ScholarAIO
Scholar All-In-One — A research infrastructure for AI agents.
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
| Feature | Details | |
|---|---|---|
| PDF Parsing | Deep structure extraction | Convert PDFs into structured Markdown while preserving formulas, figures, and layout as much as possible |
| Not Just Papers | More than papers | Journal articles, theses, patents, technical reports, standards, and lecture notes — four inbox categories with tailored metadata handling |
| Hybrid Search | Keyword + semantic fusion | Combine full-text and vector retrieval, with optional line-addressable evidence chunk search for precise source snippets |
| Topic Discovery | See what your library is about | Automatically group papers into research themes and use interactive views to grasp the overall structure quickly |
| Literature Exploration | Multi-dimensional discovery | Explore a research direction through journal, topic, author, institution, keyword, year, citation impact, and more |
| Citation Graph | References & impact | Forward citations, backward citations, and shared-reference analysis |
| Layered Reading | Read on demand | Start with metadata or the abstract, then move into conclusions or full text only when you need to |
| Local Library WebUI | Browse and inspect | Open a read-only local UI for records, audit status, Markdown abstracts/conclusions, proceedings children, and PDFs without exposing library data to remote scripts |
| Publisher PDF Fetch | Use your current access | Fetch DOI or publisher-page PDFs through the user's legal network context, with direct campus-network mode and selected/all-library PDF refetch |
| Multi-Source Import | Connect your existing library | Import directly from reference managers, fetched PDFs, local PDFs, and Markdown without rebuilding your library from scratch |
| Workspaces | Organize by project | Manage paper subsets with scoped search and BibTeX export |
| Multi-Format Export | BibTeX, RIS, Markdown, DOCX | Export your full library or a workspace for Zotero, Endnote, submission, or sharing |
| Metadata Scrub | Incremental cleanup after enrich | Review and repair low-quality titles, authors, and years for non-standard documents, then mark reviewed records to skip future passes |
| Persistent Notes | Cross-session memory | Keep analysis notes for each paper so future sessions can reuse them instead of starting over |
| Research Insights | Reading behavior analytics | Search hot keywords, most-read papers, reading trends, and semantic neighbor recommendations for papers you haven't read yet |
| Federated Discovery | Cross-library search | Search your main library, exploration libraries, and arXiv from one entry point instead of hopping across tools |
| Remote Backup | Rsync-based sync | Back up the ScholarAIO data/ workspace to configured remote targets through named rsync plans |
| AI-for-Science Runtime | Use scientific software more accurately | Use scientific software against official documentation at runtime instead of guessing commands and parameters |
| Extensible Tool Onboarding | Keep adding the tools that matter | As new scientific tools and workflows become important, the system can keep expanding |
| Academic Writing | AI-assisted writing | Router-first workflows for literature review, guided single-paper reading, paper sections, citation check, rebuttal, gap analysis, poster packages, and technical reports — with every citation traceable to your own library |
For writing tasks, start with the router-style writing entry when the deliverable is clear but the workflow is not. The current writing stack is organized around:
academic-writing: route by deliverable and writing stagenature-workflow: bridge to the upstreamnature-skillsbundle for Nature/high-impact figures, polishing, writing, reviewer critique, citation, Data Availability, paper reading, reviewer response, paper-to-PPT, and academic search; direct upstream skills are preferred when availableliterature-review: long-form review and survey writingpaper-guided-reading: guided deep reading of a single paper from fuzzy search to full-text analysispaper-writing: manuscript sections and paper-focused draftingreview-response: rebuttal and response-letter workflowsresearch-gap: gap analysis and open-question reportstechnical-report: technical briefings and topic reportsposter: poster-oriented content packagingdocument: final DOCX / PPTX packaging
See docs/guide/writing.md for the full writing map.
Works With Your Agent
ScholarAIO is designed to be agent-agnostic, but different agents expose different integration paths. Some work best when you open this repository directly; others are easier to use through plugins.
| Agent / IDE | Open this repo directly | Reuse from another project |
|---|---|---|
| Claude Code | CLAUDE.md + .claude/skills/ |
Claude plugin marketplace |
| Codex / OpenClaw | AGENTS.md + .agents/skills/ |
scholaraio setup agent |
| Cline | .clinerules + .claude/skills/ |
scholaraio setup agent --target-project ... |
| Qwen | .qwen/QWEN.md + .qwen/skills/ |
scholaraio setup agent --target-project ... |
| Cursor | .cursor/rules/scholaraio.mdc + AGENTS.md (.cursorrules legacy fallback) |
scholaraio setup agent --target-project ... |
| Windsurf | .windsurfrules |
scholaraio setup agent --target-project ... |
| GitHub Copilot | .github/copilot-instructions.md |
scholaraio setup agent --target-project ... |
Skills follow the open AgentSkills.io standard, and .agents/skills/ and .qwen/skills/ are symlinks to .claude/skills/ so different agents can discover and reuse the same skills. Qwen-specific project context lives in .qwen/QWEN.md.
For reuse from another project, run scholaraio setup agent to preview shell, skill-discovery, and project-wrapper changes; add --apply to perform the automatic steps.
Wrappers created with --target-project include