scholaraio

Your coding agent already reads code, writes code, and runs experiments. ScholarAIO adds a structured research workspace on top, so the same agent can search literature, cross-check results against papers, use scientific software more accurately, and carry the whole research workflow from one terminal.

• Your paper library becomes a reusable knowledge base for the same agent.
• When scientific software questions come up, the agent can consult official documentation at runtime instead of guessing from prompts.
• The system is built to keep expanding as new tools and workflows become worth supporting.

ScholarAIO offers more than search. It gives an AI coding agent a research workspace that supports natural-language interaction, papers and notes, more reliable use of scientific software, writing and running code, checking results against the literature, and structured academic writing.

Quick Start

The default and recommended way to use ScholarAIO is simple: install it, configure it once, and open this repository directly with your coding agent.

git clone https://github.com/ZimoLiao/scholaraio.git
cd scholaraio
pip install -e ".[full]"
scholaraio setup

Then open the repository in Codex, Claude Code, or another supported agent. In this setup, the agent gets the fullest experience: bundled instructions, local skills, the CLI, the repository knowledge map in docs/DESIGN.md, and the complete codebase context are all available directly. For Claude Code plugins, Codex/OpenClaw skill registration, and other setup paths, see docs/getting-started/agent-setup.md.

Upgrading To 1.4

ScholarAIO 1.4 is a runtime-layout upgrade. It does not migrate user data automatically during git pull, pip install -U, or normal CLI startup. That is intentional: data movement is an explicit offline operation with a migration journal and verification.

Recommended path:

# 1. Update the code/package
git pull
pip install -e ".[full]"

# 2. From the ScholarAIO runtime root, inspect and migrate explicitly
scholaraio migrate status
scholaraio migrate upgrade --migration-id upgrade-1.4.0 --confirm
scholaraio migrate verify --migration-id upgrade-1.4.0

# 3. Rebuild indexes after migrated data lands in the fresh layout
scholaraio index --rebuild

For the lowest-risk upgrade, keep or copy your old ScholarAIO folder first, then run the migration in the upgraded checkout that contains your data/, workspace/, and config*.yaml. See docs/getting-started/upgrading-to-1.4.md.

What It Does