v0.4.3

[0.4.3] 22-07-2024

Fixed:

• PhenotypeManager: prevented Pearson calculation on constant or NaN-containing arrays.
• GeneralParser: fixed error-handling on malformed input files.
• MS2DeepScoreNetworker: fixed MS2 spectra filtering for ms2deepscore algorithm.

v0.4.2

[0.4.2] 16-06-2024

Fixed

• Fixed bug in SummaryWriter: a nonexisting function was referenced, leading to premature exit of module.

v0.4.1

[0.4.1] 16-06-2024

Fixed

• Versioning

v0.3.3

[0.3.3] 06-06-2024

Fixed

• Added exception for fail of Sample Scores calculation in case of lack of spectral similarity networking data (e.g. no MS/MS data provided)

v0.3.2

[0.3.2] 05-06-2024

Fixed

• Corrected erroneous assignment of 'True' to 'module_passed' for FragmentAnnotator and NeutralLossAnnotator if no MS/MS information was provided

v0.3.1

[0.3.1] 05-06-2024

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

v0.3.0

[0.3.0] 03-06-2024

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).

v0.2.2

[0.2.2] 27-05-2024

Changed

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

v0.2.1

[0.2.1] 26-05-2024

Fixed

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

v0.2.0

[0.2.0] 26-05-2024

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 (before, 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)