ScholarAIO

Scholar All-In-One — an academic harness for AI agents.

English | 中文

Your coding agent already reasons, plans, browses, writes code, and uses tools. ScholarAIO adds the academic harness around it, so the same agent can carry evidence, project state, repeatable workflows, and reviewable outputs across the whole research process.

• Your paper library becomes a reusable knowledge base for the same agent.

• Skills and CLI contracts give the agent stable ways to search, read, organize, cite, write, and verify.

• Optional tools are integrated selectively when they strengthen that workflow and degrade cleanly when unavailable.

Here, All-in-One means one coherent academic workflow, not every scientific package in one distribution. The active agent supplies reasoning and orchestration; ScholarAIO supplies the durable academic context and operational contracts around it.

ScholarAIO offers more than search. It gives an AI coding agent a stable academic substrate for evidence, project memory, tool use, research outputs, and verification without trying to replace the agent itself.

flowchart LR
    R[Researcher] <--> A[Coding agent]
    A <--> H[ScholarAIO academic harness]
    H --> E[Evidence and context]
    H --> W[Skills, CLI, and workspaces]
    H --> O[Outputs and verification]
    H -. optional .-> X[Bounded external adapters]

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 .
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 2.0

ScholarAIO 2.0 is a product-boundary and compatibility release; it does not change the current data layout for 1.4 or 1.5 users. Upgrade the package, run scholaraio setup check, and rebuild indexes when appropriate. Users coming from 1.3 or earlier must still complete the explicit runtime migration.

See docs/getting-started/upgrading-to-2.0.md for removed surfaces, migration guidance, and the 2.x compatibility promise.

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 Search, cite, and read Filter records by field, run keyword/semantic/unified retrieval, copy canonical BibTeX, inspect audit status and Markdown summaries, and open PDFs inline or in the OS default viewer; WSL launches a stable Windows edit mirror and automatically persists embedded annotations back to the canonical library PDF

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

Backup & Restore Portable instance recovery Keep legacy data-only rsync plans or opt into a manifest-validated full-instance backup and one-click restore covering local config, data, workspaces, published outputs, and control state

Grounded Scientific Tool Use Consult exact interfaces Use versioned official documentation at runtime instead of guessing scientific-software commands and parameters

Bounded Tool Adapters Integrate only when justified Keep external tools optional, isolated, testable, and subject to the 2.x integration gate

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 stage

• nature-workflow: bridge to the upstream nature-skills bundle 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 available

• literature-review: long-form review and survey writing

• paper-guided-reading: guided deep reading of a single paper from fuzzy search to full-text analysis

• paper-writing: manuscript sections and paper-focused drafting

• review-response: rebuttal and response-letter workflows

• research-gap: gap analysis and open-question reports

• technical-report: technical briefings and topic reports

• poster: poster-oriented content packaging

• document: 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 local machine paths; review the managed block before committing