scitex 2.10.3__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/stats/mcp_server.py

@@ -0,0 +1,405 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-08
+# File: src/scitex/stats/mcp_server.py
+# ----------------------------------------
+
+"""
+MCP Server for SciTeX Stats - Statistical Testing Framework
+
+Provides tools for:
+- Recommending appropriate statistical tests
+- Running statistical tests
+- Formatting results for publication
+- Power analysis and sample size calculation
+- Multiple comparison correction
+- Descriptive statistics
+- Effect size calculation
+- Normality testing
+- Post-hoc comparisons
+"""
+
+from __future__ import annotations
+
+import asyncio
+
+# Graceful MCP dependency handling
+try:
+    import mcp.types as types
+    from mcp.server import NotificationOptions, Server
+    from mcp.server.models import InitializationOptions
+    from mcp.server.stdio import stdio_server
+
+    MCP_AVAILABLE = True
+except ImportError:
+    MCP_AVAILABLE = False
+    types = None  # type: ignore
+    Server = None  # type: ignore
+    NotificationOptions = None  # type: ignore
+    InitializationOptions = None  # type: ignore
+    stdio_server = None  # type: ignore
+
+__all__ = ["StatsServer", "main", "MCP_AVAILABLE"]
+
+
+class StatsServer:
+    """MCP Server for Statistical Testing Framework."""
+
+    def __init__(self):
+        self.server = Server("scitex-stats")
+        self.setup_handlers()
+
+    def setup_handlers(self):
+        """Set up MCP server handlers."""
+        from ._mcp_handlers import (
+            correct_pvalues_handler,
+            describe_handler,
+            effect_size_handler,
+            format_results_handler,
+            normality_test_handler,
+            p_to_stars_handler,
+            posthoc_test_handler,
+            power_analysis_handler,
+            recommend_tests_handler,
+            run_test_handler,
+        )
+        from ._mcp_tool_schemas import get_tool_schemas
+
+        @self.server.list_tools()
+        async def handle_list_tools():
+            return get_tool_schemas()
+
+        @self.server.call_tool()
+        async def handle_call_tool(name: str, arguments: dict):
+            # Test Recommendation
+            if name == "recommend_tests":
+                return await self._wrap_result(recommend_tests_handler(**arguments))
+
+            # Run Statistical Test
+            elif name == "run_test":
+                return await self._wrap_result(run_test_handler(**arguments))
+
+            # Format Results
+            elif name == "format_results":
+                return await self._wrap_result(format_results_handler(**arguments))
+
+            # Power Analysis
+            elif name == "power_analysis":
+                return await self._wrap_result(power_analysis_handler(**arguments))
+
+            # Correct P-values
+            elif name == "correct_pvalues":
+                return await self._wrap_result(correct_pvalues_handler(**arguments))
+
+            # Descriptive Statistics
+            elif name == "describe":
+                return await self._wrap_result(describe_handler(**arguments))
+
+            # Effect Size
+            elif name == "effect_size":
+                return await self._wrap_result(effect_size_handler(**arguments))
+
+            # Normality Test
+            elif name == "normality_test":
+                return await self._wrap_result(normality_test_handler(**arguments))
+
+            # Post-hoc Test
+            elif name == "posthoc_test":
+                return await self._wrap_result(posthoc_test_handler(**arguments))
+
+            # P-value to Stars
+            elif name == "p_to_stars":
+                return await self._wrap_result(p_to_stars_handler(**arguments))
+
+            else:
+                raise ValueError(f"Unknown tool: {name}")
+
+        @self.server.list_resources()
+        async def handle_list_resources():
+            """List available statistical resources."""
+            resources = [
+                types.Resource(
+                    uri="stats://tests/parametric",
+                    name="Parametric Tests",
+                    description="List of available parametric statistical tests",
+                    mimeType="application/json",
+                ),
+                types.Resource(
+                    uri="stats://tests/nonparametric",
+                    name="Non-parametric Tests",
+                    description="List of available non-parametric statistical tests",
+                    mimeType="application/json",
+                ),
+                types.Resource(
+                    uri="stats://effect-sizes",
+                    name="Effect Size Measures",
+                    description="Available effect size calculations",
+                    mimeType="application/json",
+                ),
+                types.Resource(
+                    uri="stats://correction-methods",
+                    name="Multiple Comparison Methods",
+                    description="Available p-value correction methods",
+                    mimeType="application/json",
+                ),
+            ]
+            return resources
+
+        @self.server.read_resource()
+        async def handle_read_resource(uri: str):
+            """Read a statistical resource."""
+            import json
+
+            if uri == "stats://tests/parametric":
+                content = json.dumps(
+                    {
+                        "tests": [
+                            {
+                                "name": "ttest_ind",
+                                "description": "Independent samples t-test",
+                                "groups": 2,
+                                "assumptions": ["normality", "equal_variance"],
+                            },
+                            {
+                                "name": "ttest_paired",
+                                "description": "Paired samples t-test",
+                                "groups": 2,
+                                "assumptions": ["normality"],
+                            },
+                            {
+                                "name": "ttest_1samp",
+                                "description": "One-sample t-test",
+                                "groups": 1,
+                                "assumptions": ["normality"],
+                            },
+                            {
+                                "name": "anova",
+                                "description": "One-way ANOVA",
+                                "groups": "2+",
+                                "assumptions": ["normality", "equal_variance"],
+                            },
+                            {
+                                "name": "pearson",
+                                "description": "Pearson correlation",
+                                "groups": 2,
+                                "assumptions": ["normality", "linearity"],
+                            },
+                        ]
+                    },
+                    indent=2,
+                )
+                return types.TextResourceContents(
+                    uri=uri,
+                    mimeType="application/json",
+                    text=content,
+                )
+
+            elif uri == "stats://tests/nonparametric":
+                content = json.dumps(
+                    {
+                        "tests": [
+                            {
+                                "name": "brunner_munzel",
+                                "description": "Brunner-Munzel test (recommended)",
+                                "groups": 2,
+                                "assumptions": [],
+                            },
+                            {
+                                "name": "mannwhitneyu",
+                                "description": "Mann-Whitney U test",
+                                "groups": 2,
+                                "assumptions": [],
+                            },
+                            {
+                                "name": "wilcoxon",
+                                "description": "Wilcoxon signed-rank test",
+                                "groups": 2,
+                                "assumptions": ["paired"],
+                            },
+                            {
+                                "name": "kruskal",
+                                "description": "Kruskal-Wallis H test",
+                                "groups": "2+",
+                                "assumptions": [],
+                            },
+                            {
+                                "name": "spearman",
+                                "description": "Spearman rank correlation",
+                                "groups": 2,
+                                "assumptions": [],
+                            },
+                            {
+                                "name": "kendall",
+                                "description": "Kendall tau correlation",
+                                "groups": 2,
+                                "assumptions": [],
+                            },
+                        ]
+                    },
+                    indent=2,
+                )
+                return types.TextResourceContents(
+                    uri=uri,
+                    mimeType="application/json",
+                    text=content,
+                )
+
+            elif uri == "stats://effect-sizes":
+                content = json.dumps(
+                    {
+                        "measures": [
+                            {
+                                "name": "cohens_d",
+                                "description": "Cohen's d - standardized mean difference",
+                                "type": "parametric",
+                                "interpretation": {
+                                    "small": 0.2,
+                                    "medium": 0.5,
+                                    "large": 0.8,
+                                },
+                            },
+                            {
+                                "name": "hedges_g",
+                                "description": "Hedges' g - bias-corrected Cohen's d",
+                                "type": "parametric",
+                                "interpretation": {
+                                    "small": 0.2,
+                                    "medium": 0.5,
+                                    "large": 0.8,
+                                },
+                            },
+                            {
+                                "name": "glass_delta",
+                                "description": "Glass's delta - using control group SD",
+                                "type": "parametric",
+                                "interpretation": {
+                                    "small": 0.2,
+                                    "medium": 0.5,
+                                    "large": 0.8,
+                                },
+                            },
+                            {
+                                "name": "cliffs_delta",
+                                "description": "Cliff's delta - nonparametric effect size",
+                                "type": "nonparametric",
+                                "interpretation": {
+                                    "negligible": 0.147,
+                                    "small": 0.33,
+                                    "medium": 0.474,
+                                    "large": 0.474,
+                                },
+                            },
+                        ]
+                    },
+                    indent=2,
+                )
+                return types.TextResourceContents(
+                    uri=uri,
+                    mimeType="application/json",
+                    text=content,
+                )
+
+            elif uri == "stats://correction-methods":
+                content = json.dumps(
+                    {
+                        "methods": [
+                            {
+                                "name": "bonferroni",
+                                "description": "Bonferroni correction (FWER control)",
+                                "conservative": True,
+                            },
+                            {
+                                "name": "holm",
+                                "description": "Holm-Bonferroni step-down (FWER control)",
+                                "conservative": True,
+                            },
+                            {
+                                "name": "sidak",
+                                "description": "Sidak correction (FWER control)",
+                                "conservative": True,
+                            },
+                            {
+                                "name": "fdr_bh",
+                                "description": "Benjamini-Hochberg (FDR control)",
+                                "conservative": False,
+                            },
+                            {
+                                "name": "fdr_by",
+                                "description": "Benjamini-Yekutieli (FDR control)",
+                                "conservative": False,
+                            },
+                        ]
+                    },
+                    indent=2,
+                )
+                return types.TextResourceContents(
+                    uri=uri,
+                    mimeType="application/json",
+                    text=content,
+                )
+
+            else:
+                raise ValueError(f"Unknown resource URI: {uri}")
+
+    async def _wrap_result(self, coro):
+        """Wrap handler result as MCP TextContent."""
+        import json
+
+        try:
+            result = await coro
+            return [
+                types.TextContent(
+                    type="text",
+                    text=json.dumps(result, indent=2, default=str),
+                )
+            ]
+        except Exception as e:
+            return [
+                types.TextContent(
+                    type="text",
+                    text=json.dumps({"success": False, "error": str(e)}, indent=2),
+                )
+            ]
+
+
+async def _run_server():
+    """Run the MCP server (internal)."""
+    server = StatsServer()
+    async with stdio_server() as (read_stream, write_stream):
+        await server.server.run(
+            read_stream,
+            write_stream,
+            InitializationOptions(
+                server_name="scitex-stats",
+                server_version="0.1.0",
+                capabilities=server.server.get_capabilities(
+                    notification_options=NotificationOptions(),
+                    experimental_capabilities={},
+                ),
+            ),
+        )
+
+
+def main():
+    """Main entry point for the MCP server."""
+    if not MCP_AVAILABLE:
+        import sys
+
+        print("=" * 60)
+        print("MCP Server 'scitex-stats' requires the 'mcp' package.")
+        print()
+        print("Install with:")
+        print("  pip install mcp")
+        print()
+        print("Or install scitex with MCP support:")
+        print("  pip install scitex[mcp]")
+        print("=" * 60)
+        sys.exit(1)
+
+    asyncio.run(_run_server())
+
+
+if __name__ == "__main__":
+    main()
+
+
+# EOF

scitex/stats/posthoc/_dunnett.py

@@ -332,7 +332,7 @@ if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     args = parser.parse_args([])
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys=sys,
         plt=None,
         args=args,

scitex/stats/posthoc/_games_howell.py

@@ -283,7 +283,7 @@ if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     args = parser.parse_args([])
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys=sys,
         plt=None,
         args=args,

scitex/stats/posthoc/_tukey_hsd.py

@@ -282,7 +282,7 @@ if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     args = parser.parse_args([])
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys=sys,
         plt=None,
         args=args,

scitex/stats/power/_power.py

@@ -409,7 +409,7 @@ def run_main():
 
     args = parse_args()
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,

scitex/stats/utils/_effect_size.py

@@ -968,7 +968,7 @@ def run_main():
 
     args = parse_args()
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,

scitex/stats/utils/_formatters.py

@@ -252,7 +252,7 @@ def run_main():
 
     args = parse_args()
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,

scitex/stats/utils/_power.py

@@ -409,7 +409,7 @@ def run_main():
 
     args = parse_args()
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,