Fermo-core

Changed

- Loosened typing restrictions for Feature and Sample object attributes: area and height (intensity) now accept float values.

Removed

- [Breaking change] Removed toggle 'nonbiological' from 'FragmentAnnotator' and from parameters file; 'nonbiological' fragment annotation is now performed automatically

Security

- Instead of full file paths, only filenames are now written to the 'out.fermo.session.json' file

Changed

- [Breaking change] Parameter settings for `additional_modules/feature_filtering` were changed from a list of ranges to a dictionary with explicit values.
- Reworked score assignment for qualitative phenotype data: phenotype-associated features now always receive a score of 1.0, and non-associated ones a score of 0.0.
- For all modules with runtime restriction, the 'maximum_runtime' parameter was set to a default of '0' (unlimited runtime). Therefore, runtime restriction must now be specified explicitly.
- Added a 'module_passed' parameter to all modules. This allows a more accurate description via the SummaryWriter (e.g. module was activated but timed out, and lack of e.g. annotation is due to premature ending and not because there were no hits).

Changed

- Removed 'phenotypes' as separate Feature attribute: write to Annotation object instead.
- Implemented sorting of annotation entries in descending order

Fixed

- Fixed bug in "SummaryWriter": implemented error catching.

Changed

- Replaced global logger with logger specific for `main_cli()`. `main()` now needs an argument `logger`
- Reworked output file naming: all output files now start with `out.fermo.` and a suffix specifying their type
- Removed output directory selection: the output directory is now always `results` located in the directory in which the peaktable resides.
- Features now always have default result values (previously, some Features could have an empty dictionary)
- MS2Query assignment now uses temporary directories for data reading/writing

Fixed

- Removed `sys.exit(0)` in case of successful run to fix compatibility issue with Celery task manager (`fermo_gui`)

Changed

- Implemented logging verboseness parameter for CLI interface