Picked-group-fdr

- Added support for FragPipe and Sage for LFQ data
- Support input files with byte order mark (9)
- Added tool for entrapment FDR calculation and plotting
- Gui build fix (8)
- Major code refactoring (camelCase to snake_case, new classes, better submodules)

- Added support for proteases that cleave before an amino acid, e.g. Asp-N, Lys-N
- Fix for empty score field in evidence file
- Add better detection of maxquant evidence files (7)
- Added support for combining evidence files with different proteases
- Updated GUI to support different digestion parameters per evidence file
- Fix log levels in GUI
- Added example scripts and notebook for book chapter analysis
- Add check for shared peptides to protein groups that were filtered out because they had no reliable peptides
- Change peptide count to use score cutoff for peptide FDR instead of protein FDR
- Improved log messages

- Removed proteins without any PSMs below the FDR threshold from protein groups output. Setting the new `--keep_all_proteins` flag reverts to the old behavior.
- Added support for supplying multiple evidence files
- Added support for mokapot format and allow users to specify methods with custom toml files
- Add `--fasta_contains_decoys` flag and functionality
- Update llvmlite (4)

- Added rescoring input (e.g. Prosit results) to GUI

- Added percolator input to GUI

- Add option for multiple evidence files and selecting digestion parameters in GUI