breaking: renamed detx input args to 'orcasong run' command and detx an not be given in toml anymore

- add muon bundle extractor
- add toml configs for muon bundle extractor
- move neutrino extractors from extractors.py to extractors/neutrino_chain.py (this is backward compatible thanks to __init__.py

breaking:
- rename mc_info_to_float64 to y_to_float64
- add sort_y option

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

- 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

- orcasong is now called legacy
- orcasong_2 is now called orcasong

Other changes:
- Added one line 2017 bin edges to repo
- added unittests
- added versioning for files created with orcasong
- Expanded doc
- Added check to calib if calib has been done to file already

- Added command line tools to setup.py

- Remove all optional arguments in the parser. Now, a config file is always needed! Updated docs due to this.
- Added default_config.toml file
- Implemented automatic generation of API docs
- Fix __version__.py
- Added flush_freq argument in the HDF5Sink.
- Minor other fixes.