status: complete
priority: 1
progress: 100
next: Ready for production use
type: dev
checkpoint: v0.4.0 - 256 tests passing (53% coverage), GitHub Actions CI/CD configured

# ═══════════════════════════════════════════════════════════════════
# Nexus CLI - Knowledge Workflow for Research, Teaching, Writing
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🔧 Nexus CLI Development Status
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📍 LOCATION
~/projects/dev-tools/nexus-cli/

⏰ LAST UPDATED
2025-12-25 - Test coverage expanded, CI/CD configured

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🎯 CURRENT STATUS
**ALL PHASES COMPLETE - v0.4.0 PRODUCTION READY**

Phase 9 test expansion completed:
- ✅ 256 pytest tests passing (53% coverage, +10%)
- ✅ GitHub Actions CI/CD configured (Python 3.11-3.13, Ubuntu/macOS)
- ✅ PyPI publish workflow on release
- ✅ QuartoManager tests (29 tests)
- ✅ PDFExtractor tests (25 tests)
- ✅ ZoteroClient tests (20+ tests)
- ✅ MCP server with 17 tools
- ✅ Validation, edge case, and integration tests
- ✅ Claude Code plugin installed

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📊 PROGRESS

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

Domains:
Phase 2: Knowledge         ████████████████████ 100% ✅
Phase 3: Research          ████████████████████ 100% ✅
Phase 4a: Teaching         ████████████████████ 100% ✅
Phase 4b: Writing          ████████████████████ 100% ✅
Phase 5: Claude Plugin     ████████████████████ 100% ✅
Phase 6: Testing & Docs    ████████████████████ 100% ✅

**Overall Progress**: 100% (v0.1.0 Release Ready)

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📋 ENHANCEMENTS COMPLETED (2025-12-25)

v0.4.0 improvements (current):
- [✅] Test coverage expanded (43% → 53%)
- [✅] 256 tests total (79 new tests)
- [✅] QuartoManager comprehensive tests
- [✅] PDFExtractor with mock subprocess
- [✅] ZoteroClient with mock SQLite database
- [✅] GitHub Actions CI/CD configured

v0.3.0 improvements:
- [✅] 177 tests covering all domains
- [✅] Validation tests for data models
- [✅] Edge case and error handling
- [✅] CLI integration tests

v0.2.0 improvements:
- [✅] MCP server for tool calling
- [✅] PDF text extraction improvements
- [✅] Vault graph visualization

Future improvements:
- [ ] Further test coverage improvements (target 80%)
- [ ] MkDocs documentation site

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📊 TEST SUMMARY

256 tests total, all passing (53% coverage):

Core tests:
- tests/test_config.py           - Config loading (3 tests)
- tests/test_vault.py            - Vault operations (33 tests)
- tests/test_manuscript.py       - Manuscript management (7 tests)
- tests/test_bibliography.py     - Bibliography parsing (11 tests)
- tests/test_courses.py          - Course management (10 tests)
- tests/test_cli.py              - CLI commands (19 tests)
- tests/test_zotero.py           - Zotero item (6 tests)
- tests/test_pdf.py              - PDF document (4 tests)
- tests/test_quarto.py           - Quarto project (4 tests)
- tests/test_search.py           - Unified search (30 tests)

Comprehensive tests:
- tests/test_validation.py       - Data model validation (70 tests)
- tests/test_cli_integration.py  - CLI integration (37 tests)
- tests/test_edge_cases.py       - Edge cases & errors (46 tests)

New in v0.4.0:
- tests/test_quarto_manager.py   - QuartoManager (29 tests) ⭐ NEW
- tests/test_pdf_extractor.py    - PDFExtractor (25 tests) ⭐ NEW
- tests/test_zotero_client.py    - ZoteroClient (20+ tests) ⭐ NEW

Coverage by module:
- teaching/quarto.py: 91% | utils/config.py: 80%
- research/pdf.py: 77% | writing/manuscript.py: 74%
- research/zotero.py: 73% | writing/bibliography.py: 72%
- teaching/courses.py: 70% | knowledge/vault.py: 66%
- knowledge/search.py: 60%

Run: `uv run pytest --cov=nexus`

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

🔗 RELATED PROJECTS

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

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💡 ARCHITECTURE

**Claude Integration (No API Needed)**

Four patterns:
1. **MCP Server**: 17 tools via Model Context Protocol ⭐ NEW
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, PDFs, literature
- 📚 Teaching: Courses, materials, Quarto
- ✍️ Writing: Manuscripts, bibliography, LaTeX
- 🧠 Knowledge: Vault, unified search

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📁 KEY FILES

- nexus/cli.py                  - Main CLI (Typer) - 1800+ lines
- nexus/utils/config.py         - Configuration
- nexus/knowledge/vault.py      - VaultManager (Phase 2)
- nexus/knowledge/search.py     - UnifiedSearch (Phase 2+3)
- nexus/research/zotero.py      - ZoteroClient (Phase 3)
- nexus/research/pdf.py         - PDFExtractor (Phase 3)
- nexus/teaching/courses.py     - CourseManager (Phase 4a)
- nexus/teaching/quarto.py      - QuartoManager (Phase 4a)
- nexus/writing/manuscript.py   - ManuscriptManager (Phase 4b)
- nexus/writing/bibliography.py - BibliographyManager (Phase 4b)
- tests/                        - 58 pytest tests
- pyproject.toml                - Project metadata
- install.sh                    - Installation script
- CLAUDE.md                     - Claude Code guidance
- README.md                     - User documentation

