move to uv, structured logging, us english

Author: soodoku

CLAUDE.md

@@ -319,7 +319,7 @@ export RMCP_R_TIMEOUT=300
 echo '{"debug": true, "logging": {"level": "DEBUG"}}' > ~/.rmcp/config.json
 
 # CLI options override everything
-poetry run rmcp --debug --config custom.json start
+uv run rmcp --debug --config custom.json start
 ```
 
 ### **Docker Configuration**
@@ -336,7 +336,7 @@ docker run -v $(pwd)/config.json:/etc/rmcp/config.json rmcp:latest
 - **Integration tests**: Configuration integration with HTTP/R/VFS components
 - **Environment tests**: Validation of all environment variable mappings
 
-**📖 Complete documentation**: Auto-generated from code in `docs/configuration/` (build with `poetry run sphinx-build docs docs/_build`)
+**📖 Complete documentation**: Auto-generated from code in `docs/configuration/` (build with `uv run sphinx-build docs docs/_build`)
 
 ## Universal Operation Approval System
 
@@ -545,13 +545,13 @@ Documentation is automatically generated from:
 
 ```bash
 # Build HTML documentation
-poetry run sphinx-build -b html docs docs/_build/html
+uv run sphinx-build -b html docs docs/_build/html
 
 # Build with clean rebuild
-poetry run sphinx-build -E -a -b html docs docs/_build/html
+uv run sphinx-build -E -a -b html docs docs/_build/html
 
 # Generate autosummary stubs
-poetry run sphinx-autogen docs/**/*.rst
+uv run sphinx-autogen docs/**/*.rst
 
 # Serve documentation locally
 cd docs/_build/html && python -m http.server 8080

examples/claude_desktop_v0.5.0_examples.md

@@ -228,7 +228,7 @@ After running these examples with approvals, you should find:
 **Debug Commands:**
 ```bash
 # Check RMCP status
-poetry run rmcp --debug start
+uv run rmcp --debug start
 
 # Verify file permissions
 ls -la /tmp/

pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "click>=8.1.0",        # CLI interface
     "jsonschema>=4.0.0",   # Schema validation
     "psutil>=5.0.0",       # R process management
+    "structlog>=23.1.0",   # Structured logging for MCP observability
     # subprocess module is built-in for Python 3.8+
 ]
 
@@ -188,3 +189,21 @@ exclude_lines = [
     "class .*\\bProtocol\\):",
     "@(abc\\.)?abstractmethod",
 ]
+
+[tool.deptry]
+pep621_dev_dependency_groups = ["dev"]
+extend_exclude = [
+    "scripts/",      # Development scripts have their own dependency scope
+    "streamlit/",    # Streamlit app is optional component
+    "tests/scenarios/test_deployment_scenarios.py",  # Tests all optional deps
+]
+
+[tool.deptry.per_rule_ignores]
+DEP002 = ["httpx", "pandas", "openpyxl"]  # Test-only dependencies via pandas backend
+DEP003 = ["mcp", "requests", "anthropic"] # Transitive dependencies we import directly
+DEP001 = ["package_whitelist_comprehensive"]  # Internal module
+DEP004 = ["pytest", "numpy"]           # Dev dependencies in scripts/streamlit
+
+[tool.deptry.package_module_name_map]
+structlog = "structlog"
+linkify-it-py = "linkify_it_py"

rmcp/cli.py

@@ -16,6 +16,7 @@
 from . import __version__
 from .config import get_config, load_config
 from .core.server import create_server
+from .logging_config import configure_structured_logging, get_logger
 from .registries.prompts import (
     model_diagnostic_prompt,
     panel_regression_prompt,
@@ -28,13 +29,8 @@
 from .transport.stdio import StdioTransport
 
 # Modern Python 3.10+ syntax for type hints
-# Configure logging to stderr only
-logging.basicConfig(
-    level=logging.INFO,
-    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
-    stream=sys.stderr,
-)
-logger = logging.getLogger(__name__)
+# Structured logging will be configured in CLI commands based on config
+logger = get_logger(__name__)
 
 
 async def _run_server_with_transport(server, transport) -> None:
@@ -57,8 +53,14 @@ async def _run_server_with_transport(server, transport) -> None:
     help="Path to configuration file",
 )
 @click.option("--debug", is_flag=True, help="Enable debug mode")
+@click.option(
+    "--log-format",
+    type=click.Choice(["structured", "pretty"]),
+    default="structured",
+    help="Log output format (structured=JSON, pretty=colored console)",
+)
 @click.pass_context
-def cli(ctx, config: Path, debug: bool):
+def cli(ctx, config: Path, debug: bool, log_format: str):
     """RMCP MCP Server - Comprehensive statistical analysis with 44 tools across 11 categories."""
     # Ensure context object exists
     ctx.ensure_object(dict)
@@ -71,6 +73,7 @@ def cli(ctx, config: Path, debug: bool):
 
     # Store config in context for subcommands
     ctx.obj["config"] = load_config(config_file=config, overrides=overrides)
+    ctx.obj["log_format"] = log_format
 
 
 @cli.command()
@@ -84,10 +87,15 @@ def start(ctx, log_level: str):
     """Start RMCP MCP server (default stdio transport)."""
     # Get configuration
     config = ctx.obj.get("config") or get_config()
+    log_format = ctx.obj.get("log_format", "structured")
 
-    # Set logging level (CLI option overrides config)
+    # Configure structured logging
     effective_log_level = log_level or config.logging.level
-    logging.getLogger().setLevel(getattr(logging, effective_log_level.upper()))
+    configure_structured_logging(
+        level=effective_log_level,
+        development_mode=(log_format == "pretty" or config.debug),
+        enable_console=True,
+    )
 
     logger.info(f"Starting RMCP MCP Server v{__version__}")
     if config.debug:
@@ -291,6 +299,14 @@ def serve_http(
 
     # Get configuration
     config = ctx.obj.get("config") or get_config()
+    log_format = ctx.obj.get("log_format", "structured")
+
+    # Configure structured logging for HTTP transport
+    configure_structured_logging(
+        level=config.logging.level,
+        development_mode=(log_format == "pretty" or config.debug),
+        enable_console=True,
+    )
 
     # Use CLI options or fall back to config
     effective_host = host or config.http.host

rmcp/config/loader.py

@@ -221,25 +221,24 @@ def _load_environment_config(self) -> dict[str, Any]:
 
     def _convert_env_value(self, env_var: str, value: str) -> Any:
         """Convert environment variable string to appropriate type."""
-        # Boolean conversion
-        if env_var.endswith(("_READ_ONLY", "_DEBUG", "_STDERR_OUTPUT")):
-            return value.lower() in ("true", "1", "yes", "on")
-
-        # Integer conversion
-        if env_var.endswith(
-            ("_PORT", "_TIMEOUT", "_MAX_SESSIONS", "_MAX_WORKERS", "_MAX_FILE_SIZE")
-        ):
-            try:
-                return int(value)
-            except ValueError:
-                raise ConfigError(f"Invalid integer value for {env_var}: {value}")
-
-        # List conversion (comma-separated)
-        if env_var.endswith(("_ORIGINS", "_PATHS", "_MIME_TYPES")):
-            return [item.strip() for item in value.split(",") if item.strip()]
-
-        # String value
-        return value
+        match env_var:
+            case var if var.endswith(("_READ_ONLY", "_DEBUG", "_STDERR_OUTPUT")):
+                # Boolean conversion
+                return value.lower() in ("true", "1", "yes", "on")
+            case var if var.endswith(
+                ("_PORT", "_TIMEOUT", "_MAX_SESSIONS", "_MAX_WORKERS", "_MAX_FILE_SIZE")
+            ):
+                # Integer conversion
+                try:
+                    return int(value)
+                except ValueError:
+                    raise ConfigError(f"Invalid integer value for {env_var}: {value}")
+            case var if var.endswith(("_ORIGINS", "_PATHS", "_MIME_TYPES")):
+                # List conversion (comma-separated)
+                return [item.strip() for item in value.split(",") if item.strip()]
+            case _:
+                # String value
+                return value
 
     def _set_nested_value(self, config_dict: dict[str, Any], path: str, value: Any):
         """Set a nested dictionary value using dot notation."""

rmcp/config/models.py

@@ -33,6 +33,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from ..types import CORSOrigin, LogLevel
+
 
 @dataclass(slots=True)
 class HTTPConfig:
@@ -87,7 +89,7 @@ class HTTPConfig:
     ssl_keyfile_password: str | None = None
     """SSL private key password if the key file is encrypted."""
 
-    cors_origins: list[str] = field(
+    cors_origins: list[CORSOrigin] = field(
         default_factory=lambda: [
             "http://localhost:*",
             "http://127.0.0.1:*",
@@ -283,7 +285,7 @@ class LoggingConfig:
             )
     """
 
-    level: str = "INFO"
+    level: LogLevel = "INFO"
     """Logging level. Must be DEBUG, INFO, WARNING, ERROR, or CRITICAL."""
 
     format: str = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"

rmcp/core/server.py

@@ -1060,16 +1060,17 @@ async def _handle_notification(self, method: str, params: dict[str, Any]) -> Non
             - notifications/initialized: Client initialization complete
         """
         logger.info(f"Received notification: {method}")
-        if method == "notifications/cancelled":
-            # Handle cancellation notification
-            request_id = params.get("requestId")
-            if request_id:
-                await self.cancel_request(request_id)
-        elif method == "notifications/initialized":
-            # MCP initialization complete
-            logger.info("MCP client initialization complete")
-        else:
-            logger.warning(f"Unknown notification method: {method}")
+        match method:
+            case "notifications/cancelled":
+                # Handle cancellation notification
+                request_id = params.get("requestId")
+                if request_id:
+                    await self.cancel_request(request_id)
+            case "notifications/initialized":
+                # MCP initialization complete
+                logger.info("MCP client initialization complete")
+            case _:
+                logger.warning(f"Unknown notification method: {method}")
 
 
 def create_server(