Version 2.6.1

Compatibility fix to support IdentiPy pepXML files.

Version 2.6

• New general parameters: "plot summary histogram" and "summary histogram dpi".
• Fix several warnings and errors.
• Fix incorrect results with NumPy 2+ (the fix slightly changes AA_stat results).
• Fix for Pyteomics 4.7.3+ (it is now required).
• Create a JSON file with shift interpretation data.

Version 2.5.6

• Fix #13 and a couple of issues with HTML report generation.

• Updated the following version requirements:

  Dependency	Required version
  Python	>=3.8
  Pyteomics	>4.6
  Pandas	>=1.4
  Jinja2	>=3.1.2

Version 2.5.5

• Reduce memory usage.
• Fix errors with CSV files. Add new parameters --fmods, --vmods and --enzyme to make up for metadata that was
  extracted from pepXML. Also new sections in config file can be used for the same purpose:
  modifications, configured fixed modifications and modifications, configured variable modifications.
• Add CLI argument --processes to control the maximum number of processes used.

Version 2.5.4

• Fix error message when no input files are found.
• Fix FutureWarrnings in HTML report generation.
• Fix error with DBSCAN min_samples parameter being float instead of int.

Version 2.5.3

• Fix a bug in same_residue which resulted in a KeyError when recalculating recommended modifications.

Version 2.5.2

• Fix the issue that clustering results were saved in the wrong directory.
• Fix number formatting in HTML report.

Version 2.5

GUI changes:

• Add buttons to load, edit and save AA_stat parameters.
• Add --create-shortcut option for AA_stat_GUI.
• Refine GUI text, add tooltips.

Version 2.4

Add a simple GUI based on Tkinter. Start it by running AA_stat_GUI.

Version 2.3

• Fix error on Windows (#3).
• Fix for MSFragger 3.2 (#6).
• Better support for terminal and protein-terminal variable modifications in input.
• By default, support both "DECOY_" and "rev_" decoy prefixes.
• Improve error messaging on data reading.
• Support whole directories instead of file lists on command line (#7).
• Save clustering figures to a single multi-page PDF for each input file.
• Better account for configured variable modifications in recommending variable modifications.