mcp-vector-search 0.12.0__tar.gz → 0.12.2__tar.gz

{mcp_vector_search-0.12.0 → mcp_vector_search-0.12.2}/.gitignore

@@ -299,3 +299,6 @@ pip-wheel-metadata/
 site/
 temp/
 tmp/
+
+# MCP Ticketer
+.mcp-ticketer/

mcp_vector_search-0.12.2/CLAUDE.md

@@ -0,0 +1,49 @@
+# Project Memory Configuration
+
+This project uses KuzuMemory for intelligent context management.
+
+## Project Information
+- **Path**: /Users/masa/Projects/mcp-vector-search
+- **Language**: Python
+- **Framework**: Unknown
+
+## Memory Integration
+
+KuzuMemory is configured to enhance all AI interactions with project-specific context.
+
+### Available Commands:
+- `kuzu-memory enhance <prompt>` - Enhance prompts with project context
+- `kuzu-memory learn <content>` - Store learning from conversations (async)
+- `kuzu-memory recall <query>` - Query project memories
+- `kuzu-memory stats` - View memory statistics
+
+### MCP Tools Available:
+When interacting with Claude Desktop, the following MCP tools are available:
+- **kuzu_enhance**: Enhance prompts with project memories
+- **kuzu_learn**: Store new learnings asynchronously
+- **kuzu_recall**: Query specific memories
+- **kuzu_stats**: Get memory system statistics
+
+## Project Context
+
+CLI-first semantic code search with MCP integration
+
+## Key Technologies
+- Python
+
+## Development Guidelines
+- Use kuzu-memory enhance for all AI interactions
+- Store important decisions with kuzu-memory learn
+- Query context with kuzu-memory recall when needed
+- Keep memories project-specific and relevant
+
+## Memory Guidelines
+
+- Store project decisions and conventions
+- Record technical specifications and API details
+- Capture user preferences and patterns
+- Document error solutions and workarounds
+
+---
+
+*Generated by KuzuMemory Claude Hooks Installer*

mcp_vector_search-0.12.2/INVESTIGATION_EXPANSION_BUG.md

@@ -0,0 +1,229 @@
+# Investigation Report: Node Expansion Not Working
+
+## Summary
+User reports that directory/file nodes show expand/collapse icons ("+"/"-") but clicking them doesn't expand/collapse the hierarchy.
+
+## Code Analysis
+
+### 1. Click Handler Attachment ✓ CORRECT
+**Location**: `/Users/masa/Projects/mcp-vector-search/src/mcp_vector_search/visualization/index.html:481`
+
+```javascript
+.on("click", handleNodeClick)
+```
+
+The click handler IS correctly attached to each node group (`<g>` element).
+
+### 2. Pointer Events ✓ CORRECT
+**Locations**: Lines 123, 130, 542
+
+All text elements (labels, icons, expand indicators) have `pointer-events: none`, which correctly allows clicks to pass through to the parent `<g>` element where the handler is attached.
+
+### 3. hasChildren() Function ✓ CORRECT
+**Location**: Line 586-590
+
+```javascript
+function hasChildren(node) {
+    return allLinks.some(l => (l.source.id || l.source) === node.id);
+}
+```
+
+This correctly checks if a node is a parent (source) in any link. The `(l.source.id || l.source)` pattern handles both:
+- **Before D3 mutation**: `l.source` is a string (e.g., "dir_abc")
+- **After D3 mutation**: `l.source` is an object with `.id` property
+
+### 4. handleNodeClick() Function ✓ LOGIC CORRECT
+**Location**: Line 593-624
+
+The logic flow is correct:
+1. Show content pane (always)
+2. Check if node has children
+3. If yes, toggle collapse/expand state
+4. Call `renderGraph()` to update visualization
+
+### 5. expandNode() Function ✓ LOGIC CORRECT
+**Location**: Line 626-654
+
+Correctly:
+1. Removes node from `collapsedNodes`
+2. Finds children by filtering `allLinks` for links where source matches node ID
+3. Adds each child to `visibleNodes`
+4. Adds each child to `collapsedNodes` (children start collapsed)
+
+### 6. Data Structure ✓ VERIFIED
+**File**: `/Users/masa/Projects/mcp-vector-search/chunk-graph.json`
+
+```
+Total nodes: 7015
+Total links: 7006
+Directory nodes: 26
+Root directories: 5 (docs, examples, scripts, src, tests)
+```
+
+Sample link structure:
+```json
+{
+  "source": "dir_9f40c524",
+  "target": "dir_504f9a81",
+  "type": "dir_hierarchy"
+}
+```
+
+Example: `docs` directory has 22 child links, confirming hierarchy is correctly structured.
+
+## Debugging Added
+
+I've added comprehensive console logging to help diagnose the issue:
+
+### Initial State Logging (Line 445-450)
+Logs on page load:
+- Total nodes and links
+- Root nodes identified
+- Initial visible and collapsed node sets
+
+### Click Handler Logging (Line 594-623)
+Logs on every node click:
+- Node name, type, and ID
+- Whether node has children
+- Whether node is collapsed
+- Which action is taken (expand/collapse)
+
+### hasChildren() Logging (Line 587-590)
+Logs every time it's called:
+- Node name
+- Result (true/false)
+- Number of links checked
+
+### expandNode() Logging (Line 627-653)
+Logs during expansion:
+- Node being expanded
+- Number of child links found
+- Number of child nodes found
+- Each child being added to visibleNodes
+- Final visibleNodes size
+
+### renderGraph() Logging (Line 456-467)
+Logs on every render:
+- Size of visibleNodes and collapsedNodes sets
+- Number of nodes being rendered
+- Number of links being rendered
+
+## Testing Instructions
+
+1. **Open the visualization**:
+   ```bash
+   cd /Users/masa/Projects/mcp-vector-search/src/mcp_vector_search/visualization
+   open index.html
+   ```
+
+2. **Open Browser DevTools**:
+   - Press F12 or Cmd+Option+I (Mac)
+   - Go to the Console tab
+
+3. **Check Initial State**:
+   - You should see "=== INITIAL STATE ===" logged
+   - Verify root nodes are identified correctly
+   - Should show 5-9 root nodes
+
+4. **Click a Directory Node**:
+   - Click on "docs", "src", or another directory node
+   - Watch console for "=== NODE CLICKED ===" messages
+   - Check what happens:
+
+### Expected Behavior:
+```
+=== NODE CLICKED ===
+Node: docs Type: directory ID: dir_9f40c524
+hasChildren(docs): true Checking 7006 links for node ID: dir_9f40c524
+Node has children: true
+Node is collapsed: true
+Expanding node...
+expandNode(docs): Removing from collapsedNodes
+  Found 22 child links for node dir_9f40c524
+  Found 22 child nodes: [_archive, analysis, architecture, ...]
+    Adding child to visibleNodes: _archive (dir_504f9a81)
+    Adding child to visibleNodes: analysis (dir_abc123)
+    ...
+  visibleNodes now has 27 items
+=== renderGraph() called ===
+visibleNodes.size: 27
+Rendering 27 visible nodes
+Rendering XX visible links
+```
+
+### Possible Issues to Look For:
+
+#### Issue A: hasChildren() Returns False
+**Symptom**: Console shows `Node has children: false`
+**Cause**: Links not properly structured or node ID mismatch
+**Check**:
+- Are node IDs consistent between nodes and links?
+- Are links properly loaded?
+
+#### Issue B: No Children Found
+**Symptom**: Console shows `Found 0 child links`
+**Cause**: Link source/target ID mismatch or D3 mutation issue
+**Check**:
+- What is the format of `l.source` (string or object)?
+- Does `l.source` or `l.source.id` match the node ID?
+
+#### Issue C: Children Added But Not Rendered
+**Symptom**: Console shows children added to visibleNodes, but renderGraph() shows same count
+**Cause**: visibleNodes not being updated correctly
+**Check**:
+- Does `visibleNodes.size` increase after expansion?
+- Are the new nodes actually being rendered?
+
+#### Issue D: Click Handler Not Firing
+**Symptom**: No "=== NODE CLICKED ===" in console
+**Cause**: Event handler not attached or being blocked
+**Check**:
+- Are there any JavaScript errors on page load?
+- Try clicking different parts of the node (center, edge, icon area)
+
+## Potential Root Causes
+
+Based on the code analysis, here are the most likely issues:
+
+### 1. D3 Link Mutation Issue (MOST LIKELY)
+**Problem**: D3's `forceLink()` mutates link objects, replacing string IDs with object references.
+
+When `visibleLinks` is created by filtering `allLinks`, it creates a new array but **shares the same link objects**. When D3 mutates `visibleLinks`, it also mutates `allLinks`.
+
+**Impact**: After first render, all links in `allLinks` have object references instead of strings. The `hasChildren()` function should still work due to the `(l.source.id || l.source)` pattern, but there could be edge cases.
+
+**Test**: Check console to see if `hasChildren()` is returning the correct value after clicking.
+
+### 2. Event Propagation Issue
+**Problem**: Click events might be consumed by drag handler or other events.
+
+**Test**: Check if "=== NODE CLICKED ===" appears in console when clicking.
+
+### 3. Render Not Updating Visual State
+**Problem**: Even if expansion logic works, the visual update might fail.
+
+**Test**: Check if `renderGraph()` logs show increasing node counts after expansion.
+
+## Next Steps
+
+1. **Run the visualization with debugging**
+2. **Open browser console**
+3. **Click a directory node**
+4. **Copy all console output**
+5. **Analyze which of the above issues is occurring**
+
+## Files Modified
+
+- `/Users/masa/Projects/mcp-vector-search/src/mcp_vector_search/visualization/index.html`
+  - Added comprehensive console.log() debugging throughout
+  - No logic changes - only added logging
+
+## Conclusion
+
+The code logic appears correct. The issue is likely:
+
+1. **D3 link mutation** causing unexpected behavior in `hasChildren()` or `expandNode()`
+2. **Event handling** issue preventing clicks from being registered
+3. **Visual update** issue where expansion logic works but rendering doesn't update
+
+The added debugging will help pinpoint the exact issue. Please run the visualization and check the browser console output when clicking nodes.

{mcp_vector_search-0.12.0 → mcp_vector_search-0.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcp-vector-search
-Version: 0.12.0
+Version: 0.12.2
 Summary: CLI-first semantic code search with MCP integration
 Project-URL: Homepage, https://github.com/bobmatnyc/mcp-vector-search
 Project-URL: Documentation, https://mcp-vector-search.readthedocs.io
@@ -39,6 +39,7 @@ Classifier: Topic :: Software Development :: Code Generators
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.11
 Requires-Dist: aiofiles>=23.0.0
+Requires-Dist: authlib>=1.6.4
 Requires-Dist: chromadb>=0.5.0
 Requires-Dist: click-didyoumean>=0.3.0
 Requires-Dist: httpx>=0.25.0
@@ -110,49 +111,68 @@ cd mcp-vector-search
 uv sync && uv pip install -e .
 ```
 
-### Complete Setup with Install Command
+### Complete Setup (One Command)
 
-The new **enhanced install command** provides a complete one-step setup:
+The **hierarchical install command** (v0.13.0) provides complete project setup and MCP integration management:
 
 ```bash
-# Interactive setup with MCP configuration
+# Quick setup (recommended)
 mcp-vector-search install
 
-# Setup without MCP configuration
-mcp-vector-search install --no-mcp
+# This will:
+# 1. Initialize your project configuration
+# 2. Automatically index your codebase
+# 3. Provide next-step hints for MCP integration
 
-# Setup for specific MCP tool
-mcp-vector-search install --mcp-tool "Claude Code"
-
-# Setup without automatic indexing
-mcp-vector-search install --no-index
+# Install with all MCP integrations at once
+mcp-vector-search install --with-mcp
 
 # Custom file extensions
 mcp-vector-search install --extensions .py,.js,.ts,.dart
+
+# Skip automatic indexing
+mcp-vector-search install --no-auto-index
 ```
 
-The install command:
-- Initializes your project configuration
-- Detects and configures MCP tools (Claude Code, Cursor, Windsurf, VS Code)
-- Automatically indexes your codebase
-- Provides rich progress indicators and next-step hints
+### Add MCP Integration for AI Tools
 
-### Basic Usage
+```bash
+# Add Claude Code integration (project-scoped)
+mcp-vector-search install claude-code
+
+# Add Cursor IDE integration (global)
+mcp-vector-search install cursor
+
+# Add Claude Desktop integration (global)
+mcp-vector-search install claude-desktop
+
+# See all available platforms
+mcp-vector-search install list
+```
+
+### Remove MCP Integrations
 
 ```bash
-# Initialize your project
-mcp-vector-search init
+# Remove specific platform
+mcp-vector-search uninstall claude-code
 
-# Index your codebase
-mcp-vector-search index
+# Remove all integrations
+mcp-vector-search uninstall --all
+
+# List configured integrations
+mcp-vector-search uninstall list
+```
 
+### Basic Usage
+
+```bash
 # Search your code
 mcp-vector-search search "authentication logic"
 mcp-vector-search search "database connection setup"
 mcp-vector-search search "error handling patterns"
 
-# Setup automatic reindexing (recommended)
-mcp-vector-search auto-index setup --method all
+# Index your codebase (if not done during install)
+mcp-vector-search index
 
 # Check project status
 mcp-vector-search status
@@ -191,7 +211,50 @@ See [docs/VERSIONING_WORKFLOW.md](docs/VERSIONING_WORKFLOW.md) for complete docu
 
 ### Commands
 
-#### `init` - Initialize Project
+#### `install` - Install Project and MCP Integrations (v0.13.0)
+```bash
+# Quick setup (recommended)
+mcp-vector-search install
+
+# Install with all MCP integrations
+mcp-vector-search install --with-mcp
+
+# Custom file extensions
+mcp-vector-search install --extensions .py,.js,.ts
+
+# Skip automatic indexing
+mcp-vector-search install --no-auto-index
+
+# Platform-specific MCP integration
+mcp-vector-search install claude-code      # Project-scoped
+mcp-vector-search install claude-desktop   # Global
+mcp-vector-search install cursor           # Global
+mcp-vector-search install windsurf         # Global
+mcp-vector-search install vscode           # Global
+
+# List available platforms
+mcp-vector-search install list
+```
+
+#### `uninstall` - Remove MCP Integrations (v0.13.0)
+```bash
+# Remove specific platform
+mcp-vector-search uninstall claude-code
+
+# Remove all integrations
+mcp-vector-search uninstall --all
+
+# List configured integrations
+mcp-vector-search uninstall list
+
+# Skip backup creation
+mcp-vector-search uninstall claude-code --no-backup
+
+# Alias (same as uninstall)
+mcp-vector-search remove claude-code
+```
+
+#### `init` - Initialize Project (Simple)
 ```bash
 # Basic initialization
 mcp-vector-search init
@@ -427,6 +490,10 @@ uv sync
 # Install in development mode
 uv pip install -e .
 
+# Test CLI from source (recommended during development)
+./dev-mcp version        # Shows [DEV] indicator
+./dev-mcp search "test"  # No reinstall needed after code changes
+
 # Run tests
 uv run pytest
 
@@ -435,6 +502,8 @@ uv run ruff check
 uv run mypy src/
 ```
 
+For detailed development workflow and `dev-mcp` usage, see the [Development](#-development) section below.
+
 ### Adding Language Support
 
 1. Create a new parser in `src/mcp_vector_search/parsers/`
@@ -507,10 +576,64 @@ uv sync && uv pip install -e .
 # Run development tests
 ./scripts/dev-test.sh
 
-# Test CLI locally
+# Run CLI from source (recommended during development)
+./dev-mcp version        # Visual [DEV] indicator
+./dev-mcp status         # Any command works
+./dev-mcp search "auth"  # Immediate feedback on changes
+
+# Alternative: use uv run directly
 uv run mcp-vector-search version
 ```
 
+#### Using the `dev-mcp` Development Helper
+
+The `./dev-mcp` script provides a streamlined way to run the CLI from source code during development, eliminating the need for repeated installations.
+
+**Key Features:**
+- **Visual [DEV] Indicator**: Shows `[DEV]` prefix to distinguish from installed version
+- **No Reinstall Required**: Reflects code changes immediately
+- **Complete Argument Forwarding**: Works with all CLI commands and options
+- **Verbose Mode**: Debug output with `--verbose` flag
+- **Built-in Help**: Script usage with `--help`
+
+**Usage Examples:**
+```bash
+# Basic commands (note the [DEV] prefix in output)
+./dev-mcp version
+./dev-mcp status
+./dev-mcp index
+./dev-mcp search "authentication logic"
+
+# With CLI options
+./dev-mcp search "error handling" --limit 10
+./dev-mcp index --force
+
+# Script verbose mode (shows Python interpreter, paths)
+./dev-mcp --verbose search "database"
+
+# Script help (shows dev-mcp usage, not CLI help)
+./dev-mcp --help
+
+# CLI command help (forwards --help to the CLI)
+./dev-mcp search --help
+./dev-mcp index --help
+```
+
+**When to Use:**
+- **`./dev-mcp`** → Development workflow (runs from source code)
+- **`mcp-vector-search`** → Production usage (runs installed version via pipx/pip)
+
+**Benefits:**
+- **Instant Feedback**: Changes to source code are reflected immediately
+- **No Build Step**: Skip the reinstall cycle during active development
+- **Clear Context**: Visual `[DEV]` indicator prevents confusion about which version is running
+- **Error Handling**: Built-in checks for uv installation and project structure
+
+**Requirements:**
+- Must have `uv` installed (`pip install uv`)
+- Must run from project root directory
+- Requires `pyproject.toml` in current directory
+
 **Stage B: Local Deployment Testing**
 ```bash
 # Build and test clean deployment