# CLI Reference

This document describes all available commands in the paperlib CLI.

## Global Options

All commands support these global options:

- `--help`, `-h`: Show help message
- `--version`: Show version information

Many commands also support:
- `--library`, `-L`: Specify library root directory (default: current directory)
- `--json`: Output machine-readable JSON instead of human-readable format

## Commands

### `paperlib init [PATH]`

Initialize a paper library directory structure.

**Arguments:**
- `PATH`: Directory to initialize (default: current directory)

**Examples:**
```bash
# Initialize library in current directory
paperlib init

# Initialize library in specific directory
paperlib init /path/to/my/papers

# Initialize and create parent directories
paperlib init ~/Documents/research/papers
```

**Behavior:**
- Creates standard directory structure (config/, papers/, db/, etc.)
- Safe to run multiple times (idempotent)
- Creates parent directories if they don't exist

---

### `paperlib import`

Import papers into the library from various sources.

**Required (one of):**
- `--pdf PATH`: Import a local PDF file
- `--arxiv ID`: Import paper from arXiv by ID or URL

**Options:**
- `--title TEXT`: Override paper title (for local PDFs)
- `--notes TEXT`: Add notes about the paper
- `--tags TAG1 TAG2`: Add tags to the paper
- `--library PATH`: Specify library directory

**Examples:**
```bash
# Import local PDF
paperlib import --pdf paper.pdf --title "My Research" --tags ml ai

# Import from arXiv
paperlib import --arxiv 2212.06340

# Import with arXiv URL
paperlib import --arxiv https://arxiv.org/abs/2212.06340

# Import to specific library
paperlib import --pdf paper.pdf --library ~/research
```

**Behavior:**
- Generates stable paper ID based on content (local) or arXiv ID
- Copies PDF to structured storage location
- Creates meta.json with paper metadata
- Prevents duplicate imports (same content/ID)
- Indexes paper in search database

---

### `paperlib list`

List all papers in the library with their current status.

**Options:**
- `--library PATH`: Specify library directory
- `--json`: Output in JSON format

**Examples:**
```bash
# List all papers
paperlib list

# List papers in specific library
paperlib list --library ~/research

# Get machine-readable output
paperlib list --json
```

**Output Format:**
```
Found 3 papers:

📄 arxiv-2212_06340
   The new discontinuous Galerkin methods based numerical relativity program Nmesh
   By: Wolfgang Tichy, Liwei Ji, Ananya Adhikari (+2 more)
   Categories: gr-qc

⏳ local-a1b2c3d4e5f6
   Machine Learning Applications in Physics
   Categories: cs.AI, physics.comp-ph
```

**Status Indicators:**
- ⏳ Paper imported, conversion pending
- 📄 PDF converted to Markdown
- 📝 AI summary generated
- ❌ Conversion or processing failed

---

### `paperlib show PAPER_ID`

Show detailed information about a specific paper.

**Arguments:**
- `PAPER_ID`: The unique paper identifier

**Options:**
- `--library PATH`: Specify library directory
- `--json`: Output in JSON format

**Examples:**
```bash
# Show paper details
paperlib show arxiv-2212_06340

# Show with JSON output
paperlib show local-a1b2c3d4 --json
```

**Output includes:**
- All metadata fields
- Processing status
- File locations and existence
- Import timestamp
- Tags and notes

---

### `paperlib convert`

Convert papers from PDF to Markdown using MinerU.

**Options:**
- `--library PATH`: Specify library directory
- `--paper-id ID`: Convert specific paper only

**Examples:**
```bash
# Convert all pending papers
paperlib convert

# Convert specific paper
paperlib convert --paper-id arxiv-2212_06340

# Convert in specific library
paperlib convert --library ~/research
```

**Behavior:**
- Processes papers with `conversion_status: pending`
- Uses MinerU for PDF to Markdown conversion
- Updates metadata with conversion status
- Creates conversion logs in `logs/` directory
- Handles conversion failures gracefully

---

### `paperlib reindex`

Rebuild the search index from stored paper metadata.

**Options:**
- `--library PATH`: Specify library directory

**Examples:**
```bash
# Rebuild index
paperlib reindex

# Rebuild index for specific library
paperlib reindex --library ~/research
```

**Behavior:**
- Clears existing SQLite database
- Scans all meta.json files in papers/ directory
- Rebuilds full-text search index
- Reports statistics on completion
- Safe to run anytime (repairs corrupted index)

---

### `paperlib status`

Show library configuration and layout information.

**Options:**
- `--library PATH`: Specify library directory
- `--json`: Output in JSON format

**Examples:**
```bash
# Show current library status
paperlib status

# Show specific library status
paperlib status --library ~/research
```

**Output:**
```
root: /home/user/papers
config: /home/user/papers/config/config.toml
database: /home/user/papers/db/paperlib.sqlite3
papers: /home/user/papers/papers
inbox: /home/user/papers/inbox
cache: /home/user/papers/cache
```

---

## Future Commands

These commands are planned but not yet implemented:

### `paperlib search QUERY`
Search papers by content and metadata.

### `paperlib summarize [PAPER_ID]`
Generate AI summaries for papers.

### `paperlib export FORMAT`
Export papers in various formats.

### `paperlib doctor`
Diagnose and repair library issues.

---

## Exit Codes

paperlib commands return standard exit codes:

- `0`: Success
- `1`: General error (file not found, invalid arguments, etc.)
- `2`: Command line argument error

## Configuration

paperlib looks for configuration in these locations (in order):
1. `$LIBRARY_ROOT/config/config.toml`
2. `~/.config/paperlib/config.toml`
3. Built-in defaults

## JSON Output Format

When using `--json`, commands output structured data suitable for programmatic consumption:

```json
{
  "papers": [
    {
      "paper_id": "arxiv-2212_06340",
      "title": "Example Paper",
      "authors": ["Alice Smith", "Bob Jones"],
      "conversion_status": "success",
      "imported_at": "2024-01-15T10:30:00"
    }
  ],
  "total": 1
}
```

This format is stable across paperlib versions for reliable automation.