fermo_core - v0.6.4

[0.6.4] 13-05-2025

Changed

• Improved README for publication
• Switched installer option from hatch to uv

- Python
Published by mmzdouc 10 months ago

fermo_core - v0.6.3

[0.6.3] 16-04-2025

Changed

• Changed key names in params json file/schema to better align with output parameter designation

- Python
Published by mmzdouc 10 months ago

fermo_core - v0.6.2

[0.6.2] 12-04-2025

Fixed

• Fixed sorting error when fermo and mzmine ion adduct annotations are mixed

- Python
Published by mmzdouc 11 months ago

fermo_core - v0.6.1

[0.6.1] 10-04-2025

Added

• Retrieve library and ion identity annotation from mzmine3/4 file

- Python
Published by mmzdouc 11 months ago

fermo_core - v0.6.0

[0.6.0] 10-04-2025

Changed

• Flattened parameter .json format
• Module logic: all modules must be specified explicitly, no module runs by default
• Removed all default values from data models to omit redundancy
• Spectral library now accepts a dir of files (e.g. multiple mgf files), not a single file
• Removed automatic timeout of long-running functions

Nota bene: parameter.json files from <=5.1 are not compatible with this version (0.6.0)

- Python
Published by mmzdouc 11 months ago

fermo_core - v0.5.1

[0.5.1] 05-04-2025

Fixed

• Fixed publishing to PyPI

- Python
Published by mmzdouc 11 months ago

fermo_core - v0.5.0

[0.5.0] 05-04-2025

Added

• Implemented compatibility with mzmine4 output

Changed

• QuantPhenotype: reimplemented, allowing for flexible FDR
• SpecLibMgfParser: implemented lazy loading to better deal with large libraries, filter out invalid spectra

Fixed

• Fixed bug in mzmine parser hanging on "NaN to integer"

- Python
Published by mmzdouc 11 months ago

fermo_core - 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.

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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.

- Python
Published by mmzdouc over 1 year ago

fermo_core - v0.4.1

[0.4.1] 16-06-2024

Fixed

• Versioning

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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)

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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).

- Python
Published by mmzdouc over 1 year ago

fermo_core - 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

- Python
Published by mmzdouc over 1 year ago

fermo_core - v0.2.1

[0.2.1] 26-05-2024

Fixed

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

- Python
Published by mmzdouc almost 2 years ago

fermo_core - 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)

- Python
Published by mmzdouc almost 2 years ago

fermo_core - v0.1.1

Modifying argparse (addition of logging verboseness control). Improvements to README.

- Python
Published by mmzdouc almost 2 years ago

fermo_core - v0.1.0

Initial release of fermo_core.

- Python
Published by mmzdouc almost 2 years ago