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Change Log

All notable changes to this project will be documented in this file.

  • 01_10_2025:

    • fixing missing headers issue when writing a previously not existing csv file.
    • optimizing peaks filter with Numba just-in-time (jit)

  • 26_09_2025:

    • remove peaks with intensity <= 0.
    • bugfix with json update

  • 15_09_2025:

    • replace UNKNOWN by NOT FOUND for missing value
    • improve JSON output with pretty humane-readable JSON.
    • adding De Novo fragments formula calculations.
    • adding safety checks to the GUI start button.
    • adding file hash to spectrums (SHA-256 of the file size).
    • disabling automatic instrument deduction (e.g., inferring LC if ESI is found).

  • 05_06_2025:

    • replace RETENTIONTIME default field by RT.
    • Return to the main window when FINISH is pressed.
    • Correction of spectra moved to in-silico if FragHub output is used as input.
    • Deduplicate now on SPLASH and INCHIKEY. spectra without INCHIKEY are not deleted at the beginning of the process.

  • 14_05_2025:

    • fix adduct in silico correction

  • 18_04_2025:

    • fix adduct regex pattern
    • improve spectrum deletion callback by writing deleted spectrum in DELETION_REASONS sub folder with a detailed reason.
    • extend precursormz and adduct checks exception to all GC spectrums.
    • modifiy adduct ionmode check with "pos", "neg" in adduct dico.
    • direct integration of spectra-hash (https://github.com/berlinguyinca/spectra-hash) into fraghub.
    • Correcting and adduct some adducts to adduct dict
    • Adding loading screen to GUI
    • adding new gc instruments to instrument dict.
    • auto add [M+H]+ or [M-H]- in In-Silico if adduct is missing.
    • creating FragHub executable for Windows, Linux, and macOS with Python fully integrated.

  • 03_04_2025:

    • fixing missing last msp spectrum in msp files in some cases.

  • 25_03_2025:

    • fixing peaks list regex parsing error when formulas in peaks comment.

  • 29_01_2025:

    • changing licence from MIT to CC-BY-NC 4.0

  • 27_01_2025:

    • Refactoring updates and project logic.

  • 24_01_2025:

    • deleting spectrum if neg adduct in pos spectrum, or pos adduct in neg spectrum
    • bug(fix): let thread safely terminate in no new spectrum to process
    • removing no or bad adduct spectrum
    • refactoring adduct normalization
    • adding report.txt in output directory

  • 20_12_2024:

    • New modern GUI (Graphical User Interface).
    • Adding dependencies to requirements.txt
    • Removing MacOS and Linux support 😢 (this is just good-bye).
    • Refactoring duplicatas removal, now by sames SPLASH key.
    • Refactoring filtering logic with GC case.
    • Adding logs to GUI for monitoring suppressed spectrum.
    • Now completing NAMES and descriptor from RDkit and PubChem datas (offline).
    • Now completing Classyfire and NPclassifier from local datas.
    • Auto calculating chunk size for multi threading pool.
    • Now deleting spectrum with no SMILES no InChI AND no inchikey.
    • Refactoring .json reader for standard ISO/IEC 20802-2:2016 .json and non-standard formats.
    • Moving all globals variables to a single file.