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

scitex/scholar/pdf_download/ScholarPDFDownloader.py

@@ -660,7 +660,7 @@ def run_main() -> None:
 
     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/scholar/pipelines/ScholarPipelineBibTeX.py

@@ -316,7 +316,7 @@ def run_main() -> None:
 
     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/scholar/pipelines/ScholarPipelineParallel.py

@@ -406,7 +406,7 @@ def run_main() -> None:
 
     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/scholar/pipelines/ScholarPipelineSingle.py

@@ -694,7 +694,7 @@ def run_main() -> None:
 
     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/scholar/storage/PaperIO.py

@@ -438,7 +438,7 @@ def run_main() -> None:
 
     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/session/README.md

@@ -22,7 +22,7 @@ def main(
     CONFIG=scitex.INJECTED,
     plt=scitex.INJECTED,
     COLORS=scitex.INJECTED,
-    rng_manager=scitex.INJECTED,
+    rng=scitex.INJECTED,
 ):
     """Args injected by @scitex.session decorator"""
     print(f"Session ID: {CONFIG['ID']}")
@@ -46,7 +46,7 @@ def main(
     CONFIG=scitex.INJECTED,
     plt=scitex.INJECTED,
     COLORS=scitex.INJECTED,
-    rng_manager=scitex.INJECTED,
+    rng=scitex.INJECTED,
 ):
     """Args injected by @scitex.session decorator"""
     print(f"Session ID: {CONFIG['ID']}")
@@ -59,7 +59,7 @@ The decorator automatically injects the following parameters:
 - `CONFIG`: Configuration dictionary with session metadata
 - `plt`: Configured matplotlib.pyplot module
 - `COLORS`: Color cycle dictionary
-- `rng_manager`: RandomStateManager instance
+- `rng`: RandomStateManager instance
 
 Using `scitex.INJECTED` as default values makes it explicit that these parameters are injected by the decorator.
 
@@ -249,4 +249,4 @@ if __name__ == "__main__":
 - Automatically fixes seeds for all libraries
 - Reproducible across runs
 
-<!-- EOF -->
+<!-- EOF -->

scitex/session/__init__.py

@@ -22,7 +22,7 @@ Usage:
     from scitex import session
     
     # Start a session
-    CONFIG, sys.stdout, sys.stderr, plt, COLORS, rng_manager = session.start(sys, plt)
+    CONFIG, sys.stdout, sys.stderr, plt, COLORS, rng = session.start(sys, plt)
     
     # Your experiment code here
     

scitex/session/_decorator.py

@@ -79,7 +79,7 @@ def session(
             # - CONFIG: Session configuration dict
             # - plt: Matplotlib pyplot (configured for session)
             # - COLORS: Custom Colors
-            # - rng_manager: RandomStateManager (fixes seeds, creates named generators)
+            # - rng: RandomStateManager (fixes seeds, creates named generators)
             logger.info(f"Session ID: {CONFIG['ID']}")
             logger.info(f"Output directory: {CONFIG['SDIR_RUN']}")
             # ... training code ...
@@ -100,8 +100,8 @@ def session(
         - CONFIG (dict): Session configuration with ID, SDIR, paths, etc.
         - plt (module): matplotlib.pyplot configured with session settings
         - COLORS (CustomColors): Custom Colors for consistent plotting
-        - rng_manager (RandomStateManager): Manages reproducibility by fixing global seeds
-                                             and creating named generators via rng_manager("name")
+        - rng (RandomStateManager): Manages reproducibility by fixing global seeds
+                                             and creating named generators via rng("name")
     """
 
     def decorator(func: Callable) -> Callable:
@@ -163,7 +163,7 @@ def _run_with_session(
     # Start session
     import matplotlib.pyplot as plt
 
-    CONFIG, stdout, stderr, plt, COLORS, rng_manager = start(
+    CONFIG, stdout, stderr, plt, COLORS, rng = start(
         sys=sys_module,
         plt=plt,
         args=cleaned_args,
@@ -182,7 +182,7 @@ def _run_with_session(
     func_globals["CONFIG"] = CONFIG
     func_globals["plt"] = plt
     func_globals["COLORS"] = COLORS
-    func_globals["rng_manager"] = rng_manager
+    func_globals["rng"] = rng
     func_globals["logger"] = script_logger
 
     # Log injected globals for user awareness (only in verbose mode)
@@ -195,7 +195,7 @@ def _run_with_session(
         _decorator_logger.info(f"      - CONFIG['PID']: {CONFIG['PID']}")
         _decorator_logger.info("  • plt - matplotlib.pyplot (configured for session)")
         _decorator_logger.info("  • COLORS - CustomColors (for consistent plotting)")
-        _decorator_logger.info("  • rng_manager - RandomStateManager (for reproducibility)")
+        _decorator_logger.info("  • rng - RandomStateManager (for reproducibility)")
         _decorator_logger.info("  • logger - SciTeX logger (configured for your script)")
         _decorator_logger.info("=" * 60)
 
@@ -216,7 +216,7 @@ def _run_with_session(
             "CONFIG": CONFIG,
             "plt": plt,
             "COLORS": COLORS,
-            "rng_manager": rng_manager,
+            "rng": rng,
             "logger": script_logger,
         }
 
@@ -419,7 +419,7 @@ Global Variables Injected by @session Decorator:
             plt.plot(x, y, color=COLORS.blue)
             plt.plot(x, y, color=COLORS['blue'])
 
-    rng_manager (RandomStateManager)
+    rng (RandomStateManager)
         Manages reproducible randomness
 
     logger (SciTeXLogger)
@@ -596,7 +596,7 @@ def run(func: Callable, parse_args: Callable = None, **session_kwargs) -> Any:
     # Start session
     import matplotlib.pyplot as plt
 
-    CONFIG, stdout, stderr, plt, COLORS, rng_manager = start(
+    CONFIG, stdout, stderr, plt, COLORS, rng = start(
         sys=sys_module,
         plt=plt,
         args=args,

scitex/session/_lifecycle.py

@@ -411,12 +411,12 @@ def start(
     Returns
     -------
     tuple
-        (CONFIGS, stdout, stderr, plt, COLORS, rng_manager)
+        (CONFIGS, stdout, stderr, plt, COLORS, rng)
         - CONFIGS: Configuration dictionary
         - stdout, stderr: Redirected output streams
         - plt: Configured matplotlib.pyplot module
         - COLORS: Color cycle dictionary
-        - rng_manager: Global RandomStateManager instance for reproducible random generation
+        - rng: Global RandomStateManager instance for reproducible random generation
     """
     IS_DEBUG = _get_debug_mode()
     ID, PID = _initialize_env(IS_DEBUG)
@@ -516,7 +516,7 @@ def start(
             pass
 
     # Initialize RandomStateManager (automatically fixes all seeds)
-    rng_manager = RandomStateManager(seed=seed, verbose=verbose)
+    rng = RandomStateManager(seed=seed, verbose=verbose)
     if verbose:
         logger.info(f"Initialized RandomStateManager with seed {seed}")
 
@@ -554,9 +554,9 @@ def start(
 
     # Return appropriate values based on whether sys was provided
     if sys is not None:
-        return CONFIGS, sys.stdout, sys.stderr, plt, COLORS, rng_manager
+        return CONFIGS, sys.stdout, sys.stderr, plt, COLORS, rng
     else:
-        return CONFIGS, None, None, plt, COLORS, rng_manager
+        return CONFIGS, None, None, plt, COLORS, rng
 
 
 def _format_diff_time(diff_time):

scitex/session/template.py

@@ -16,7 +16,7 @@ def main(
     CONFIG=INJECTED,
     plt=INJECTED,
     COLORS=INJECTED,
-    rng_manager=INJECTED,
+    rng=INJECTED,
     logger=INJECTED,
 ):
     """Demonstration for scitex.session.session"""

scitex/stats/__init__.py

@@ -57,21 +57,21 @@ from .auto import (
 )
 
 # =============================================================================
-# Stats Schema - Use scitex.fts.Stats as single source of truth
+# Stats Schema - Use scitex.io.bundle.Stats as single source of truth
 # =============================================================================
 
-# For backward compatibility, re-export from fts
+# Re-export Stats from bundle module
 try:
-    from scitex.fts import Stats
+    from scitex.io.bundle import Stats
 
-    FTS_AVAILABLE = True
+    BUNDLE_AVAILABLE = True
 except ImportError:
     Stats = None
-    FTS_AVAILABLE = False
+    BUNDLE_AVAILABLE = False
 
 
 def test_result_to_stats(result: dict) -> "Stats":
-    """Convert test result dict to FTS Stats schema.
+    """Convert test result dict to Stats schema.
 
     Parameters
     ----------
@@ -92,26 +92,24 @@ def test_result_to_stats(result: dict) -> "Stats":
     Returns
     -------
     Stats
-        FTS Stats object suitable for bundle storage
+        Stats object suitable for bundle storage
 
     Example
     -------
     >>> result = stats.t_test(x, y)
-    >>> fts_stats = stats.test_result_to_stats(result)
-    >>> bundle.stats = fts_stats
+    >>> stat_obj = stats.test_result_to_stats(result)
+    >>> bundle.stats = stat_obj
     """
-    if not FTS_AVAILABLE:
-        raise ImportError("scitex.fts is required for Stats conversion")
+    if not BUNDLE_AVAILABLE:
+        raise ImportError("scitex.io.bundle is required for Stats conversion")
 
     import uuid
 
-    from scitex.fts._stats._dataclasses._Stats import (
+    from scitex.io.bundle._stats._dataclasses._Stats import (
         Analysis,
         EffectSize,
         StatMethod,
-    )
-    from scitex.fts._stats._dataclasses._Stats import (
-        StatResult as FTSStatResult,
+        StatResult,
     )
 
     # Handle legacy flat format vs new nested format
@@ -134,7 +132,7 @@ def test_result_to_stats(result: dict) -> "Stats":
                 ci_lower=ci[0] if len(ci) > 0 else None,
                 ci_upper=ci[1] if len(ci) > 1 else None,
             )
-        stat_result = FTSStatResult(
+        stat_result = StatResult(
             statistic=result.get("statistic", 0.0),
             statistic_name=result.get("statistic_name", ""),
             p_value=result.get("p_value", 1.0),
@@ -164,7 +162,7 @@ def test_result_to_stats(result: dict) -> "Stats":
                 ci_upper=es.get("ci_upper"),
             )
 
-        stat_result = FTSStatResult(
+        stat_result = StatResult(
             statistic=results_data.get("statistic", 0.0),
             statistic_name=results_data.get("statistic_name", ""),
             p_value=results_data.get("p_value", 1.0),
@@ -189,25 +187,25 @@ def test_result_to_stats(result: dict) -> "Stats":
 
 
 # =============================================================================
-# .statsz Bundle Support - Using FTS
+# .stats Bundle Support
 # =============================================================================
 
 
-def save_statsz(
+def save_stats(
     comparisons,
     path,
     metadata=None,
     as_zip=False,
 ):
     """
-    Save statistical results as an FTS bundle.
+    Save statistical results as a SciTeX bundle.
 
     Parameters
     ----------
     comparisons : list of dict
         List of comparison results.
     path : str or Path
-        Output path (e.g., "results.zip").
+        Output path (e.g., "results.stats" or "results.stats.zip").
     metadata : dict, optional
         Additional metadata.
     as_zip : bool, optional
@@ -220,14 +218,14 @@ def save_statsz(
     """
     from pathlib import Path
 
-    from scitex.fts import FTS
+    from scitex.io.bundle import Bundle
 
     p = Path(path)
     if as_zip and not p.suffix == ".zip":
         p = p.with_suffix(".zip")
 
-    # Create FTS bundle
-    bundle = FTS(p, create=True, node_type="stats")
+    # Create bundle
+    bundle = Bundle(p, create=True, bundle_type="stats")
 
     # Convert comparisons to Stats
     if comparisons:
@@ -246,14 +244,14 @@ def save_statsz(
     return p
 
 
-def load_statsz(path):
+def load_stats(path):
     """
-    Load a stats bundle using FTS.
+    Load a stats bundle.
 
     Parameters
     ----------
     path : str or Path
-        Path to bundle.
+        Path to bundle (.stats or .stats.zip).
 
     Returns
     -------
@@ -262,9 +260,9 @@ def load_statsz(path):
         Each comparison is a flat dict with:
         - name, method, p_value, effect_size, ci95, formatted
     """
-    from scitex.fts import FTS
+    from scitex.io.bundle import Bundle
 
-    bundle = FTS(path)
+    bundle = Bundle(path)
 
     comparisons = []
     if bundle.stats and bundle.stats.analyses:
@@ -317,9 +315,8 @@ __all__ = [
     "describe",
     # Torch availability flag (for GPU acceleration)
     "TORCH_AVAILABLE",
-    # Stats schema (from FTS)
+    # Stats schema
     "Stats",
-    "FTS_AVAILABLE",
     # Auto module convenience exports
     "StatContext",
     "TestRule",
@@ -334,8 +331,8 @@ __all__ = [
     # Conversion utilities
     "test_result_to_stats",
     # Bundle functions
-    "save_statsz",
-    "load_statsz",
+    "save_stats",
+    "load_stats",
 ]
 
 __version__ = "2.2.0"

scitex/stats/__main__.py

@@ -0,0 +1,281 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-08
+# File: src/scitex/stats/__main__.py
+# ----------------------------------------
+
+"""Stats CLI entry point.
+
+Subcommand-based interface:
+- recommend: Recommend statistical tests based on data characteristics
+- test: Run a statistical test
+- power: Power analysis and sample size calculation
+- mcp: Start MCP server for LLM integration
+"""
+
+from __future__ import annotations
+
+import argparse
+import asyncio
+import json
+import sys
+
+
+def create_parser():
+    """Create main argument parser with subcommands."""
+    parser = argparse.ArgumentParser(
+        prog="python -m scitex.stats",
+        description="""
+SciTeX Stats - Statistical Testing Framework
+═══════════════════════════════════════════
+
+Subcommand interface:
+  recommend - Recommend statistical tests
+  test      - Run a statistical test
+  power     - Power analysis
+  mcp       - Start MCP server for LLM integration
+        """,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    subparsers = parser.add_subparsers(
+        dest="command",
+        help="Available commands",
+        required=True,
+    )
+
+    # ========================================
+    # Subcommand: recommend
+    # ========================================
+    recommend_parser = subparsers.add_parser(
+        "recommend",
+        help="Recommend statistical tests",
+        description="Recommend appropriate statistical tests based on data characteristics",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    recommend_parser.add_argument(
+        "--n-groups",
+        type=int,
+        default=2,
+        help="Number of groups to compare (default: 2)",
+    )
+    recommend_parser.add_argument(
+        "--sample-sizes",
+        type=int,
+        nargs="+",
+        help="Sample sizes for each group",
+    )
+    recommend_parser.add_argument(
+        "--outcome",
+        type=str,
+        choices=["continuous", "ordinal", "categorical", "binary"],
+        default="continuous",
+        help="Outcome variable type (default: continuous)",
+    )
+    recommend_parser.add_argument(
+        "--design",
+        type=str,
+        choices=["between", "within", "mixed"],
+        default="between",
+        help="Study design (default: between)",
+    )
+    recommend_parser.add_argument(
+        "--paired",
+        action="store_true",
+        help="Data is paired/matched",
+    )
+    recommend_parser.add_argument(
+        "--has-control",
+        action="store_true",
+        help="Has a control group",
+    )
+    recommend_parser.add_argument(
+        "--top-k",
+        type=int,
+        default=3,
+        help="Number of recommendations (default: 3)",
+    )
+
+    # ========================================
+    # Subcommand: test
+    # ========================================
+    test_parser = subparsers.add_parser(
+        "test",
+        help="Run a statistical test",
+        description="Execute a statistical test on provided data",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    test_parser.add_argument(
+        "test_name",
+        type=str,
+        help="Name of the test to run",
+    )
+    test_parser.add_argument(
+        "--data",
+        type=str,
+        help="JSON array of group data, e.g., '[[1,2,3],[4,5,6]]'",
+    )
+    test_parser.add_argument(
+        "--alternative",
+        type=str,
+        choices=["two-sided", "less", "greater"],
+        default="two-sided",
+        help="Alternative hypothesis (default: two-sided)",
+    )
+
+    # ========================================
+    # Subcommand: power
+    # ========================================
+    power_parser = subparsers.add_parser(
+        "power",
+        help="Power analysis",
+        description="Calculate statistical power or required sample size",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    power_parser.add_argument(
+        "--test-type",
+        type=str,
+        choices=["ttest", "anova", "correlation", "chi2"],
+        default="ttest",
+        help="Type of statistical test (default: ttest)",
+    )
+    power_parser.add_argument(
+        "--effect-size",
+        type=float,
+        help="Expected effect size (Cohen's d, f, r, or w)",
+    )
+    power_parser.add_argument(
+        "--n",
+        type=int,
+        help="Sample size per group (for power calculation)",
+    )
+    power_parser.add_argument(
+        "--power",
+        type=float,
+        default=0.8,
+        help="Desired power (default: 0.8)",
+    )
+    power_parser.add_argument(
+        "--alpha",
+        type=float,
+        default=0.05,
+        help="Significance level (default: 0.05)",
+    )
+
+    # ========================================
+    # Subcommand: mcp
+    # ========================================
+    subparsers.add_parser(
+        "mcp",
+        help="Start MCP server for LLM integration",
+        description="Start the MCP (Model Context Protocol) server for Claude/LLM integration",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    return parser
+
+
+def run_recommend(args):
+    """Run test recommendation."""
+    from scitex.stats.auto import StatContext, recommend_tests
+    from scitex.stats.auto._rules import TEST_RULES
+
+    ctx = StatContext(
+        n_groups=args.n_groups,
+        sample_sizes=args.sample_sizes or [30] * args.n_groups,
+        outcome_type=args.outcome,
+        design=args.design,
+        paired=args.paired,
+        has_control_group=args.has_control,
+        n_factors=1,
+    )
+
+    tests = recommend_tests(ctx, top_k=args.top_k)
+
+    print("\n=== Recommended Statistical Tests ===\n")
+    for i, test_name in enumerate(tests, 1):
+        rule = TEST_RULES.get(test_name)
+        if rule:
+            print(f"{i}. {test_name}")
+            print(f"   Family: {rule.family}")
+            print(f"   Priority: {rule.priority}")
+            if rule.needs_normality:
+                print("   Requires: normality assumption")
+            if rule.needs_equal_variance:
+                print("   Requires: equal variance assumption")
+            print()
+
+    return 0
+
+
+def run_test(args):
+    """Run a statistical test."""
+    if not args.data:
+        print("Error: --data is required")
+        return 1
+
+    data = json.loads(args.data)
+
+    from scitex.stats._mcp_handlers import run_test_handler
+
+    result = asyncio.run(
+        run_test_handler(
+            test_name=args.test_name,
+            data=data,
+            alternative=args.alternative,
+        )
+    )
+
+    print(json.dumps(result, indent=2))
+    return 0 if result.get("success") else 1
+
+
+def run_power(args):
+    """Run power analysis."""
+    from scitex.stats._mcp_handlers import power_analysis_handler
+
+    result = asyncio.run(
+        power_analysis_handler(
+            test_type=args.test_type,
+            effect_size=args.effect_size,
+            n=args.n,
+            power=args.power,
+            alpha=args.alpha,
+        )
+    )
+
+    print(json.dumps(result, indent=2))
+    return 0 if result.get("success") else 1
+
+
+async def run_mcp_server():
+    """Run MCP server."""
+    from .mcp_server import main as mcp_main
+
+    print("Starting Stats MCP server...", file=sys.stderr)
+    await mcp_main()
+    return 0
+
+
+def main():
+    """Main entry point."""
+    parser = create_parser()
+    args = parser.parse_args()
+
+    if args.command == "recommend":
+        return run_recommend(args)
+    elif args.command == "test":
+        return run_test(args)
+    elif args.command == "power":
+        return run_power(args)
+    elif args.command == "mcp":
+        return asyncio.run(run_mcp_server())
+    else:
+        print(f"Unknown command: {args.command}")
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())
+
+
+# EOF