jfox-cli 0.2.2__tar.gz → 0.3.2__tar.gz

{jfox_cli-0.2.2 → jfox_cli-0.3.2}/CLAUDE.md

@@ -56,7 +56,7 @@ Notes are Markdown files with YAML frontmatter stored under `~/.zettelkasten/<kb
 
 | Module | Role |
 |--------|------|
-| `cli.py` | All CLI commands (~1800 lines). Commands follow pattern: `@app.command()` → `_xxx_impl()` helper for reuse |
+| `cli.py` | All CLI commands (~2500 lines). Commands follow pattern: `@app.command()` → `_xxx_impl()` helper for reuse |
 | `config.py` | `ZKConfig` + `use_kb()` context manager for multi-KB switching |
 | `global_config.py` | `GlobalConfigManager` managing `~/.zk_config.json` |
 | `kb_manager.py` | Knowledge base lifecycle (create, rename, remove) |
@@ -66,7 +66,8 @@ Notes are Markdown files with YAML frontmatter stored under `~/.zettelkasten/<kb
 | `models.py` | `Note` data model with frontmatter serialization |
 | `search_engine.py` | `HybridSearchEngine` with `SearchMode` enum, RRF fusion |
 | `bm25_index.py` | BM25 keyword search index |
-| `embedding_backend.py` | Sentence-transformers embedding backend |
+| `embedding_backend.py` | Sentence-transformers embedding backend（支持 daemon 代理） |
+| `daemon/` | Embedding 模型 HTTP 守护进程，`jfox daemon start/stop/status` |
 | `vector_store.py` | ChromaDB vector store for semantic search |
 | `graph.py` | NetworkX knowledge graph from links/backlinks |
 | `template.py` / `template_cli.py` | Jinja2 template system for structured note creation |
@@ -97,6 +98,7 @@ Notes are Markdown files with YAML frontmatter stored under `~/.zettelkasten/<kb
 - **Adding a CLI command**: Add `@app.command()` in `cli.py`, implement `_xxx_impl()` helper, add `--kb` and `--format json` support
 - **Adding a search mode**: Add to `SearchMode` enum in `search_engine.py`, implement in `HybridSearchEngine.search()`, update CLI `--mode` help text
 - **Modifying data models**: Update `Note` class in `models.py`, update `to_markdown()`/`from_markdown()`, consider backward compat
+- **Viewing note content**: `jfox show <id_or_title>` 复用 `find_note_id_by_title_or_id` 定位笔记，只读输出完整 Markdown
 
 ## Test Infrastructure
 

jfox_cli-0.3.2/PKG-INFO

@@ -0,0 +1,463 @@
+Metadata-Version: 2.4
+Name: jfox-cli
+Version: 0.3.2
+Summary: JFox - Zettelkasten 知识管理 CLI 工具
+Project-URL: Homepage, https://github.com/zhuxixi/jfox
+Project-URL: Repository, https://github.com/zhuxixi/jfox
+Author-email: User <user@example.com>
+License: MIT
+Keywords: cli,jfox,knowledge-management,note-taking,zettelkasten
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Requires-Dist: chromadb>=0.5.0
+Requires-Dist: fastapi>=0.110.0
+Requires-Dist: jinja2>=3.0
+Requires-Dist: networkx>=3.0
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rank-bm25>=0.2.2
+Requires-Dist: rich>=13.0.0
+Requires-Dist: sentence-transformers>=3.0
+Requires-Dist: typer>=0.12.0
+Requires-Dist: uvicorn[standard]>=0.27.0
+Requires-Dist: watchdog>=3.0
+Provides-Extra: dev
+Requires-Dist: black>=23.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0; extra == 'dev'
+Requires-Dist: pytest-timeout>=2.0; extra == 'dev'
+Requires-Dist: pytest-xdist>=3.0; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# JFox
+
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](pyproject.toml)
+[![Platform](https://img.shields.io/badge/platform-Windows%20%7C%20macOS%20%7C%20Linux-lightgrey.svg)](#)
+
+> A local-first Zettelkasten knowledge management CLI.
+> Bidirectional links, semantic search, knowledge graphs — all offline, all on CPU.
+
+**JFox** (**J** + **Fox** / "box") is a command-line tool that helps you build a personal knowledge base using the [Zettelkasten method](https://en.wikipedia.org/wiki/Zettelkasten). Notes live as plain Markdown files on your disk, connected by `[[wiki links]]` and indexed for instant semantic search.
+
+---
+
+## Table of Contents
+
+- [Features](#features)
+- [Architecture](#architecture)
+- [Data Flows](#data-flows)
+- [Quick Start](#quick-start)
+- [Command Reference](#command-reference)
+- [Note Format](#note-format)
+- [Contributing](#contributing)
+- [License](#license)
+
+---
+
+## Features
+
+- **Three note types** — Fleeting (quick capture), Literature (reading notes), Permanent (refined knowledge)
+- **Bidirectional links** — Write `[[Note Title]]` to connect notes; backlinks are auto-generated
+- **Hybrid search** — BM25 keyword search + semantic vector search, fused with Reciprocal Rank Fusion
+- **Knowledge graph** — NetworkX-powered link analysis: clusters, orphans, hubs, shortest paths
+- **File watcher** — Real-time index updates when you edit notes with any editor
+- **Multi knowledge bases** — Manage separate KBs for work, personal, research, etc.
+
+---
+
+## Architecture
+
+### Three-Layer Design
+
+```mermaid
+graph TB
+    subgraph CLI ["CLI Layer"]
+        cmd["jfox commands<br/>(Typer)"]
+    end
+    subgraph Storage ["Storage Layer"]
+        note[note.py]
+        models[models.py]
+        md[("Markdown Files<br/>YAML Frontmatter")]
+    end
+    subgraph Index ["Index Layer"]
+        se[search_engine.py<br/>HybridSearchEngine]
+        vs[vector_store.py<br/>ChromaDB]
+        bm[bm25_index.py<br/>BM25Okapi]
+        emb[embedding_backend.py<br/>all-MiniLM-L6-v2]
+        daemon["daemon/<br/>HTTP Server"]
+    end
+    subgraph Analysis ["Analysis Layer"]
+        gph["graph.py<br/>NetworkX DiGraph"]
+    end
+    subgraph Watcher ["File Watcher"]
+        idx[indexer.py<br/>watchdog]
+    end
+
+    cmd --> note & se & gph
+    note --> models --> md
+    se --> vs & bm
+    vs --> emb
+    emb -.->|"preferred"| daemon
+    idx --> vs
+```
+
+### Module Map
+
+| Module | Role |
+|--------|------|
+| `cli.py` | All CLI commands (~2500 lines). Each command delegates to a `_xxx_impl()` helper |
+| `config.py` | Per-KB config (`ZKConfig`) + `use_kb()` context manager for KB switching |
+| `global_config.py` | Multi-KB registry in `~/.zk_config.json` |
+| `kb_manager.py` | KB lifecycle: create, rename, remove, switch |
+| `note.py` | CRUD on Markdown files with dual-index updates |
+| `models.py` | `Note` dataclass with YAML frontmatter serialization |
+| `search_engine.py` | `HybridSearchEngine` — dispatches to semantic/keyword/hybrid with RRF fusion |
+| `vector_store.py` | ChromaDB wrapper with cosine similarity search |
+| `bm25_index.py` | BM25 keyword index with Chinese/English tokenizer |
+| `embedding_backend.py` | Lazy-loaded SentenceTransformer (`all-MiniLM-L6-v2`, 384-dim vectors) |
+| `daemon/` | Embedding HTTP 守护进程，常驻模型避免重复加载 |
+| `graph.py` | NetworkX DiGraph built from links + wiki links; BFS, clusters, hubs |
+| `indexer.py` | File watcher (watchdog) with debounce for incremental ChromaDB updates |
+| `formatters.py` | Output in JSON, CSV, YAML, Table, Paths, Tree formats |
+| `performance.py` | Batch processing, model caching, bulk import pipeline |
+
+---
+
+## Data Flows
+
+### Note Creation
+
+When you run `jfox add`, the system parses wiki links, creates the Markdown file, updates both indexes, and propagates backlinks:
+
+```mermaid
+sequenceDiagram
+    participant U as User
+    participant CLI as cli.py
+    participant NM as note.py
+    participant MD as Filesystem
+    participant VS as VectorStore
+    participant BM as BM25Index
+    participant T as Target Note
+
+    U->>CLI: jfox add "content with [[Link]]"
+    CLI->>CLI: extract_wiki_links() → ["Link"]
+    CLI->>CLI: find_note_id_by_title_or_id()
+    Note over CLI: Match: exact ID → exact title → substring
+    CLI->>NM: create_note(content, links=[id1])
+    NM->>NM: generate_id() → timestamp + random
+    NM->>MD: write Markdown + YAML frontmatter
+    NM->>VS: add_note() → embed + store in ChromaDB
+    NM->>BM: add_document() → tokenize + update index
+    CLI->>T: load target → append backlink → save
+```
+
+### Index Rebuild
+
+`jfox index rebuild` reconstructs both the vector index and the keyword index from all Markdown files on disk:
+
+```mermaid
+sequenceDiagram
+    participant U as User
+    participant CLI as cli.py
+    participant IDX as Indexer
+    participant VS as VectorStore
+    participant BM as BM25Index
+    participant FS as Filesystem
+
+    U->>CLI: jfox index rebuild
+    CLI->>VS: clear() — wipe ChromaDB collection
+    CLI->>FS: rglob("*.md") — scan all notes
+    loop Each note file
+        FS-->>IDX: parse Markdown + frontmatter
+        IDX->>VS: add_or_update_note()
+        Note over VS: embed → store in ChromaDB
+    end
+    CLI->>FS: list all notes
+    CLI->>BM: rebuild_from_notes()
+    Note over BM: tokenize all → rebuild BM25Okapi → persist
+```
+
+### Hybrid Search (BM25 + Semantic → RRF)
+
+`jfox search` runs two independent search paths in parallel and fuses results using Reciprocal Rank Fusion:
+
+```mermaid
+sequenceDiagram
+    participant U as User
+    participant SE as HybridSearchEngine
+    participant VS as VectorStore
+    participant BM as BM25Index
+    participant EMB as EmbeddingBackend
+
+    U->>SE: search("knowledge management", mode=hybrid)
+    par Semantic Path
+        SE->>EMB: encode(query) → 384-dim vector
+        EMB-->>VS: cosine similarity search
+        VS-->>SE: ranked results with scores
+    and Keyword Path
+        SE->>BM: tokenize(query) → BM25 scoring
+        BM-->>SE: ranked results with scores
+    end
+    Note over SE: Graceful fallback if one path fails
+    SE->>SE: RRF Fusion: score = Σ 1/(k + rank), k=60
+    SE-->>U: merged, re-ranked results
+```
+
+### Query with Graph Traversal
+
+`jfox query` combines hybrid search with knowledge graph BFS to find semantically related notes and their neighbors:
+
+```mermaid
+sequenceDiagram
+    participant U as User
+    participant CLI as cli.py
+    participant SE as SearchEngine
+    participant KG as KnowledgeGraph
+    participant NX as NetworkX
+
+    U->>CLI: jfox query "Luhmann's methodology" --depth 2
+    CLI->>SE: hybrid search → top results
+    SE-->>CLI: ranked search results
+    CLI->>KG: build() — 3-pass graph construction
+    Note over KG: Pass 1: nodes from files<br/>Pass 2: edges from frontmatter links<br/>Pass 3: edges from [[wiki links]]
+    loop For each search result
+        CLI->>KG: get_related(note_id, depth=2)
+        KG->>NX: BFS traversal (predecessors + successors)
+        NX-->>KG: neighbors grouped by depth
+    end
+    CLI-->>U: results enriched with graph context
+```
+
+---
+
+## Quick Start
+
+### Install
+
+```bash
+# Recommended
+uv tool install "git+https://github.com/zhuxixi/jfox.git"
+
+# Or with pip
+pip install -e ".[dev]"
+```
+
+See [Installation Guide](docs/installation.md) for details, Windows PATH setup, and uninstall instructions.
+
+### Create Your First Note
+
+```bash
+jfox init
+jfox add "The Zettelkasten method uses atomic notes connected by links" \
+    --title "Zettelkasten Introduction" --type permanent
+```
+
+### Add Links
+
+```bash
+jfox add "[[Zettelkasten Introduction]] was invented by Niklas Luhmann" \
+    --title "Luhmann and the Card Box" --type permanent
+```
+
+The `[[Zettelkasten Introduction]]` syntax automatically creates a bidirectional link. Backlinks are propagated to the target note.
+
+### Search
+
+```bash
+# Semantic + keyword hybrid search
+jfox search "knowledge management method"
+
+# Hybrid search + graph traversal
+jfox query "Luhmann's methodology" --depth 2
+```
+
+---
+
+## Command Reference
+
+### Knowledge Base
+
+| Command | Description |
+|---------|-------------|
+| `jfox init` | Initialize a knowledge base |
+| `jfox init --name work --desc "Work notes"` | Initialize a named KB |
+| `jfox kb list` | List all knowledge bases |
+| `jfox kb use work` | Switch default KB |
+| `jfox kb info work` | Show KB details and stats |
+| `jfox kb rename old new` | Rename a KB |
+| `jfox kb remove name --force` | Delete a KB and its data |
+
+### Notes
+
+| Command | Description |
+|---------|-------------|
+| `jfox add "content" --title "Title" --type permanent` | Create a note |
+| `jfox add --content-file note.txt --title "Title"` | Create from file content |
+| `jfox list` | List all notes |
+| `jfox list --type permanent --limit 20` | Filter by type |
+| `jfox status` | Show knowledge base status |
+| `jfox edit NOTE_ID` | Edit note in `$EDITOR` |
+| `jfox delete NOTE_ID --force` | Delete a note |
+| `jfox daily` | Show today's notes |
+| `jfox daily --date 2026-03-20` | Show notes for a date |
+| `jfox inbox` | Show fleeting notes |
+| `jfox suggest-links "content"` | Suggest notes to link from content |
+| `jfox bulk-import notes.json` | Bulk import from JSON (optimized) |
+| `jfox ingest-log` | Import git commit history as notes |
+| `jfox show NOTE_ID` | View full note content in terminal |
+
+### Search & Analysis
+
+| Command | Description |
+|---------|-------------|
+| `jfox search "query"` | Hybrid search (default) |
+| `jfox search "query" --mode semantic` | Semantic search only |
+| `jfox search "query" --mode keyword` | BM25 keyword search only |
+| `jfox query "concept" --depth 2` | Search + graph traversal |
+| `jfox refs` | Show link statistics for all notes |
+| `jfox refs --search "keyword"` | Filter refs by title |
+| `jfox refs --note NOTE_ID` | Show links for a specific note |
+| `jfox graph --stats` | Graph statistics |
+| `jfox graph --orphans` | Find isolated notes |
+| `jfox graph --note NOTE_ID --depth 2` | Subgraph around a note |
+
+### Index Management
+
+| Command | Description |
+|---------|-------------|
+| `jfox index status` | Show index health |
+| `jfox index rebuild` | Rebuild vector + BM25 indexes |
+| `jfox index verify` | Cross-check files vs indexed entries |
+
+### Templates
+
+| Command | Description |
+|---------|-------------|
+| `jfox template list` | List built-in and custom templates |
+| `jfox template show quick` | Display template content |
+| `jfox template create my-template` | Create a custom template |
+| `jfox template edit my-template` | Edit in `$EDITOR` |
+| `jfox template remove my-template` | Delete a custom template |
+
+### Performance & Debug
+
+| Command | Description |
+|---------|-------------|
+| `jfox perf report` | Show performance metrics |
+| `jfox perf clear-cache` | Clear embedding model cache |
+
+### Daemon
+
+| Command | Description |
+|---------|-------------|
+| `jfox daemon start` | Start embedding daemon (background process) |
+| `jfox daemon stop` | Stop embedding daemon |
+| `jfox daemon status` | Show daemon PID, port, model info |
+
+### Global Options
+
+| Option | Description |
+|--------|-------------|
+| `--kb NAME` | Target a specific knowledge base |
+| `--format json\|table\|csv\|yaml\|paths\|tree` | Output format |
+| `--json` | Shortcut for `--format json` |
+| `--version` | Show version |
+
+---
+
+## Note Format
+
+### Directory Structure
+
+```
+~/.zettelkasten/
+├── default/                # Default knowledge base
+│   ├── notes/
+│   │   ├── fleeting/       # Quick captures
+│   │   ├── literature/     # Reading notes
+│   │   └── permanent/      # Refined knowledge
+│   └── .zk/
+│       ├── chroma_db/      # Vector index
+│       ├── bm25_index.pkl  # Keyword index
+│       ├── templates/      # Jinja2 templates
+│       └── config.yaml     # KB config
+├── work/                   # Named KB example
+│   ├── notes/
+│   └── .zk/
+└── ~/.zk_config.json       # Global KB registry
+```
+
+### File Format
+
+Each note is a Markdown file with YAML frontmatter:
+
+```markdown
+---
+id: '20260321011528'
+title: Machine Learning Overview
+type: permanent
+created: '2026-03-21T01:15:28'
+updated: '2026-03-21T01:15:28'
+tags:
+- ml
+- ai
+links:
+- 20260321011546
+backlinks:
+- 20260321011550
+---
+
+# Machine Learning Overview
+
+[[Deep Learning]] is a subfield of machine learning...
+```
+
+### Note Types
+
+| Type | Purpose | Filename |
+|------|---------|----------|
+| `fleeting` | Quick ideas, temporary captures | `YYYYMMDD-HHMMSSNNNN.md` |
+| `literature` | Reading notes, paper summaries | `YYYYMMDDHHMMSSNNNN-slug.md` |
+| `permanent` | Refined, lasting knowledge | `YYYYMMDDHHMMSSNNNN-slug.md` |
+
+### Link Resolution
+
+`[[Link Text]]` matches notes by priority:
+
+1. **Exact ID** — if text matches a note ID
+2. **Exact title** — case-insensitive title match
+3. **Substring** — title contains the link text
+
+---
+
+## Contributing
+
+```bash
+git clone https://github.com/zhuxixi/jfox.git
+cd jfox
+uv sync --extra dev
+uv run pytest tests/ -v
+```
+
+See [Troubleshooting](docs/troubleshooting.md) for common issues.
+
+## License
+
+[MIT](LICENSE)
+
+## Acknowledgments
+
+- [sentence-transformers](https://www.sbert.net/) — text embeddings
+- [ChromaDB](https://www.trychroma.com/) — vector database
+- [NetworkX](https://networkx.org/) — graph algorithms
+- [Typer](https://typer.tiangolo.com/) — CLI framework
+- [Rich](https://rich.readthedocs.io/) — terminal formatting