Scipion-em-relion

- initial EER support for motion correction and polishing, not available yet
- consider hot pixels from relion mc for polishing
- refactor mc protocol and viewer
- replace xmipp by eman2 for psd calculation
- add 3.1.2 binary
- remove Relion 3.0 protocols and code, but users can still import old star files
- fix 278, 274, 277, 257
- add a test to read old star format
- fix shifts conversion for pre-3.1 (origins are in px already)
- fix accuracy label, use Angstroms by default
- add a warning about polishing gain bug
- subtract protocol supports non-Relion input (thanks rmarabini)
- add a protocol to "gentle clean" all Relion jobs

- quick fixes for issues from PR 282, 283 (thanks to rmarabini)

- Scipion 3.0.0 support, migration to python 3
- GPLv2 to v3
- Add Relion 3.1 support, remove relion 2.x support
- New STAR file parser (emtable package)
- New protocol to assign optics groups
- Sort protocol will be deleted soon (gone in relion 3.1)
- Extract particle movies is gone
- Updated drift plot for motioncor, added new plot for drift per frame
- convertMask changed so that it uses relion_image_handler to change box/pix size/threshold
- movie refinement is gone and fully replaced by bayesian polishing
- picker protocols code cleanup
- get rid of shell=true in subprocess
- refactor viewers code
- xmipp metadata is gradually replaced by the Table class from new star file parser
- new protocol to export coordinates to star format
- new protocol to remove preferential views
- new protocol to compress movies
- new protocol to resize / rescale volume
- add new Falcon 4 MTFs
- updated extra labels list for particles
- set PARTICLE_EXTRA_LABELS inside ClassesLoader and refine3d _updateParticle
- fill random subset by default
- Autoscale input vol refs with relion not xmipp
- Add missing ProtRelionExportParticles to protocol tree
- Fix default values for missing extra ctf attrs
- Use abs paths when creating symlinks
- Add warning about dm4 gain flip by xmipp
- Optimize imports
- Assign gain and defects file from input or star file, transform gain if required
- use getVar for cuda vars
- update optics from image set upon conversion
- fix wrong MicrographOriginalPixelSize
- update priors help
- add PSD calculation for mc
- add missing frame grouping param for mc
- picking wizards removed
- optimize mode removed in relion reference-based picker
- fix --odir param for pickers
- add min_avg_noise to picker
- add skip_gridding to 3d jobs (True by default)
- add missing flatten_solvent to init3d
- remove unrequired params from polishing
- add RELION_CUDA_LIB var
- Hide Allow coarser sampling if doing no alignments
- Hide some args in continue mode for classification/refinement/init model protocols
- Fix healpix arg for autopicking, add missing ctf param
- Fixed matching between particles and movies by using micName in polishing
- Fixed generation of the local motion table when needed (e.g when only some movies failed to align)
- Allowed to display ctf-refinement results with matplotlib (still need to find the proper color map)
- Fixed function splitCTFGroups, now replaced with class DefocusGroups and not using Xmipp metadata
- Now use proper pixelSize label depending on input set
- Remove failing reconstruct rot-shift-flip test as we don't support flip in 3D
- add the colorScale wizard to the LocalRes viewer
- chimeraX support
1.0.9: Fixed multibody output bug. Added a test for it.