Oktoberfest

🚀 Features

* Changed hierarchy in usage principles (109) victorgiurcoiu
* Added logfile for mokapot (107) victorgiurcoiu
* added SA distribution plot and density to rt_vs_irt plot (104) picciama
* Changed percolator folder name, percolator variables depending on fdr… (106) victorgiurcoiu
* Added progress during prediction, corrected counting in check_pool (105) victorgiurcoiu
* Feature/mass tolerance config (102) picciama
* Read input/output paths from config and restructure it (96) victorgiurcoiu
* Feature/documentation (95) victorgiurcoiu
* fragmentation_grpc column / support for PTM models (87) picciama

🐛 Bug Fixes

* Fix/integration test (94) picciama
* Fix/check rawfile exists (89) picciama

🧰 Maintenance

* Changed hierarchy in usage principles (109) victorgiurcoiu
* Changed percolator folder name, percolator variables depending on fdr… (106) victorgiurcoiu
* Feature/mass tolerance config (102) picciama
* Read input/output paths from config and restructure it (96) victorgiurcoiu
* Feature/documentation (95) victorgiurcoiu
* Fix/integration test (94) picciama
* Chore/thermorawfileparser ext dep (88) picciama

:package: Dependencies

* [DEPENDABOT]: Bump actions/cache from 2.1.7 to 3.3.1 (58) dependabot
* [DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 3.1.1 to 4.1.0 (17) dependabot
* [DEPENDABOT]: Bump actions/setup-python from 3 to 4 (1) dependabot

Changes

* Documentation (60) victorgiurcoiu
* Update ce_calibration.py (54) qussai96
* cleanup ce_calibration (68) picciama
* line128 in spectral_library.py: UnboundLocalError-local-variable-'predictions'-referenced-before-assignment (55) qussai96

🚀 Features

* Added mokapot as an alternative fdr_estimation_method for percolator (70) victorgiurcoiu
* Feature/koina grpc (75) picciama
* Feature/plotting (72) picciama
* Made flags in the config case insensitive (51) victorgiurcoiu
* Feature/flag curve fitting method (49) victorgiurcoiu
* Feature/add mz for cosine (48) victorgiurcoiu
* Feature/searchtype/lowercase check (41) victorgiurcoiu

🐛 Bug Fixes

* Update documentation for running with docker (73) (77) MatthewThe

🧰 Maintenance

* Update documentation for running with docker (73) (77) MatthewThe
* Added mokapot as an alternative fdr_estimation_method for percolator (70) victorgiurcoiu
* Feature/flag curve fitting method (49) victorgiurcoiu
* Feature/searchtype/lowercase check (41) victorgiurcoiu

Changes

* Fix/docker build (28) MatthewThe

🚀 Features

* support capital .RAW and lowercase .raw ext (33) picciama

🐛 Bug Fixes

* Vg/minor fixes (37) WassimG
* Fix/docker build (35) picciama
* Fix/docker build (30) MatthewThe
* fix remaining actions on development (29) picciama
* Fixed everything related to pre-commit (12) picciama

🧰 Maintenance

* Vg/minor fixes (34) victorgiurcoiu
* Fix/docker build (30) MatthewThe
* Added plotting (31) victorgiurcoiu
* Fixed everything related to pre-commit (12) picciama