Pre-release v1.1.0

[nttg8100]

Description

• Changed to GPLv3.0 license
• Added graphical abstract
  This pull request introduces significant changes to support running the backend using PyPy for improved performance, updates the development and deployment workflow, and makes several related improvements across the codebase and documentation. The most important changes are grouped below.

Backend Runtime and Dependency Management

• Switched the backend Docker image to use pypy:3.11-slim instead of python:3.12.11-slim, updated dependency installation, and adjusted file copying in backend/Dockerfile to optimize for PyPy.
• Added Makefile targets and logic to download and install PyPy locally for development, and updated backend commands (including database migrations, server start, and Celery worker) to use the installed PyPy interpreter and socketify server instead of uvicorn. [1] [2] [3]
• Removed the legacy backend/dev.py development entrypoint, as development now uses PyPy and socketify directly.
• Updated .dockerignore, .gitignore, and related ignore files to exclude PyPy binaries and artifacts. [1] [2] [3]

Database and Dependency Updates

• Migrated from the deprecated postgres:// URI scheme to the modern psycopg:// scheme in backend/app/db.py for all environments.
• Updated backend dependencies: removed uvicorn, uvloop, and asyncpg, and added socketify, psycopg[binary], psycopg-pool, and anyio to backend/requirements.txt. [1] [2]
• Changed the server startup command in backend/run_server.sh to use pypy -m socketify instead of uvicorn, and set the number of workers dynamically.

Performance and Benchmarking

• Added a new backend/perf directory with configuration (pixi.toml, requirements.txt, .gitignore, .gitattributes), a minimal app.py for performance testing, and an install.sh script to automate PyPy setup and run benchmarks comparing socketify, uvicorn, and granian servers. [1] [2] [3] [4] [5] [6]

Documentation and Licensing

• Updated the README to include a graphical overview image, revised the license section to use GPLv3 instead of Creative Commons, and updated license badges. [1] [2]
• Updated developer documentation to show how to use pixi instead of micromamba for analysis environments.

Miscellaneous Fixes and Improvements

• Improved dynamic Traefik configuration generation logic in backend/app/utils/executor/ssh.py for cleaner TLS block handling and fixed a minor logging bug. [1] [2] [3] [4]
• Added extra Pixi configuration steps for channel setup and dependency installation in generated scripts.
• Minor debug print added in backend/app/main.py (likely temporary).
• Restricted backend pixi.toml to only support linux-64 platform.

These changes collectively modernize the backend stack, improve performance through PyPy and socketify, and streamline development and deployment workflows.