united layout with other tools from doctopts to argparse, no more natsort, separete folder for config

Daniel Guderian authored 4 years ago and Stefan Reck committed 4 years ago

event id and run id are nowints and no more arrays in the y info. this caused a problem and is solved by taking [0] of it

- remove correct_timeslew (this is part of kp.calib now)
- subtract t0 from mchit times for now

- column_names of point maker no longer saved as title, but as attributes --> auto read out in OrcaNet
- properly implement h5shuffle in tools and add unittests
- concatenate copies over attributes
- add option to keep dtype of mcinfo
- now all infos in the blob are kept for the mc_info_extr, including classical reco
- add overwrite option to BaseProcessor

- restructured the FileBinner to be more flexible and added the FileGraph for preprocessing into graphs
- header and rawheader are now kept if existing
- add tests for the core classes
- add time slew option
- adjust EventSkipper for km3pipe bug
- update docs
- remove deprecated os2 and muon mc_info_extractor

- add shuffle filter
- add option to conc individual files
- remove hardcoded x/y/event_info
- improve tests

- overhaul concatenate.py and move to main repo
- Add 4line bin edges
- timing of modules
- subtract t0 option
- warning for when mcinfo maker produces more then one line

- Added codacy badge
- Added docker
- Added singularity file.