chatspatial 1.1.0__py3-none-any.whl

chatspatial/__init__.py

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+"""
+ChatSpatial
+
+Agentic workflow orchestration platform for spatial transcriptomics analysis.
+Integrates 60 methods from Python and R ecosystems via Model Context Protocol.
+"""
+
+__version__ = "1.0.0"
+
+# Import configuration to set up environment
+from . import config as config  # noqa: F401

chatspatial/__main__.py

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+"""
+Entry point for ChatSpatial.
+
+This module provides the command-line interface for starting the
+ChatSpatial server using either stdio or SSE transport.
+"""
+
+import os
+import sys
+import traceback
+import warnings
+from pathlib import Path
+
+import click
+
+# Suppress warnings to speed up startup
+warnings.filterwarnings("ignore", category=FutureWarning)
+warnings.filterwarnings("ignore", category=UserWarning)
+
+# CRITICAL: Disable all progress bars to prevent stdout pollution in MCP protocol
+# MCP uses JSON-RPC over stdio, any non-JSON output breaks communication
+os.environ["TQDM_DISABLE"] = "1"  # Disable tqdm globally
+
+# Configure scientific libraries to suppress output
+try:
+    import scanpy as sc
+
+    sc.settings.verbosity = 0  # Suppress scanpy output
+except ImportError:
+    pass  # scanpy may not be installed yet
+
+# IMPORTANT: Intelligent working directory handling
+# Only change cwd when it's clearly problematic, otherwise respect user configuration
+PROJECT_ROOT = Path(__file__).parent.resolve()
+user_cwd = Path.cwd()
+
+# Identify problematic working directories that should be changed
+problematic_cwds = [
+    Path("/"),  # Root directory
+    Path("/tmp"),  # Temp directory
+    Path("/var"),  # System directory
+    Path("/usr"),  # System directory
+    Path("/etc"),  # System directory
+]
+
+# Check if current cwd is problematic
+is_problematic = (
+    # Check exact match
+    user_cwd in problematic_cwds
+    or
+    # Check if cwd is a parent of problematic directories
+    any(user_cwd == p.parent for p in problematic_cwds)
+    or
+    # Check if directory doesn't exist
+    not user_cwd.exists()
+    or
+    # Check if it's a temporary npx directory (common MCP issue)
+    "_npx" in str(user_cwd)
+    or ".npm" in str(user_cwd)
+)
+
+if is_problematic:
+    print(
+        f"WARNING:Working directory appears problematic: {user_cwd}\n"
+        f"   Changing to project root: {PROJECT_ROOT}\n"
+        f"   (This ensures file operations work correctly)",
+        file=sys.stderr,
+    )
+    os.chdir(PROJECT_ROOT)
+else:
+    print(
+        f"Using configured working directory: {user_cwd}\n"
+        f"  (Project root: {PROJECT_ROOT})",
+        file=sys.stderr,
+    )
+    # Keep user's configured cwd - don't change it!
+
+from .server import mcp  # noqa: E402
+
+
+@click.group()
+def cli():
+    """ChatSpatial - AI-powered spatial transcriptomics analysis"""
+    pass
+
+
+@cli.command()
+@click.option("--port", default=8000, help="Port to listen on for SSE transport")
+@click.option(
+    "--transport",
+    type=click.Choice(["stdio", "sse"]),
+    default="stdio",
+    help="Transport type (stdio or sse)",
+)
+@click.option(
+    "--host",
+    default="127.0.0.1",  # nosec B104 - Default to localhost for security
+    help="Host to bind to for SSE transport",
+)
+@click.option(
+    "--log-level",
+    type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
+    default="INFO",
+    help="Logging level",
+)
+def server(port: int, transport: str, host: str, log_level: str):
+    """Start the ChatSpatial server.
+
+    This command starts the ChatSpatial server using either stdio or SSE transport.
+    For stdio transport, the server communicates through standard input/output.
+    For SSE transport, the server starts an HTTP server on the specified host and port.
+    """
+    try:
+        # Configure server settings
+        print(
+            f"Starting ChatSpatial server with {transport} transport...",
+            file=sys.stderr,
+        )
+
+        # Set server settings
+        mcp.settings.host = host
+        mcp.settings.port = port
+        mcp.settings.log_level = log_level
+
+        # Run the server with the specified transport
+        # This is the recommended way to run a FastMCP server
+        mcp.run(transport=transport)
+
+    except Exception as e:
+        print(f"Error starting MCP server: {e}", file=sys.stderr)
+        traceback.print_exc(file=sys.stderr)
+        sys.exit(1)
+
+
+def main():
+    """Main entry point for ChatSpatial CLI"""
+    cli()
+
+
+if __name__ == "__main__":
+    main()

chatspatial/cli/__init__.py

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+"""
+ChatSpatial Command Line Interface module.
+
+Provides the main CLI entry point for the ChatSpatial server.
+"""
+
+__all__: list[str] = []

chatspatial/config.py

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+"""
+Configuration module for ChatSpatial
+"""
+
+import os
+import warnings
+
+# Configure Dask to use new DataFrame implementation
+os.environ.setdefault("DASK_DATAFRAME__QUERY_PLANNING", "True")
+
+# Try to import and configure dask
+try:
+    import dask
+
+    dask.config.set({"dataframe.query-planning": True})
+except ImportError:
+    pass  # Dask not installed
+
+
+# Suppress specific warnings
+def configure_warnings():
+    """Configure warning filters for known issues"""
+    # Suppress dask legacy dataframe warning
+    warnings.filterwarnings(
+        "ignore",
+        message="The legacy Dask DataFrame implementation is deprecated",
+        category=FutureWarning,
+    )
+
+    # Suppress spatialdata functools.partial warnings
+    warnings.filterwarnings(
+        "ignore",
+        message="functools.partial will be a method descriptor",
+        category=FutureWarning,
+    )
+
+    # Suppress numba nopython warning
+    warnings.filterwarnings(
+        "ignore",
+        message="nopython is set for njit and is ignored",
+        category=RuntimeWarning,
+    )
+
+    # Suppress anndata read_text warning
+    warnings.filterwarnings(
+        "ignore",
+        message="Importing read_text from `anndata` is deprecated",
+        category=FutureWarning,
+    )
+
+
+# Configure on import
+configure_warnings()

chatspatial/models/__init__.py

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+"""
+Data models for spatial transcriptomics analysis.
+"""
+
+# Import result models from analysis module
+from .analysis import (
+    AnnotationResult,
+    BaseAnalysisResult,
+    CellCommunicationResult,
+    CellTypeComparisonResult,
+    CNVResult,
+    ConditionComparisonResult,
+    DEGene,
+    DeconvolutionResult,
+    DifferentialExpressionResult,
+    EnrichmentResult,
+    IntegrationResult,
+    PreprocessingResult,
+    RNAVelocityResult,
+    SpatialDomainResult,
+    SpatialStatisticsResult,
+    SpatialVariableGenesResult,
+    TrajectoryResult,
+)
+
+# Import parameter models from data module
+from .data import (
+    AnnotationParameters,
+    CellCommunicationParameters,
+    CNVParameters,
+    ColumnInfo,
+    ConditionComparisonParameters,
+    DeconvolutionParameters,
+    DifferentialExpressionParameters,
+    EnrichmentParameters,
+    IntegrationParameters,
+    PreprocessingParameters,
+    RNAVelocityParameters,
+    SpatialDataset,
+    SpatialDomainParameters,
+    SpatialStatisticsParameters,
+    SpatialVariableGenesParameters,
+    TrajectoryParameters,
+    VisualizationParameters,
+)
+
+__all__ = [
+    # Base class
+    "BaseAnalysisResult",
+    # Result models
+    "AnnotationResult",
+    "CellCommunicationResult",
+    "CellTypeComparisonResult",
+    "CNVResult",
+    "ConditionComparisonResult",
+    "DEGene",
+    "DeconvolutionResult",
+    "DifferentialExpressionResult",
+    "EnrichmentResult",
+    "IntegrationResult",
+    "PreprocessingResult",
+    "RNAVelocityResult",
+    "SpatialDomainResult",
+    "SpatialStatisticsResult",
+    "SpatialVariableGenesResult",
+    "TrajectoryResult",
+    # Parameter models
+    "AnnotationParameters",
+    "CellCommunicationParameters",
+    "CNVParameters",
+    "ColumnInfo",
+    "ConditionComparisonParameters",
+    "DeconvolutionParameters",
+    "DifferentialExpressionParameters",
+    "EnrichmentParameters",
+    "IntegrationParameters",
+    "PreprocessingParameters",
+    "RNAVelocityParameters",
+    "SpatialDataset",
+    "SpatialDomainParameters",
+    "SpatialStatisticsParameters",
+    "SpatialVariableGenesParameters",
+    "TrajectoryParameters",
+    "VisualizationParameters",
+]