# bibox
<p align="center">
<img src="assets/bbox_bass.png" alt="bibox" width="320">
</p>
[](https://crates.io/crates/bibox)
[](LICENSE)
**Using AI agents (OpenClaw) to search and summarize papers?**
**Let them manage your bibliography and notes too.**
**You just browse the TUI. bibox makes it work.**
Just give your agent the GitHub link. It'll figure out the rest.
For humans: browse and edit in the TUI. For agents: manage entries and notes through the CLI.
> **Best for:** researchers who use AI agents for literature review and want papers, notes, and BibTeX in one Git-syncable folder.
>
> **Not for:** GUI, PDF annotation, or Word integration. Use Zotero instead.
**Sources:** Crossref, Open Library, arXiv, Unpaywall
**Formats:** BibTeX, YAML, RIS, CSV, Markdown
**Import:** `.bib` from Zotero, Mendeley, EndNote
## Features
- **Smart import** - Drop a PDF and bibox extracts the DOI, fetches metadata from Crossref, and files it automatically
- **Multiple sources** - Add entries via PDF, DOI, ISBN, arXiv ID, URL, or title search
- **Three-panel TUI** - Collections, entries, and preview (info / notes / PDF) side by side
- **Vim-style navigation** - `hjkl`, `gg`/`G`, `{n}j`, `Ctrl+d/u`, multi-select with `Space`
- **Fetch & refresh** - Press `f` to pull metadata from Crossref, preview changes, pick which fields to update
- **Undo/redo** - `Ctrl+z`/`Ctrl+y` with in-memory snapshots
- **AI-agent-friendly** - Every command supports `--json`. Notes have `--stdin`, `--section`, `--template` for programmatic access
- **Markdown notes** - Per-entry notes with section-level updates, rendered with syntax highlighting in the TUI
- **Sub-collections** - Hierarchical collections with path notation (`digest/2026-04`). Unlimited depth, works like a filesystem
- **Portable home** - `bibox init` puts everything in one Git-syncable folder
- **Export** - BibTeX, YAML, RIS, CSV, notes (`.md`). Include PDFs. Copy to clipboard. Zip it up.
- **Templates** - Built-in and custom note templates with `{{variable}}` substitution
- **Doctor** - `bibox doctor` diagnoses and auto-repairs DB issues: bad citekeys, LaTeX escapes, orphaned files
## Install
**With Rust (macOS / Linux desktop):**
```bash
cargo install bibox
```
**With cargo-binstall (fast, no compile):**
```bash
cargo binstall bibox
```
**On a server (no Rust needed):**
```bash
curl -L https://github.com/namil-k/bibox/releases/latest/download/bibox-x86_64-unknown-linux-musl -o ~/.local/bin/bibox
chmod +x ~/.local/bin/bibox
```
Pre-built binaries for Linux x86_64, macOS arm64, and macOS x86_64 are available on the [releases page](https://github.com/namil-k/bibox/releases/latest).
**Update:**
```bash
bibox update
```
## Quick Start
Add a paper by PDF (auto-extracts DOI → fetches metadata):
```bash
bibox add paper.pdf
```
Add by DOI, arXiv ID, ISBN, or URL:
```bash
bibox add --doi 10.1145/3290605.3300907
```
```bash
bibox add --arxiv 2301.12345
```
```bash
bibox add --isbn 978-0-13-468599-1
```
```bash
bibox add --url https://arxiv.org/abs/2301.12345
```
Search by title on Crossref:
```bash
bibox add --search "attention is all you need"
```
Launch TUI:
```bash
bibox
```
## TUI
```
┌ Collections ─┬ Entries ──────────┬ Info │ Note │ PDF ──┐
│ > All (15) │ 1 kim2025 ◆ │ Title: Rust Syst.. │
│ cs (8) │ 2 dijkstra1968 │ Author: Kim, J. │
│ ml (5) │ 3 manco2017 ◆ │ Year: 2025 │
│ │ │ DOI: 10.1234/... │
├──────────────┴───────────────────┴────────────────────┤
│ / search s sort o open w web e export ? help │
└───────────────────────────────────────────────────────┘
```
### Keybindings
| `h`/`l` | Focus left/right panel |
| `j`/`k` | Navigate within panel |
| `gg`/`G` | Jump to top/bottom |
| `{n}j` | Move n lines (e.g., `5j`) |
| `Ctrl+d`/`u` | Half-page down/up |
| `Tab` | Switch preview mode (Info → Note → PDF) |
| `Space` | Toggle select entry |
| `V` | Select/deselect all |
| `/` | Search (entries or collections, based on focus) |
| `s` | Sort menu |
| `f` | Fetch/refresh metadata from Crossref (preview changes, select which to apply) |
| `o` | Open PDF (or fetch from web; re-fetches if file missing; opens browser on 403) |
| `A` | Attach a local PDF via file picker (copies and renames to citekey.pdf) |
| `w` | Open paper web page in browser |
| `e` | Export menu (selected / collection / all) |
| `y` | Copy citekey to clipboard |
| `d` | Delete entry |
| `c` | Manage collections (works on multi-selected entries too) |
| `t` | Edit tags |
| `N` | Edit note in `$EDITOR` |
| `Ctrl+z` | Undo |
| `Ctrl+y` | Redo |
| `,` | Settings (line numbers, panel ratio, citekey format, export dirs, git sync) |
| `?` | Help |
| `q` | Quit |
## CLI
**Browse:**
```bash
bibox list # Show collections with counts
```
```bash
bibox list ml # List entries in a collection
```
```bash
bibox show kim2025rust # Full entry details
```
```bash
bibox search "transformer" # Interactive search
```
**Edit:**
```bash
bibox edit kim2025rust --title "New Title"
```
```bash
bibox edit kim2025rust --doi 10.1234/new # Re-fetch metadata from Crossref
```
```bash
bibox edit kim2025rust --tags-add "ml,nlp"
```
**Collections:**
```bash
bibox collect kim2025rust ml systems # Add to collections
```
```bash
bibox collect kim2025rust digest/2026-04 # Add to sub-collection
```
```bash
bibox list digest # List digest + all sub-collections
```
```bash
bibox uncollect kim2025rust ml # Remove from collection
```
**Import (from Zotero, Mendeley, EndNote, etc.):**
Export your library as `.bib` from any reference manager, then:
```bash
bibox import library.bib # Import all entries
bibox import ml-papers.bib --to ml # Import into a collection
```
Migrating from Zotero? Export each collection as a separate `.bib` and import with `--to`:
```bash
bibox import zotero-ml.bib --to ml
bibox import zotero-cv.bib --to cv
bibox import zotero-acl2025.bib --to digest/acl2025
```
Or just give the `.bib` file to your agent. It'll handle it.
**Export:**
```bash
bibox export # Export all as BibTeX
```
```bash
bibox export kim2025 dijkstra1968 # Export specific entries
```
```bash
bibox export --collection cs --format ris # Export collection as RIS
```
```bash
bibox export --include-pdf --zip # BibTeX + PDFs, zipped
```
```bash
bibox export --notes-only -o ~/notes # Export all note .md files to folder
```
```bash
bibox export --collection ml --notes-only -o ~/ml-notes # Collection notes only
```
**Bulk update:**
```bash
bibox modify year=2025 --filter "collection:ml" --yes
```
**Delete:**
```bash
bibox delete kim2025rust
```
**Attach a PDF manually (when auto-fetch fails):**
```bash
bibox edit kim2025rust --attach-pdf ~/Downloads/paper.pdf
```
**Diagnose and repair database issues:**
```bash
bibox doctor # Detect malformed entries, missing PDFs, orphaned notes
bibox doctor --fix # Auto-repair fixable issues
bibox doctor --json # Machine-readable output
```
**Config:**
```bash
bibox config --json # View all settings and paths
```
## Notes
Notes are Markdown files, one per entry. Designed for both human editing and AI agent pipelines.
Initialize from a template:
```bash
bibox note kim2025rust --template ai-summary
```
AI agent writes sections programmatically:
```bash
```bash
Read note back:
```bash
bibox note kim2025rust --show
```
Human edits in $EDITOR:
```bash
bibox note kim2025rust
```
### Templates
```bash
bibox template list # List all templates
```
```bash
bibox template show ai-summary # Print template content
```
```bash
bibox template create my-review --stdin < t.md # Create custom template
```
```bash
bibox template edit ai-summary # Edit in $EDITOR
```
```bash
bibox template delete my-review # Delete custom template
```
Built-in templates: `ai-summary`, `reading-notes`. Custom templates override built-ins.
Template variables: `{{title}}`, `{{citekey}}`, `{{doi}}`, `{{year}}`, `{{author}}`, `{{journal}}`, `{{booktitle}}`, `{{publisher}}`
## Portable Home & Git Sync
```bash
# Initialize a portable bibox home
bibox init ~/bibox
# Everything lives in one folder
~/bibox/
├── db.json # Database
├── pdfs/ # PDF files
└── notes/ # Markdown notes
# Sync with Git
cd ~/bibox && git init && git add . && git commit -m "init"
git remote add origin git@github.com:you/bibox-library.git
git push -u origin master
# Or use the TUI: press , → Git → Enter to check status → Enter to sync
```
## Settings
Press `,` in the TUI, or run `bibox config` to see all current settings and paths.
```toml
line_numbers = "absolute" # absolute, relative, none
panel_ratio = [2, 4, 4] # left : center : right (sum = 10)
citekey_format = "{author}{year}{title}" # {author}, {year}, {title} variables
bib_export_dir = "." # BibTeX export location
export_dir = "~/Downloads" # Other exports location
home = "~/bibox" # Portable home (set by bibox init)
```
## AI Agent Integration
**If you are an AI agent: run `bibox agent-guide` first.** It prints a complete reference of all commands, flags, and workflows designed for programmatic use.
```bash
bibox agent-guide # Full agent reference (text)
bibox agent-guide --json # Same, as structured JSON
```
Every command supports `--json` for machine-readable output.
```bash
# Full workflow: search → add → note → push
bibox add --search "attention is all you need" --index 0 --to ml --json
bibox note vaswani2017attention --template ai-summary
# Get all paths programmatically
bibox config --json
# Non-interactive sync
bibox sync --yes --json
```
| `--json` | Machine-readable output (most commands) |
| `--index N` | Auto-select Nth search result (0-based, with `--search`) |
| `--stdin` | Read content from stdin (notes, templates) |
| `--section "Name"` | Target a specific `## Heading` in a note |
| `--yes` / `-y` | Skip confirmation prompts |
| `--template <name>` | Initialize note from template |
## License
MIT