copick-mcp 0.1.0__tar.gz

copick_mcp-0.1.0/.gitignore

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copick_mcp-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 copick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

copick_mcp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: copick-mcp
+Version: 0.1.0
+Summary: MCP server for Copick.
+Project-URL: Repository, https://github.com/copick/copick-mcp
+Project-URL: Issues, https://github.com/copick/copick-mcp/issues
+Project-URL: Documentation, https://github.com/copick/copick-mcp#readme
+Author-email: Kyle Harrington <czi@kyleharrington.com>, "Utz H. Ermel" <utz@ermel.me>
+License: MIT License
+        
+        Copyright (c) 2025 copick
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: annotation,copick,cryo-et,cryoet,mcp,model-context-protocol,tomography
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.9
+Requires-Dist: click>=8.0
+Requires-Dist: copick-torch
+Requires-Dist: copick-utils
+Requires-Dist: copick>=1.15.0
+Requires-Dist: fastmcp>=0.1.0
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == 'dev'
+Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'
+Requires-Dist: hatchling>=1.25.0; extra == 'dev'
+Requires-Dist: ipython>=8.18.1; extra == 'dev'
+Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
+Requires-Dist: ruff>=0.12.0; extra == 'dev'
+Provides-Extra: test
+Requires-Dist: pytest-cov>=6.2.1; extra == 'test'
+Requires-Dist: pytest>=8.4.1; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Copick MCP Server
+
+A Model Context Protocol (MCP) server for Copick that provides two sets of tools:
+1. **Data Exploration Tools** - Browse and query copick project contents (read-only)
+2. **CLI Introspection Tools** - Discover and validate copick CLI commands for building processing pipelines
+
+## Features
+
+- **Read-only data exploration** - List and inspect runs, picks, segmentations, meshes, tomograms, and project metadata
+- **CLI discovery** - Dynamically discover all available copick CLI commands with full documentation
+- **Command validation** - Validate copick CLI command syntax using Click's native parsing
+- **Smart caching** - Efficient caching of copick project roots
+- **Easy setup** - Simple CLI for registering with Claude Desktop
+
+## Installation
+
+```bash
+cd copick-mcp
+pip install -e .
+```
+
+## Quick Setup
+
+### Register with Claude Desktop
+
+Use the copick CLI to register the MCP server with Claude Desktop:
+
+```bash
+# Basic setup (default settings)
+copick setup mcp
+
+# Setup with custom server name
+copick setup mcp --server-name "my-copick-server"
+
+# Setup with default config path (optional - can be provided per-request)
+copick setup mcp --config-path "/path/to/default/config.json"
+
+# Check registration status
+copick setup mcp-status
+```
+
+After setup:
+1. Restart Claude Desktop completely
+2. The Copick MCP tools should now be available
+3. The server starts automatically when Claude Desktop connects
+
+### Manual Configuration (Optional)
+
+If you prefer manual setup, add this to your Claude Desktop configuration file:
+
+**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
+
+**Windows**: `%APPDATA%/Claude/claude_desktop_config.json`
+
+```json
+{
+  "mcpServers": {
+    "copick-mcp": {
+      "command": "python",
+      "args": ["-m", "copick_mcp.main"],
+      "env": {}
+    }
+  }
+}
+```
+
+## Available Tools
+
+### Data Exploration Tools (Read-Only)
+
+All data exploration tools require a `config_path` parameter pointing to your copick configuration file.
+
+#### `list_runs`
+List all runs in a Copick project.
+- **Args**: `config_path` (str)
+- **Returns**: List of run names
+
+#### `get_run_details`
+Get detailed information about a specific run including voxel spacings, picks, meshes, and segmentations.
+- **Args**: `config_path` (str), `run_name` (str)
+- **Returns**: Comprehensive run details
+
+#### `list_objects`
+List all pickable objects defined in the project.
+- **Args**: `config_path` (str)
+- **Returns**: List of objects with properties (name, type, label, color, radius, etc.)
+
+#### `list_picks`
+List picks for a run with optional filtering.
+- **Args**: `config_path` (str), `run_name` (str), `object_name` (optional), `user_id` (optional), `session_id` (optional)
+- **Returns**: List of picks with point counts and sample coordinates
+
+#### `list_meshes`
+List meshes for a run with optional filtering.
+- **Args**: `config_path` (str), `run_name` (str), `object_name` (optional), `user_id` (optional), `session_id` (optional)
+- **Returns**: List of meshes
+
+#### `list_segmentations`
+List segmentations for a run with optional filtering.
+- **Args**: `config_path` (str), `run_name` (str), `voxel_size` (optional), `name` (optional), `user_id` (optional), `session_id` (optional), `is_multilabel` (optional)
+- **Returns**: List of segmentations with metadata
+
+#### `list_tomograms`
+List tomograms for a specific run and voxel spacing.
+- **Args**: `config_path` (str), `run_name` (str), `voxel_spacing` (float)
+- **Returns**: List of tomograms with feature information
+
+#### `list_voxel_spacings`
+List all voxel spacings available for a run.
+- **Args**: `config_path` (str), `run_name` (str)
+- **Returns**: List of voxel spacings with tomogram counts
+
+#### `get_project_info`
+Get general project information and statistics.
+- **Args**: `config_path` (str)
+- **Returns**: Project metadata and entity counts
+
+#### `get_json_config`
+Get the raw JSON configuration of the project.
+- **Args**: `config_path` (str)
+- **Returns**: Complete configuration dictionary
+
+### CLI Introspection Tools
+
+These tools help LLMs discover and validate copick CLI commands for building processing pipelines.
+
+#### `list_copick_cli_commands`
+List all available copick CLI commands hierarchically organized by group.
+- **Returns**: Complete command tree including:
+  - `main`: Core commands (add, browse, config, deposit, info, new, stats, sync)
+  - `inference`: Inference commands (e.g., membrain-seg)
+  - `training`: Training commands
+  - `evaluation`: Evaluation commands
+  - `process`: Processing commands (downsample, fit-spline, hull, skeletonize, etc.)
+  - `convert`: Conversion commands (picks2seg, mesh2seg, seg2picks, etc.)
+  - `logical`: Logical operations (clipmesh, clippicks, meshop, segop, etc.)
+
+#### `get_copick_cli_command_info`
+Get detailed information about a specific command.
+- **Args**: `command_path` (str) - e.g., "convert.picks2seg" or "add"
+- **Returns**: Full command details including:
+  - Help text and short description
+  - All parameters with types, defaults, and help text
+  - Required vs optional parameters
+  - Usage examples (if present in help)
+  - Command group
+
+#### `validate_copick_cli_command`
+Validate a copick CLI command string using Click's syntax validation.
+- **Args**: `command_string` (str) - e.g., "copick convert picks2seg --config /path/to/config.json ..."
+- **Returns**: Validation result including:
+  - Valid/invalid status
+  - Missing required parameters
+  - Parameter type errors
+  - Helpful error messages from Click
+
+## Usage Examples
+
+### Data Exploration Workflow
+
+```
+User: "Show me all runs in my copick project at /data/my_project/config.json"
+
+Assistant uses: list_runs(config_path="/data/my_project/config.json")
+
+User: "What picks are available for run TS_001?"
+
+Assistant uses: list_picks(config_path="/data/my_project/config.json", run_name="TS_001")
+
+User: "Show me only the ribosome picks from user 'annotator1'"
+
+Assistant uses: list_picks(
+    config_path="/data/my_project/config.json",
+    run_name="TS_001",
+    object_name="ribosome",
+    user_id="annotator1"
+)
+```
+
+### CLI Discovery Workflow
+
+```
+User: "I want to convert picks to a segmentation. What copick command can do that?"
+
+Assistant uses: list_copick_cli_commands()
+# Discovers convert.picks2seg command
+
+Assistant uses: get_copick_cli_command_info(command_path="convert.picks2seg")
+# Gets full documentation and parameters
+Assistant explains:
+"The picks2seg command converts picks to segmentation by painting spheres at pick locations.
+It requires:
+- --config: Path to copick config
+- --input: Picks URI (format: object_name:user_id/session_id)
+- --output: Segmentation URI (format: name:user_id/session_id@voxel_spacing)
+- --radius: Sphere radius in angstroms (default: 10.0)"
+
+User: "Can you validate this command for me: copick convert picks2seg --config /data/config.json --input 'ribosome:user1/manual-001' --output 'ribosome:picks2seg/painted-001@10.0'"
+
+Assistant uses: validate_copick_cli_command(
+    command_string="copick convert picks2seg --config /data/config.json --input 'ribosome:user1/manual-001' --output 'ribosome:picks2seg/painted-001@10.0'"
+)# Returns validation result: valid=True if syntax is correct
+```
+
+### Pipeline Building Workflow
+
+```
+User: "I want to build a pipeline that:
+1. Converts ribosome picks to meshes
+2. Computes the convex hull of those meshes
+3. Converts the hulls to segmentations"
+
+Assistant uses: list_copick_cli_commands()
+# Discovers relevant commands in convert and process groups
+
+Assistant uses: get_copick_cli_command_info(command_path="convert.picks2mesh")
+Assistant uses: get_copick_cli_command_info(command_path="process.hull")
+Assistant uses: get_copick_cli_command_info(command_path="convert.mesh2seg")
+# Gets documentation for each command
+
+Assistant suggests the pipeline:
+"Here's a three-step pipeline for your workflow:
+
+Step 1: Convert picks to meshes
+copick convert picks2mesh --config /path/to/config.json \
+    --input 'ribosome:user1/manual-001' \
+    --output 'ribosome:pipeline/step1-meshes' \
+    --method convex_hull
+
+Step 2: Compute convex hull (if not done in step 1)
+copick process hull --config /path/to/config.json \
+    --input-mesh 'ribosome:pipeline/step1-meshes' \
+    --output-mesh 'ribosome:pipeline/step2-hulls'
+
+Step 3: Convert meshes to segmentation
+copick convert mesh2seg --config /path/to/config.json \
+    --input 'ribosome:pipeline/step2-hulls' \
+    --output 'ribosome:pipeline/final-seg@10.0'"
+```
+
+## Management Commands
+
+```bash
+# Check MCP server status
+copick setup mcp-status
+
+# Remove MCP server configuration
+copick setup mcp-remove --server-name "copick-mcp"
+
+# Force removal without confirmation
+copick setup mcp-remove --server-name "copick-mcp" --force
+```
+
+## Troubleshooting
+
+1. **"MCP server not found"**: Ensure you've restarted Claude Desktop completely after configuration
+2. **"Python module not found"**: Verify the package is installed and the Python path is correct in the config
+3. **"Permission denied"**: Check that the Claude config directory is writable
+4. **"Invalid JSON"**: Use `copick setup mcp-status` to validate your configuration
+5. **"Command not found" during CLI introspection**: Ensure copick and all plugin packages (copick-torch, copick-utils) are installed
+6. **"setup command not found"**: Make sure copick-mcp is installed (`pip install -e .` from the copick-mcp directory)
+
+## Development
+
+```bash
+# Install in development mode
+cd copick-mcp
+pip install -e ".[dev]"
+
+# Format code
+black src/
+
+# Lint
+ruff check --fix src/
+
+# Run the server locally for testing
+python -m copick_mcp.main
+```
+
+## License
+
+MIT License - See LICENSE file for details.
+
+## Links
+
+- [Copick Documentation](https://copick.github.io/copick)
+- [Model Context Protocol](https://modelcontextprotocol.io)
+- [FastMCP](https://github.com/jlowin/fastmcp)