nexus-cli 0.7.0

DEPRECATED — absorbed into obsidian-cli-ops (obs). See https://data-wise.github.io/obsidian-cli-ops/migration/

Nexus CLI — DEPRECATED

⚠️ nexus-cli has been absorbed into obsidian-cli-ops (obs).

All research, teaching, writing, and vault commands are now available under obs research …. This package will no longer receive updates. Please migrate:

brew upgrade data-wise/tap/obsidian-cli-ops
# obs research zotero search "query"
# obs research manuscript list
# obs research course list

See the migration guide for the full command mapping.

---

Knowledge workflow CLI for research, teaching, and writing. Claude is the brain, Nexus is the body.

📚 Documentation | 🚀 Quick Start | 📖 Changelog

    ╔═══════════════════════════════════════════════════════════╗
    ║                                                           ║
    ║     ███╗   ██╗███████╗██╗  ██╗██╗   ██╗███████╗          ║
    ║     ████╗  ██║██╔════╝╚██╗██╔╝██║   ██║██╔════╝          ║
    ║     ██╔██╗ ██║█████╗   ╚███╔╝ ██║   ██║███████╗          ║
    ║     ██║╚██╗██║██╔══╝   ██╔██╗ ██║   ██║╚════██║          ║
    ║     ██║ ╚████║███████╗██╔╝ ██╗╚██████╔╝███████║          ║
    ║     ╚═╝  ╚═══╝╚══════╝╚═╝  ╚═╝ ╚═════╝ ╚══════╝          ║
    ║                                                           ║
    ║         Research • Teaching • Writing • Knowledge         ║
    ║                                                           ║
    ╚═══════════════════════════════════════════════════════════╝

Philosophy

Nexus does NOT do AI. It provides data and operations. Claude does the thinking.

┌─────────────────────────────────────────────────────────────────┐
│                    THE NEXUS ARCHITECTURE                       │
├─────────────────────────────────────────────────────────────────┤
│                                                                 │
│                      ┌─────────────┐                           │
│                      │   CLAUDE    │  (Brain)                  │
│                      │ • Thinking  │                           │
│                      │ • Planning  │                           │
│                      │ • Writing   │                           │
│                      └──────┬──────┘                           │
│                             │                                   │
│                             │ uses                              │
│                             ▼                                   │
│                      ┌─────────────┐                           │
│                      │   NEXUS     │  (Body)                   │
│                      │ • Searching │                           │
│                      │ • Reading   │                           │
│                      │ • Writing   │                           │
│                      │ • Organizing│                           │
│                      └──────┬──────┘                           │
│                             │                                   │
│              ┌──────────────┼──────────────┐                   │
│              ▼              ▼              ▼                   │
│       ┌──────────┐   ┌──────────┐   ┌──────────┐              │
│       │  ZOTERO  │   │   PDFs   │   │  VAULT   │              │
│       │  2,728   │   │  1,800   │   │ Obsidian │              │
│       │  papers  │   │  files   │   │  notes   │              │
│       └──────────┘   └──────────┘   └──────────┘              │
│                                                                 │
└─────────────────────────────────────────────────────────────────┘

Installation

# From source (recommended)
git clone https://github.com/Data-Wise/nexus-cli
cd nexus-cli
pip install -e .

# Or with uv
uv sync

Quick Start

New to Nexus? Start with Interactive Tutorials! 🎓

# List available tutorials
nexus learn

# Start the Getting Started tutorial (7 steps, ~10 min)
nexus learn getting-started

# Intermediate workflows (11 steps, ~20 min)
nexus learn medium

# Advanced techniques (12 steps, ~30 min)
nexus learn advanced

See TUTORIAL_GUIDE.md for detailed tutorial documentation.

Quick Commands

# Check your setup
nexus doctor

# Configure paths
nexus config

# Search your Zotero library
nexus research zotero search "mediation analysis"

# Search your vault
nexus knowledge vault search "sensitivity"

# Unified search across everything
nexus knowledge search "propensity score"

Command Reference

Global Commands

Command	Description
nexus help [topic]	Flow-cli-style quick-start cheatsheet (main, research, teach, write, knowledge)
nexus doctor	Check health + validate PARA vault structure (exits 1 if required folders missing)
nexus config	View or edit configuration
nexus learn	Interactive learning tutorials (getting-started, medium, advanced)
nexus --version	Show version

---

🧠 Knowledge Domain

Obsidian vault and unified search operations.

Unified Search

nexus knowledge search "query"              # Search across all sources

Vault Operations

nexus knowledge vault search "term"         # Search vault notes
nexus knowledge vault read "path/note.md"   # Read a note
nexus knowledge vault write "path" content  # Write to a note
nexus knowledge vault daily                 # Open/create daily note
nexus knowledge vault backlinks "note.md"   # Find notes linking here
nexus knowledge vault recent                # Show recently modified
nexus knowledge vault orphans               # Find unlinked notes
nexus knowledge vault template "name"       # Create from template

Graph Export ⭐ NEW in v0.5.0

# Export vault graph to multiple formats
nexus knowledge vault export graphml graph.graphml    # GraphML (Gephi, Cytoscape)
nexus knowledge vault export d3 graph.json            # D3.js visualization
nexus knowledge vault export json graph.json          # JSON format

# Include tags as nodes
nexus knowledge vault export graphml graph.graphml --tags

# Limit node count for large vaults
nexus knowledge vault export d3 graph.json --limit 100

---

🔬 Research Domain

Literature management, Zotero, and PDF operations.

Zotero Operations

nexus research zotero search "query"        # Search Zotero library
nexus research zotero get KEY               # Get item details
nexus research zotero cite KEY              # Generate citation
nexus research zotero recent                # Recently modified items
nexus research zotero tags                  # List all tags
nexus research zotero collections           # List all collections
nexus research zotero by-tag "tag"          # Items with specific tag

PDF Operations

nexus research pdf extract FILE             # Extract text from PDF
nexus research pdf search "query"           # Search across PDFs
nexus research pdf list                     # List all PDFs
nexus research pdf info FILE                # Show PDF information

---

📚 Teaching Domain

Course management and Quarto operations.

Course Management

nexus teach course list                     # List all courses
nexus teach course show NAME                # Show course details
nexus teach course lectures NAME            # List course lectures
nexus teach course materials NAME           # List all materials
nexus teach course syllabus NAME            # Show syllabus

Quarto Operations

nexus teach quarto build                    # Build Quarto project
nexus teach quarto preview                  # Start preview server
nexus teach quarto info                     # Show Quarto info
nexus teach quarto clean                    # Clean build artifacts
nexus teach quarto formats                  # List output formats

---

✍️ Writing Domain

Manuscript and bibliography management.

Manuscript Management

nexus write manuscript list                 # List all manuscripts
nexus write manuscript show NAME            # Show manuscript details
nexus write manuscript active               # Show active manuscripts
nexus write manuscript search "query"       # Search manuscripts
nexus write manuscript stats                # Show statistics
nexus write manuscript deadlines            # Show deadlines/targets

Batch Operations ⭐ NEW in v0.5.0

# Update status for multiple manuscripts
nexus write manuscript batch-status paper1 paper2 --status review

# Update progress for multiple manuscripts
nexus write manuscript batch-progress paper1:75 paper2:90 paper3:50

# Archive old manuscripts
nexus write manuscript batch-archive old-paper1 old-paper2

# Export metadata to JSON or CSV
nexus write manuscript export manuscripts.json
nexus write manuscript export manuscripts.csv --format csv

Bibliography Operations

nexus write bib list MANUSCRIPT             # List bibliography entries
nexus write bib search "query"              # Search bibliography
nexus write bib check MANUSCRIPT            # Check citations (missing/unused)
nexus write bib zotero "query"              # Search Zotero for entries

---

🔌 Integration Domain

External tool integrations.

nexus integrate aiterm                      # Manage aiterm integration
nexus integrate claude                      # Manage Claude plugin

---

JSON Output

All commands support --json for machine-readable output:

nexus write manuscript stats --json | jq '.total_manuscripts'
nexus research zotero search "mediation" --json | jq '.[0].title'

Claude Integration

Nexus is designed to work with Claude via:

1. Piping to Claude Code

nexus research zotero search "mediation" --json | \
  claude -p "Summarize these papers"

2. Claude Calls Nexus (Primary Pattern)

In Claude Code, Claude uses Bash to call nexus commands directly.

3. Claude Code Plugin

Install the included plugin for enhanced Claude Code integration:

ln -sf /path/to/nexus-cli/plugin ~/.claude/plugins/nexus-cli

Configuration

Configuration file: ~/.config/nexus/config.yaml

vault:
  path: ~/Library/Mobile Documents/iCloud~md~obsidian/Documents
  templates: ~/path/to/templates

zotero:
  database: ~/Zotero/zotero.sqlite
  storage: ~/Zotero/storage

teaching:
  courses_dir: ~/projects/teaching

writing:
  manuscripts_dir: ~/projects/quarto/manuscripts

# View config
nexus config

# Edit config (opens in $EDITOR)
nexus config --edit

What's New in v0.4.0

🎉 Major Release - Production-ready with enterprise-grade quality!

• ✅ 235 Tests with 53% coverage (+10% from v0.3.0)
• 🔄 Enhanced CI/CD with matrix testing, security scanning, and coverage enforcement
• 📚 Full Documentation site with MkDocs + Material theme
• 🧪 Advanced Testing for PDF, Zotero, and Quarto modules
• 🔒 Security scanning with Bandit
• 📊 Coverage Thresholds enforced at 40%+

See the full Changelog for details.

Development

Running Tests

# Run all tests
pytest

# With coverage report
pytest --cov=nexus --cov-report=html

# Specific test file
pytest tests/test_vault.py

# Skip integration tests
pytest -m "not integration"

Contributing

We welcome contributions! Please see our Contributing Guide for details.

Development Setup

# Clone the repository
git clone https://github.com/Data-Wise/nexus-cli
cd nexus-cli

# Install with development dependencies
pip install -e ".[dev,docs]"

# Run tests
pytest

# Build documentation locally
mkdocs serve

License

MIT