with excluded views in the CTF and/or in the TS.
* The same when entering with interpolated or not aligned TS.
* The xf, defocus, and tlt files are generated inside each TS extra sub-directory.
Developers:
- Update the acquisition order in the CTFTomo objects (field added to that class in scipion-em-tomo v3.7.0).
- Refactorization: avoid the excessive usage of getFirstItem.
- File generation methods (most of them in utils) adapted to the CTF-TS intersection functionality.
- Fixing sorted dictionary in ctf correction. How to access the defocus list in utils.py

- bugfix for import ctf, set missing defocus flag
- move plugin-specific import CTF protocol to the core
- add IMOD 4.11.25 version
- Prevent viewers from locking the screen focus.
- tilt series normalization: defines possible outputs
- tomo preprocess: always outputs mrc file