Releases and development updates.

Downloadable assistant conversation logs

In the AI edition, the chat sidebar now has a conversation log that you can save as a text file. It records the model and assistant level, each step the assistant took, the evidence it looked up, the changes it proposed, which ones you approved and what was finally applied. That gives you an audit trail for every AI-assisted plot change.

Optional contaminant filtering

Filter Settings gains a Filter contaminants option based on the Cambridge cRAP reference, with selectable categories. It is off by default and matches exact protein names and accessions, not gene symbols. MaxQuant CON__ and FragPipe contam_ prefixes are recognized. Normalization excludes contaminant rows from its fit, and the unfiltered data stays available.

CoPYlot has moved to the proteomics-ukj organization

The repository now lives at github.com/proteomics-ukj/ProteomicsCoPYlot. Old GitHub links redirect automatically; the interactive architecture map has moved to proteomics-ukj.github.io.

Separately, installing from source or as a Python package now requires Python 3.11 or newer. The desktop downloads bundle their own Python and are not affected.