status: released
priority: 1
progress: 100
next: v0.6.0 planning - additional exporters and interactive CLI
type: dev
checkpoint: v0.5.0 RELEASED - 302 tests passing (54% coverage), graph export & batch ops
release_date: 2025-12-25
release_url: https://github.com/Data-Wise/nexus-cli/releases/tag/v0.5.0
docs_url: https://data-wise.github.io/nexus-cli/

# ═══════════════════════════════════════════════════════════════════
# Nexus CLI - Knowledge Workflow for Research, Teaching, Writing
# ═══════════════════════════════════════════════════════════════════

🔧 Nexus CLI Development Status
────────────────────────────────────────

📍 LOCATION
~/projects/dev-tools/nexus-cli/

⏰ LAST UPDATED
2025-12-25 - v0.5.0 RELEASED - Graph Export & Batch Operations!

────────────────────────────────────────

🎉 RELEASE v0.5.0 - GRAPH EXPORT & BATCH OPERATIONS

**Feature enhancement release with productivity improvements!**

Release highlights:
- ✅ 302 tests passing (54% coverage, +9.8% from v0.4.0)
- ✅ Graph export formats (GraphML, D3.js, JSON)
- ✅ Batch manuscript operations (status, progress, archive)
- ✅ Comprehensive documentation (9,500+ lines added)
- ✅ Manuscript module: 78% coverage (+27% improvement)
- ✅ GitHub Pages updated
- ✅ GitHub Release published
- ✅ All CI/CD pipelines passing

────────────────────────────────────────

🎯 CURRENT STATUS

**v0.5.0 SHIPPED** ✅

All v0.5.0 features complete:
- ✅ Graph Export Formats (GraphML, D3.js)
- ✅ Batch Manuscript Operations
- ✅ Comprehensive Documentation (tutorials, API, architecture)
- ✅ Enhanced Test Coverage (54.35%, +4.47%)
- ✅ Manuscript Module: 78% coverage (+27%)

Release artifacts:
- Git tag: v0.5.0
- GitHub Release: https://github.com/Data-Wise/nexus-cli/releases/tag/v0.5.0
- Documentation: https://data-wise.github.io/nexus-cli/
- CI/CD: All passing ✅

────────────────────────────────────────

📊 PROGRESS

Core Infrastructure:
CLI Skeleton               ████████████████████ 100% ✅
Configuration System       ████████████████████ 100% ✅
Doctor Command             ████████████████████ 100% ✅
Project Setup              ████████████████████ 100% ✅

Domains:
Knowledge Domain           ████████████████████ 100% ✅
Research Domain            ████████████████████ 100% ✅
Teaching Domain            ████████████████████ 100% ✅
Writing Domain             ████████████████████ 100% ✅
Claude Plugin              ████████████████████ 100% ✅
Testing & CI/CD            ████████████████████ 100% ✅
Documentation              ████████████████████ 100% ✅

**Overall Progress**: 100% ✅ (v0.4.0 Released)

────────────────────────────────────────

📦 RELEASE DETAILS

Version: 0.5.0
Date: December 25, 2025
Type: Feature Enhancement Release
Status: ✅ Released

Key improvements:
1. **Graph Export Formats**
   - GraphML format (Gephi, Cytoscape, yEd)
   - D3.js format (web visualizations)
   - Enhanced JSON format with tags/limits
   - Proper XML escaping for special characters

2. **Batch Manuscript Operations**
   - Batch status updates for multiple manuscripts
   - Batch progress updates
   - Batch archiving to Archive/ directory
   - Metadata export to JSON/CSV

3. **Comprehensive Documentation** (~9,500 lines)
   - 4 tutorial pages: first-steps, vault-setup, zotero, graph-viz
   - API reference with code examples
   - MCP server documentation (17 tools)
   - Testing guide (302 tests, 54% coverage)
   - Architecture documentation

4. **Quality Improvements**
   - 27 new tests (+9.8% increase)
   - Coverage: 49.88% → 54.35% (+4.47%)
   - Manuscript module: 50.99% → 78.03% (+27%)
   - New test files: test_graph_export, test_manuscript_batch

────────────────────────────────────────

📊 TEST SUMMARY

302 tests total (301 passing, 1 skipped) - 54.35% coverage:

Core tests:
- test_config.py           - Config loading (3 tests)
- test_vault.py            - Vault operations (22 tests)
- test_manuscript.py       - Manuscript management (11 tests)
- test_bibliography.py     - Bibliography parsing (13 tests)
- test_courses.py          - Course management (9 tests)
- test_cli.py              - CLI commands (13 tests)
- test_zotero.py           - Zotero item (5 tests)
- test_pdf.py              - PDF document (3 tests)
- test_quarto.py           - Quarto project (4 tests)
- test_search.py           - Unified search (21 tests)

Integration & validation:
- test_validation.py       - Data model validation (28 tests)
- test_cli_integration.py  - CLI integration (19 tests)
- test_cli_commands.py     - CLI commands (19 tests)
- test_edge_cases.py       - Edge cases & errors (25 tests)

v0.4.0 comprehensive tests:
- test_quarto_manager.py   - QuartoManager (29 tests) ⭐
- test_pdf_extractor.py    - PDFExtractor (23 tests) ⭐
- test_zotero_client.py    - ZoteroClient (28 tests) ⭐

v0.5.0 new tests:
- test_graph_export.py     - Graph export formats (11 tests) ⭐
- test_manuscript_batch.py - Batch operations (16 tests) ⭐

Coverage by module (top performers):
- teaching/quarto.py: 91% (+4% in v0.5.0)
- utils/config.py: 80%
- writing/manuscript.py: 78% (+27% in v0.5.0) 🎯
- research/pdf.py: 77%
- research/zotero.py: 73%
- writing/bibliography.py: 72%
- teaching/courses.py: 70%
- knowledge/vault.py: 59% (+6% in v0.5.0)
- knowledge/search.py: 60%

Run: `pytest --cov=nexus --cov-report=html`

────────────────────────────────────────

🎯 NEXT STEPS (v0.6.0 Planning)

Feature enhancements:
- [ ] Additional graph export formats (GML, Cytoscape JSON)
- [ ] Batch operations for other domains (courses, bibliography)
- [ ] Interactive CLI mode with prompts
- [ ] Workflow automation commands
- [ ] Export to graph databases (Neo4j, ArangoDB)

Quality improvements:
- [ ] Increase test coverage to 60%+
- [ ] Performance benchmarks with pytest-benchmark
- [ ] Improve CLI test coverage (currently 20%)
- [ ] Additional integration tests
- [ ] User acceptance testing

Developer experience:
- [ ] Plugin system for custom exporters
- [ ] API client library
- [ ] Web UI for graph visualization
- [ ] Enhanced error messages

────────────────────────────────────────

🔗 RELATED PROJECTS

| Project | Location | Purpose |
|---------|----------|---------|
| Nexus MCP Server | ~/mcp-servers/nexus/ | MCP server with 17 tools |
| Nexus (docs) | ~/projects/dev-tools/nexus/ | Architecture & vault template |
| Statistical Research | ~/.claude/plugins/statistical-research/ | Research MCP plugin |

────────────────────────────────────────

💡 ARCHITECTURE

**Claude Integration (No API Needed)**

Four patterns:
1. **MCP Server**: 17 tools via Model Context Protocol
2. **Claude calls Nexus**: Claude runs `nexus` via Bash
3. **Piping**: `nexus search | claude -p "summarize"`
4. **Plugin skills**: Teach Claude how to use nexus

**Four Domains**:
- 🔬 Research: Zotero (2,728 papers), PDFs (~1,800 files), literature
- 📚 Teaching: Courses, materials, Quarto integration
- ✍️ Writing: Manuscripts, bibliography, LaTeX
- 🧠 Knowledge: Vault (Obsidian), unified search, graph viz

────────────────────────────────────────

📁 KEY FILES

Core:
- nexus/cli.py                  - Main CLI (Typer) - 1109 lines
- nexus/utils/config.py         - Configuration - 82 lines
- pyproject.toml                - Project metadata (v0.5.0)
- mkdocs.yml                    - Documentation config
- README.md                     - User documentation
- CLAUDE.md                     - Claude Code guidance

Domains:
- nexus/knowledge/vault.py      - VaultManager - 319 lines (59% cov) ⭐ +39 lines
- nexus/knowledge/search.py     - UnifiedSearch - 100 lines (60% cov)
- nexus/research/zotero.py      - ZoteroClient - 193 lines (73% cov)
- nexus/research/pdf.py         - PDFExtractor - 205 lines (77% cov)
- nexus/teaching/courses.py     - CourseManager - 214 lines (70% cov)
- nexus/teaching/quarto.py      - QuartoManager - 162 lines (91% cov)
- nexus/writing/manuscript.py   - ManuscriptManager - 355 lines (78% cov) ⭐ +116 lines
- nexus/writing/bibliography.py - BibliographyManager - 176 lines (72% cov)

Testing:
- tests/                        - 18 test modules, 302 tests
- .github/workflows/ci.yml      - CI/CD pipeline
- .github/workflows/docs.yml    - Documentation deployment

Documentation:
- docs/                         - MkDocs source files
- site/                         - Built documentation (gh-pages)

────────────────────────────────────────

🔧 QUICK COMMANDS

Development:
```bash
# Run tests
pytest --cov=nexus --cov-report=html

# Type check
mypy nexus/

# Lint
ruff check nexus/ tests/

# Format
ruff format nexus/ tests/

# Serve docs locally
mkdocs serve

# Deploy docs
mkdocs gh-deploy
```

Usage:
```bash
# Doctor check
nexus doctor

# Search knowledge
nexus knowledge search "mediation"

# Search Zotero
nexus research zotero search "causal inference"

# Check bibliography
nexus write bib check manuscript/

# Graph visualization
nexus knowledge vault graph --json > graph.json
```

────────────────────────────────────────

📚 DOCUMENTATION

- **Home**: https://data-wise.github.io/nexus-cli/
- **Installation**: https://data-wise.github.io/nexus-cli/getting-started/installation/
- **Quick Start**: https://data-wise.github.io/nexus-cli/getting-started/quickstart/
- **Configuration**: https://data-wise.github.io/nexus-cli/getting-started/configuration/
- **Tutorials**: https://data-wise.github.io/nexus-cli/tutorials/ ⭐ NEW
- **API Reference**: https://data-wise.github.io/nexus-cli/reference/api/ ⭐ NEW
- **Changelog**: https://data-wise.github.io/nexus-cli/changelog/
- **GitHub**: https://github.com/Data-Wise/nexus-cli
- **Release**: https://github.com/Data-Wise/nexus-cli/releases/tag/v0.5.0

────────────────────────────────────────

✅ v0.5.0 FEATURE RELEASE - RELEASED 2025-12-25
