MDCatch

- separate mdoc parser, enable bigtiff header parser
- add Cryoassess for 2D cls sorting, use it by default
- create backup_selection.star so that user can see selected 2D classes
- create .gui_projectdir to automatically "start" a new project
- create .gui_manualpickjob.star so that user can visualize picking
- sortcl2d job check for accuracy
- add FEI MRC2 extended header support
- replace Ctffind & Gctf paths by shell vars
- switch off debug for release
- update Scipion template
- update documentation

• cleanup filtered mics for topaz and cryolo
• add distance arg = half box size (when provided) to cryolo job
• remove wait time
• add a counter to stop preprocess schedule if no new mics after 2 hours

• add different picker options: cryolo, topaz, logpicker
• add back the boxsize options to GUI
• simplified Schedules: preprocess (3 options) and class2d. No cryolo retraining is used for now. Class2d is run continuously (overwriting results) until 20k ptcls is reached, then a second class2d job is launched followed by cinderella sorting. Added frame grouping param if the dose per frame < 0.8 e/A2
• add parser tests
• fixed ACL set error

• SerialEM / Scipion launch fixes
• prints job time for external jobs
• fix "wrong" cryolo model, gpu args
• batch increased to 15
• add topaz external job (not used yet)
• fix save_noDW
• use MPIs for ctffind job

- set ACL
- move more vars to config file
- major Schedules update for relion 3.1: logpicker replaced by cryolo, cinderella added
- replace symlink by copy for small files
- remove boxsizes and until_ctf options
- speed up recursive file search (replace os.walk by iglob)
- fix gain file detection
- fix wrong mask size
- update README
- add daemon mode
- fix schedules abort/stop
- new deps: emtable, watchdog

Added parsing for MRC: standard and FEI1 extended header. BigTiff parsing works but not used for now. Some code refactoring for the parser, small fixes.

First pip release

0.9.2:
- Scipion 3 scheduling works, however relion 3.1 is not ready for streaming
- added more parameters to xml parser: VPP options, gun lens, spot size, beam size, EPU version
- fix "do until ctf"

0.9.1:
- refactored xml parser, now it should not depend on EPU version
- launching Relion schedules in a separate subprocess, return shell immediately
- code clean up
- fix wrong ptcl diameter for preprocess schedule
- remove shell=True to increase security
- initial preparation for scipion 3 workflow
- created SCOPE_DICT, now parser is not LMB-specific