CAFE_v3.1.0

New

1. Session persistence: loaded data now survives a browser refresh (F5) instead of resetting, so long analyses no longer lose state.

Changed

1. Desktop & HPC only: the web-hosted mode has been removed; run CAFE locally (cafe) or on HPC (cafe-hpc).
2. Updated dependencies: refreshed the full stack (Streamlit, scanpy, and others) for better stability and performance.
3. Refreshed theme and landing page polish.

Fixed

1. Numerous fixes across data processing and clustering (annotation, evaluation, downsampling, merging, and selective clustering).

CAFE_v3.0.0

Highlights

• New design system with unified color palette, shared headers, and consistent info cards across all pages.
• Redesigned Data Processing as a guided step-by-step wizard.
• Package restructure: app moved from bin/ into an installable src/cafe_app/ layout.
• New direct installation using uv, and the global 'cafe' command for quicker access to the web app
• Removed visual clutter
• Resolved Streamlit use_container_width deprecation.
• Bug fixes

CAFE_v2.0.2

• Bug fixes for Selective Clustering tab
• Minor changes in instruction
• Updated readme

Alternative download link using curl:

curl -L -o CAFE_v2.0.2.zip https://github.com/mhbsiam/cafe/releases/download/v2.0.2/CAFE_v2.0.2.zip && unzip CAFE_v2.0.2.zip

CAFE_v2.0.1

• Bug fixes for windows where download buttons won't appear in cluster annotation and merging tabs.
• Minor improvements in instructions
• Updated cafe.yaml

CAFE_v2.0.0

CAFE v2 released!

• Updated support for Streamlit 1.41.0, Scanpy 1.10.4, and Watchdog 6
• Restructured resource files for better managements
• Specified custom theme colors for consistency using config.toml
• Set streamlit telemetry to false
• Added Leiden resolution as adata file name extension
• Added support for website deployment
• Improved flowchart images for instruction using Napkin.
• Improved installation instruction
• Added known issues for windows
• Updated citations
• Various styling changes

CAFE_v1.0.3

• Minor improvements

CAFE_v1.0.2

• Default PCA variance set to 95%
• Default dimension metric of Leiden set to X_pca
• Bug fixing
• Minor improvement

CAFE_v1.0.1

Release Notes:

1. Included high resolution images
2. Added workflow image
3. Bug fixes

CAFE_v1.0.0

This marks the first major release of CAFE (Cell Analyzer for Flow Experiment).