@QingQ77: A local-first academic paper management desktop application supporting paper discovery, management, and visualization from sources like arXiv. https://github.com/linxiv-dev/linXiv… A local paper management tool for researchers, all data stored locally, nothing uploaded to any external service…

A local-first desktop application for managing academic papers, supporting paper discovery, management, and visualization from sources like arXiv. https://github.com/linxiv-dev/linXiv… A local paper management tool for researchers—all data stays on your device, nothing is uploaded to external services. It integrates a SQLite database, Google Gemini AI tagging, Obsidian note integration, and paper network graph visualization into a Tauri desktop app (React + TypeScript frontend, Python backend). You can upload PDFs directly, create projects, write notes, add tags, and search for papers via arXiv, DOI, OpenAlex, or CrossRef. — # linxiv-dev/linXiv Source: https://github.com/linxiv-dev/linXiv # linXiv A local-first desktop application for discovering, managing, and visualizing academic papers from arXiv and other sources. Combines a local SQLite database, optional AI-powered tagging, Obsidian vault integration, and an interactive network graph (Cytoscape rendering with a D3 force simulation), wrapped in a Tauri desktop shell (React + TypeScript frontend, Python backend). Upload your PDFs, create projects, manage notes, tags, and more to organize your files — all locally, without sending your data anywhere. This project aims to be a one-stop-shop for researchers who want to manage their literature, with the near-term goal of extending to research groups who seek to share knowledge without going to the web. > Development status: The database schema and paper identifier format are actively changing. source_id values are being migrated to a namespaced format (arxiv:2204.12985, doi:10.48550/..., openalex:W3123456789, local:{hash}). Until that work lands, pre-v0.1.2 (current version) existing papers.db files will not be compatible with new builds — delete papers.db and let it rebuild on first run. No stable release has been cut yet. ## Table of Contents - Features - Project Structure - Setup - Prerequisites - Install dependencies - Environment variables - Run - Building the Tauri App - Tauri prerequisites - Development - Production build - Usage - Projects - Notes - Search and save papers - Add by DOI - AI tools - Download PDFs - Database queries - Graph Visualization - Acknowledgements ## Features - Paper search — Search arXiv by keyword, fetch by ID, or look up by DOI; results saved to a local SQLite DB with version tracking - Interactive graph — Force-directed network of papers and authors (D3 force simulation, Cytoscape rendering); real-time force controls (center, repel, link distance, link strength) - Projects — Organise papers into projects; add notes per paper scoped to a project; composable SQL query builder (Q) for filtering - TeX rendering — MathJax renders LaTeX math in titles and abstracts inside the search UI - AI tools — Google Gemini structured output for tag generation, paper summarization, and semantic similarity - Obsidian integration — Auto-generate markdown notes with YAML frontmatter for your vault - PDF & TeX downloads — Batch download PDFs and TeX source tarballs ## Project Structure linXiv/ ├── AI_tools.py # Gemini: tag(), summarize(), find_related(); PaperContent input type ├── linxiv_cli.py # CLI entry point (linxiv command via pyproject.toml) ├── linxiv_mcp.py # MCP server for Claude integration ├── config.py # App-wide configuration constants ├── user_settings.py # User-editable settings (API keys, paths) ├── pyproject.toml # Package metadata + CLI/MCP entry points ├── assets/ │ ├── app_icon.png # Application icon │ └── wide_logo.png # Wide logo (README header) ├── api/ │ ├── __main__.py # Entry point: python -m api │ ├── app.py # FastAPI routes (REST API incl. /api/graph) │ ├── graph_payload.py # Graph JSON (tags + projects) for /api/graph │ └── run_api.py # uvicorn launcher helper ├── sources/ │ ├── base.py # PaperSource protocol + PaperMetadata model │ ├── arxiv_source.py # ArxivSource: search and fetch from arXiv API │ ├── crossref_source.py # CrossRefSource: fetch by DOI, search by title │ ├── openalex_source.py # OpenAlexSource: lookup via OpenAlex │ ├── doi_resolve.py # DOI resolution (arXiv, Semantic Scholar, CrossRef fallback) │ ├── fetch_paper_metadata.py# High-level fetch/search helpers + Obsidian note generation │ ├── pdf_metadata.py # PDF metadata extraction and resolution pipeline │ └── arxiv_downloads.py # PDF and TeX source download helpers ├── service/ │ ├── paper.py # Paper service: get, get_all, get_many, upsert, graph data │ ├── author.py # Author service: get, upsert, link/unlink to papers │ ├── tag.py # Tag service: get, upsert, paper/project tag management │ ├── note.py # Note service: get, upsert, count by paper/project │ ├── project.py # Project service: get, upsert, filter, status management │ ├── export_import.py # Export/import projects as .lxproj archives │ ├── vault.py # On-disk LaTeX vault for the embedded editor │ ├── editor_project.py # Note-link layer for the embedded editor │ ├── files.py # File utilities for paper sources │ └── models/ # Typed return types (PaperDetails, ProjectDetails, etc.) ├── storage/ │ ├── db.py # SQLite DB: versioned paper storage, graph data queries │ ├── authors.py # Author CRUD and paper linkage │ ├── tags.py # Tag CRUD │ ├── projects.py # Projects: Project data model + CRUD (Status/Q imported) │ ├── notes.py # Notes: per-paper annotations scoped to projects │ ├── paths.py # Filesystem paths (project root, DB, PDFs) │ ├── config/ │ │ ├── core.py # Schema application: apply_sql_schema, init_db │ │ ├── queries.py # Typed query helpers + composable Q predicate builder │ │ └── sql/ # SQL table, view, and index definitions │ └── migrations/ # One-off schema migration scripts ├── formats/ │ ├── bibtex.py # BibTeX import/export │ ├── csv_fmt.py # CSV import/export │ ├── json_fmt.py # JSON import/export │ ├── markdown.py # Markdown / Obsidian import/export │ ├── table_format.md # YAML frontmatter template for Obsidian notes │ └── arxiv_paper.md # Plain-text paper card template ├── public/ │ └── graph/ # Graph viewer (graph.html/js/css), loaded in an iframe ├── src/ # React + TypeScript frontend (Vite) ├── src-tauri/ # Tauri shell (Rust) + bundled sidecar binaries ├── tests/ # pytest suite (API, CLI, DB, sources, DOI, notes, projects) ├── docs/ # Development notes and technical debt log └── pdfs/ # Downloaded PDFs (gitignored) ## Setup ### Prerequisites - Python 3.10+ - Node.js (https://nodejs.org/) 18+ (for frontend / Tauri dev) - Rust toolchain (https://rustup.rs/) (for Tauri) - uv (https://github.com/astral-sh/uv) (recommended Python package manager) ### Install dependencies bash uv sync # Python dependencies (backend + dev) npm install # Node dependencies (frontend) > Add --extra mcp if you need the MCP server: uv pip install -e ".[mcp]" ### Environment variables Create a .env file in the project root: env GENAI_API_KEY_TAG_GEN=your_google_gemini_api_key ### Run HTTP API (JSON backend) bash uv run python -m api # http://127.0.0.1:8000 — see /docs for OpenAPI CLI Install once (editable install via uv): bash uv pip install -e . Then run from anywhere: bash linxiv --version # Search papers (arxiv, openalex, or crossref) linxiv search "attention is all you need" --max 5 linxiv search "diffusion models" --source openalex --max 10 linxiv search "lattice QCD" --source crossref --max 3 # Fetch and save a paper by ID linxiv fetch 2204.12985 linxiv fetch W3123456789 --source openalex # List papers in the database linxiv list --limit 20 --offset 0 --category cs.LG # Paper management linxiv paper get 2204.12985 linxiv paper versions 2204.12985 linxiv paper delete 2204.12985 # Tag management linxiv tag add 2204.12985 transformers attention deep-learning linxiv tag remove 2204.12985 attention linxiv tag list 2204.12985 linxiv tag list-all linxiv tag create my-tag linxiv tag delete 42 # Project management linxiv project list linxiv project list --status active # active | archived | deleted linxiv project get 1 linxiv project create "Diffusion Models" --description "Score-based generative models" linxiv project update 1 --name "Diffusion Models v2" --description "Updated" linxiv project add-paper 1 2006.11239 linxiv project remove-paper 1 2006.11239 linxiv project delete 1 # Note management linxiv note create 2204.12985 "Key insight: scaled dot-product attention" --title "Reading notes" linxiv note create 2204.12985 "Follow-up question" --project-id 1 linxiv note get 7 linxiv note list --paper-id 2204.12985 linxiv note list --project-id 1 linxiv note delete 7 # PDF management linxiv pdf path 2204.12985 linxiv pdf path 2204.12985 --version 2 linxiv pdf download 2204.12985 https://arxiv.org/pdf/2204.12985 linxiv pdf storage All commands output JSON (or a formatted markdown card for fetch). Pass --help to any subcommand for full options. MCP server (Claude integration) Install with the mcp extra: bash uv pip install -e ".[mcp]" Register with Claude Code: bash claude mcp add linxiv -- linxiv-mcp Or add manually to .claude/settings.json: json { "mcpServers": { "linxiv": { "command": "linxiv-mcp" } } } > Without an editable install, fall back to uv run: > json > { "command": "uv", "args": ["run", "linxiv_mcp.py"], "cwd": "/absolute/path/to/linxiv" } > Once registered, Claude can call the linXiv tools directly — for example search_papers, fetch_paper, and list_papers. Full tool documentation will be added soon. ## Building the Tauri App The Tauri desktop app wraps the React/Vite frontend and bundles the Python backend as sidecar binaries compiled with PyInstaller. ### Tauri prerequisites - Node.js (https://nodejs.org/) 18+ - Rust toolchain (https://rustup.rs/) (stable) - uv (https://github.com/astral-sh/uv) - The Tauri build pulls the tauri-plugin-texbrain crate as a git dependency (github.com/linxiv-dev/tex-brain-linxiv-plugin, pinned in Cargo.lock) — no extra checkout needed - System Tauri dependencies — follow the Tauri v2 prerequisites guide (https://tauri.app/start/prerequisites/) for your OS (WebKit2GTK on Linux, Xcode Command Line Tools on macOS, Microsoft C++ Build Tools on Windows) ### Development Start the Python API and the Tauri dev window in separate terminals: bash # terminal 1 — Python backend uv run python -m api # http://127.0.0.1:8000 # terminal 2 — Tauri dev window (also starts Vite, hot-reloads on frontend changes) npm run tauri dev The Python API sidecar is not bundled in dev mode — the app talks to the locally running API on port 8000. ### Production build The Python entry points (API, CLI, MCP server) are compiled to self-contained binaries with PyInstaller and staged into src-tauri/binaries/ before Tauri bundles the app. 1. Build and stage the Python sidecars: bash npm run build:sidecar This runs PyInstaller on linxiv-api.spec, linxiv-cli.spec, and linxiv-mcp.spec, then copies the outputs to src-tauri/binaries/ with the correct Tauri target-triple suffix. 2. Build the Tauri app: bash npm run tauri build Or run both steps at once: bash npm run build:all The final installer/bundle is written to src-tauri/target/release/bundle/. Installing the CLI After installing the desktop app, open Settings and click Install CLI to symlink the bundled linxiv binary to ~/.local/bin/linxiv (Linux/macOS) or add a shim to your PATH (Windows). ## Usage ### Projects python from storage import Project, filter_projects, Q, Status, get_paper # Create and save a project p = Project(name="Diffusion Models", color=0x5b8dee, project_tags=["generative"]) p.save() # Add papers — add_papers takes integer SOURCE_FKs (papers must already be in the DB) p.add_papers([get_paper(sid)["source_fk"] for sid in ("2006.11239", "2010.02502", "2112.10752")]) # Query with composable predicates active = filter_projects(Q("status = ?", Status.ACTIVE)) not_deleted = filter_projects(~Q("status = ?", Status.DELETED)) blue_diffusion = filter_projects( Q("status = ?", Status.ACTIVE) & Q("color = ?", 0x5b8dee) & Q("name LIKE ?", "%diffusion%") ) ### Notes python from storage import Note, get_notes, count_paper_notes, ensure_notes_db, get_paper ensure_notes_db() # Notes attach to a paper by its integer SOURCE_FK sfk = get_paper("2006.11239")["source_fk"] # Add a project-scoped note on a paper note = Note(source_fk=sfk, project_id=p.id, title="Key insight", content="...") note.save() # Retrieve project_notes = get_notes(sfk, project_id=p.id) count = count_paper_notes(sfk, project_id=p.id) ### Search and save papers python from sources import search_papers from storage import init_db, save_papers init_db() papers = search_papers("lattice QCD", max_results=25) # returns arxiv.Result objects save_papers(papers) # persist them to the DB ### Add by DOI python from sources import resolve_doi result = resolve_doi("10.48550/arXiv.1706.03762") ### AI tools python from AI_tools import tag, summarize, find_related, PaperContent content = PaperContent(abstract=paper.summary) tags = tag(content) # ["#quantum_computing", ...] tags = tag(content, file_path="tags.md") # also appends to file s = summarize(content) print(s.tldr) print(s.key_contributions) # Semantic edges for the graph from storage import list_papers candidates = [(r["paper_id"], r["summary"]) for r in list_papers()] related_ids = find_related(content, candidates) ### Download PDFs python from sources.arxiv_downloads import download_pdf, download_pdf_batch, download_source_batch download_pdf(paper, dirpath="pdfs/") download_pdf_batch(papers, dirpath="pdfs/") download_source_batch(papers, dirpath="source/") ### Database queries python from storage import get_paper, get_all_versions, list_papers, get_graph_data get_paper("2204.12985") # latest version get_paper("2204.12985", version=2) get_all_versions("2204.12985") # all stored versions nodes, edges = get_graph_data() # for the graph viewer ## Graph Visualization Papers (circles, in your theme’s accent color — blue by default) and authors (gold diamonds) form a force-directed network. Edges connect each paper to its authors. The control panel has four real-time sliders: | Slider | Effect | |—|—| | Center force | Pulls/pushes nodes toward the center | | Repel force | Controls node-to-node repulsion | | Link distance | Target edge length | | Link strength | Stiffness of paper–author edges | ## Notes - papers.db, pdfs/, source/, and vault contents are gitignored. - MathJax, D3, and the Inter UI font are all bundled locally — no external CDN calls, so the interface works fully offline. - PaperContent accepts abstract, full_text (TeX source), or pdf (bytes) — Gemini will use the richest available source. ## Acknowledgements linXiv owes a debt to Qiqqa (https://github.com/jimmejardine/qiqqa-open-source), the open-source research management tool originally created by Jimme Jardine. PDF text and metadata extraction uses pypdf (https://github.com/py-pdf/pypdf), a pure-Python PDF library maintained by the py-pdf (https://github.com/py-pdf) organization. pypdf is licensed under the BSD 3-Clause License (https://github.com/py-pdf/pypdf/blob/main/LICENSE).