DeepLC integration

[RalfG]

Integrate DeepLC to further improve PSM rescoring.

• [x] Continue restructuring code
  • [x] Move tests out of package directory
  • [x] Move code in init to main, config_parser, runner
  • [x] Fix publish workflow and test file paths
• [x] New module peptide_record to handle PEPREC files (should be moved to MS²PIP)
• [x] Integrate DeepLC
• [x] Propagate required columns to peprec (psm_score and observed_retention_time)
  • [x] MaxQuant pipeline
  • [x] PeptideShaker pipeline
  • [x] X!Tandem pipeline
  • [ ] MS-GF+ pipeline
• [x] Update documentation