nexus-cli 0.3.0__py3-none-any.whl

nexus_cli-0.3.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: nexus-cli
+Version: 0.3.0
+Summary: Knowledge workflow CLI for research, teaching, and writing - Claude's body for academic work
+Project-URL: Homepage, https://github.com/Data-Wise/nexus-cli
+Project-URL: Documentation, https://data-wise.github.io/nexus-cli
+Project-URL: Repository, https://github.com/Data-Wise/nexus-cli
+Author-email: DT <dt@example.com>
+License: MIT
+Keywords: claude,cli,knowledge-management,obsidian,research,zotero
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: pydantic-settings>=2.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: typer>=0.12.0
+Provides-Extra: dev
+Requires-Dist: bandit[toml]>=1.7.0; extra == 'dev'
+Requires-Dist: coverage-badge>=1.1.0; extra == 'dev'
+Requires-Dist: mypy>=1.10.0; extra == 'dev'
+Requires-Dist: pytest-benchmark>=4.0.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest-mock>=3.12.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.4.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-git-revision-date-localized-plugin>=1.2.0; extra == 'docs'
+Requires-Dist: mkdocs-material>=9.0.0; extra == 'docs'
+Requires-Dist: mkdocs>=1.5.0; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.24.0; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# Nexus CLI
+
+[![CI](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml/badge.svg)](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml)
+[![Documentation](https://github.com/Data-Wise/nexus-cli/actions/workflows/docs.yml/badge.svg)](https://data-wise.github.io/nexus-cli)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Version](https://img.shields.io/badge/version-0.4.0-blue.svg)](https://github.com/Data-Wise/nexus-cli/releases)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![codecov](https://codecov.io/gh/Data-Wise/nexus-cli/branch/main/graph/badge.svg)](https://codecov.io/gh/Data-Wise/nexus-cli)
+[![Tests](https://img.shields.io/badge/tests-235%20passing-success.svg)](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml)
+[![Coverage](https://img.shields.io/badge/coverage-53%25-yellow.svg)](https://codecov.io/gh/Data-Wise/nexus-cli)
+
+> **Knowledge workflow CLI for research, teaching, and writing.**
+> Claude is the brain, Nexus is the body.
+
+**📚 [Documentation](https://data-wise.github.io/nexus-cli)** | **🚀 [Quick Start](https://data-wise.github.io/nexus-cli/getting-started/quickstart/)** | **📖 [Changelog](https://data-wise.github.io/nexus-cli/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
+
+```bash
+# 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
+
+```bash
+# 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 doctor` | Check Nexus health and integrations |
+| `nexus config` | View or edit configuration |
+| `nexus --version` | Show version |
+
+---
+
+### 🧠 Knowledge Domain
+
+Obsidian vault and unified search operations.
+
+#### Unified Search
+```bash
+nexus knowledge search "query"              # Search across all sources
+```
+
+#### Vault Operations
+```bash
+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
+```
+
+---
+
+### 🔬 Research Domain
+
+Literature management, Zotero, and PDF operations.
+
+#### Zotero Operations
+```bash
+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
+```bash
+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
+```bash
+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
+```bash
+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
+```bash
+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
+```
+
+#### Bibliography Operations
+```bash
+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.
+
+```bash
+nexus integrate aiterm                      # Manage aiterm integration
+nexus integrate claude                      # Manage Claude plugin
+```
+
+---
+
+## JSON Output
+
+All commands support `--json` for machine-readable output:
+
+```bash
+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
+```bash
+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:
+```bash
+ln -sf /path/to/nexus-cli/plugin ~/.claude/plugins/nexus-cli
+```
+
+## Configuration
+
+Configuration file: `~/.config/nexus/config.yaml`
+
+```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
+```
+
+```bash
+# 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](https://data-wise.github.io/nexus-cli/changelog/) for details.
+
+## Development
+
+### Running Tests
+
+```bash
+# 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](https://github.com/Data-Wise/nexus-cli/blob/main/CONTRIBUTING.md) for details.
+
+### Development Setup
+
+```bash
+# 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

nexus_cli-0.3.0.dist-info/RECORD

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nexus_cli-0.3.0.dist-info/entry_points.txt

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+[console_scripts]
+nexus = nexus.cli:app