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

scitex/repro/_RandomStateManager.py

@@ -14,7 +14,7 @@ __DIR__ = os.path.dirname(__FILE__)
 Clean, simple RandomStateManager for scientific reproducibility.
 
 Main API:
-    rng_manager = RandomStateManager(seed=42)   # Create instance
+    rng = RandomStateManager(seed=42)   # Create instance
     gen = rng("name")                   # Get named generator
     rng.verify(obj, "name")             # Verify reproducibility
 """
@@ -44,11 +44,11 @@ class RandomStateManager:
     >>> import scitex as stx
     >>>
     >>> # Method 1: Direct usage
-    >>> rng_manager = stx.rng.RandomStateManager(seed=42)
+    >>> rng = stx.rng.RandomStateManager(seed=42)
     >>> data = rng("data").random(100)
     >>>
     >>> # Method 2: From session.start
-    >>> CONFIG, stdout, stderr, plt, CC, rng_manager = stx.session.start(seed=42)
+    >>> CONFIG, stdout, stderr, plt, CC, rng = stx.session.start(seed=42)
     >>> model = rng("model").normal(size=(10, 10))
     >>>
     >>> # Verify reproducibility
@@ -98,7 +98,7 @@ class RandomStateManager:
             np.random.seed(self.seed)
             # Also set default_rng for new API
             self._np = np
-            self._np_default_rng_manager = np.random.default_rng(self.seed)
+            self._np_default_rng = np.random.default_rng(self.seed)
             fixed_modules.append("numpy")
         except ImportError:
             self._np = None
@@ -159,7 +159,7 @@ class RandomStateManager:
 
         Examples
         --------
-        >>> rng_manager = RandomStateManager(42)
+        >>> rng = RandomStateManager(42)
         >>> gen = rng.get_np_generator("data")
         >>> values = gen.random(100)
         >>> perm = gen.permutation(100)
@@ -427,7 +427,7 @@ class RandomStateManager:
 
         Examples
         --------
-        >>> rng_manager = RandomStateManager(42)
+        >>> rng = RandomStateManager(42)
         >>> from sklearn.model_selection import train_test_split
         >>> X_train, X_test = train_test_split(
         ...     X, test_size=0.2,
@@ -455,7 +455,7 @@ class RandomStateManager:
 
         Examples
         --------
-        >>> rng_manager = RandomStateManager(42)
+        >>> rng = RandomStateManager(42)
         >>> gen = rng.get_torch_generator("model")
         >>> torch.randn(5, 5, generator=gen)
         """
@@ -503,7 +503,7 @@ class RandomStateManager:
 
         Examples
         --------
-        >>> rng_manager = RandomStateManager(42)
+        >>> rng = RandomStateManager(42)
         >>> rng.clear_cache()  # Clear all
         >>> rng.clear_cache("old_data")  # Clear specific
         >>> rng.clear_cache(["test1", "test2"])  # Clear multiple
@@ -559,7 +559,7 @@ def get(verbose: bool = False) -> RandomStateManager:
     Examples
     --------
     >>> import scitex as stx
-    >>> rng_manager = stx.rng.get()
+    >>> rng = stx.rng.get()
     >>> data = rng("data").random(100)
     """
     global _GLOBAL_INSTANCE
@@ -589,7 +589,7 @@ def reset(seed: int = 42, verbose: bool = False) -> RandomStateManager:
     Examples
     --------
     >>> import scitex as stx
-    >>> rng_manager = stx.repro.reset(seed=123)
+    >>> rng = stx.repro.reset(seed=123)
     """
     global _GLOBAL_INSTANCE
     _GLOBAL_INSTANCE = RandomStateManager(seed, verbose=verbose)
@@ -626,8 +626,8 @@ def main(args):
     print(f"Seed: {args.seed}")
 
     # Get named generators
-    data_gen = rng_manager("data")
-    model_gen = rng_manager("model")
+    data_gen = rng("data")
+    model_gen = rng("model")
 
     # Generate data
     print(f"\n{'Data Generation':-^60}")
@@ -641,7 +641,7 @@ def main(args):
 
     # Verify reproducibility
     print(f"\n{'Verification':-^60}")
-    rng_manager.verify(data, "demo_data")
+    rng.verify(data, "demo_data")
     print("✓ Data reproducibility verified")
 
     print(f"\n{'=' * 60}")
@@ -660,7 +660,7 @@ if __name__ == "__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/repro/_gen_ID.py

@@ -114,7 +114,7 @@ if __name__ == "__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/repro/_gen_timestamp.py

@@ -91,7 +91,7 @@ if __name__ == "__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/repro/_hash_array.py

@@ -72,8 +72,8 @@ def main(args):
     print(f"Array size: {args.size}")
     print(f"Seed: {args.seed}")
 
-    # Generate arrays using rng_manager
-    gen = rng_manager("demo")
+    # Generate arrays using rng
+    gen = rng("demo")
 
     # Create array and hash it
     print(f"\n{'Hash Generation':-^60}")
@@ -95,7 +95,7 @@ def main(args):
 
     # Reset generator and create same data
     print(f"\n{'Reproducibility Check':-^60}")
-    gen_repro = rng_manager("demo")  # Same name = same seed
+    gen_repro = rng("demo")  # Same name = same seed
     data3 = gen_repro.random(args.size)
     hash3 = hash_array(data3)
     print(f"Array 3 hash (reproduced): {hash3}")
@@ -115,7 +115,7 @@ if __name__ == "__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/schema/__init__.py

@@ -5,10 +5,10 @@
 SciTeX Schema Module - DEPRECATED
 
 This module is scheduled for removal. All schemas are being consolidated
-in scitex.fts as the single source of truth.
+in scitex.io.bundle as the single source of truth.
 
-For new code, import from scitex.fts:
-    from scitex.fts import FTS, Node, Encoding, Theme, Stats
+For new code, import from scitex.io.bundle:
+    from scitex.io.bundle import FTS, Node, Encoding, Theme, Stats
 
 This module exists temporarily for backward compatibility.
 """
@@ -16,31 +16,28 @@ This module exists temporarily for backward compatibility.
 import warnings
 
 warnings.warn(
-    "scitex.schema is deprecated. Import from scitex.fts instead. "
+    "scitex.schema is deprecated. Import from scitex.io.bundle instead. "
     "This module will be removed in a future version.",
     DeprecationWarning,
-    stacklevel=2
+    stacklevel=2,
 )
 
 # Schema version
 SCHEMA_VERSION = "0.2.0"
 
 # =============================================================================
-# Re-export from scitex.fts (new single source of truth)
+# Re-export from scitex.io.bundle (new single source of truth)
 # =============================================================================
 try:
-    from scitex.fts import (
-        # Core bundle classes
+    from scitex.io.bundle import (  # Core bundle classes; Encoding and Theme; Stats
         FTS,
-        Node,
         BBox,
-        SizeMM,
         DataInfo,
-        # Encoding and Theme
         Encoding,
-        Theme,
-        # Stats
+        Node,
+        SizeMM,
         Stats,
+        Theme,
     )
 except ImportError:
     # FTS not fully configured yet
@@ -52,21 +49,10 @@ except ImportError:
 
 # =============================================================================
 # Independent schemas (still defined here temporarily)
-# These will be migrated to scitex.fts in subsequent phases
+# These will be migrated to scitex.io.bundle in subsequent phases
 # =============================================================================
 
 # Stats schema (GUI-focused version - to be merged with FTS Stats)
-from scitex.schema._stats import (
-    Position,
-    PositionMode,
-    StatPositioning,
-    StatResult,
-    StatStyling,
-    SymbolStyle,
-    UnitType,
-    create_stat_result,
-)
-
 # Encoding schema
 from scitex.schema._encoding import (
     ENCODING_VERSION,
@@ -87,48 +73,58 @@ from scitex.schema._figure_elements import (
     generate_caption_markdown,
 )
 
-# Theme schema
-from scitex.schema._theme import (
-    THEME_VERSION,
-    ColorScheme,
-    LegendStyle,
-    LineDefaults,
-    MarkerDefaults,
-    PlotTheme,
-    Typography,
-)
-from scitex.schema._theme import TraceStyle as ThemeTraceStyle
-
 # Plot schema
 from scitex.schema._plot import (
     DPI_FALLBACK,
     PLOT_GEOMETRY_VERSION,
     PLOT_SPEC_VERSION,
     PLOT_STYLE_VERSION,
+    AxesLabels,
+    AxesLimits,
+    AxesSpecItem,
     BboxPx,
     BboxRatio,
     CoordinateSpace,
+    DataSourceSpec,
+    FontSpec,
+    HitRegionEntry,
     LegendLocation,
+    LegendSpec,
+    PlotGeometry,
+    PlotSpec,
+    PlotStyle,
+    RenderedArtist,
+    RenderedAxes,
+    RenderManifest,
+    SelectableRegion,
+    SizeSpec,
+    ThemeSpec,
+    TraceSpec,
+    TraceStyleSpec,
     TraceType,
 )
-from scitex.schema._plot import AxesLabels as PltzAxesLabels
-from scitex.schema._plot import AxesLimits as PltzAxesLimits
-from scitex.schema._plot import AxesSpecItem as PltzAxesItem
-from scitex.schema._plot import DataSourceSpec as PltzDataSource
-from scitex.schema._plot import FontSpec as PltzFont
-from scitex.schema._plot import HitRegionEntry as PltzHitRegion
-from scitex.schema._plot import LegendSpec as PltzLegendSpec
-from scitex.schema._plot import PlotGeometry as PltzGeometry
-from scitex.schema._plot import PlotSpec as PltzSpec
-from scitex.schema._plot import PlotStyle as PltzStyle
-from scitex.schema._plot import RenderedArtist as PltzRenderedArtist
-from scitex.schema._plot import RenderedAxes as PltzRenderedAxes
-from scitex.schema._plot import RenderManifest as PltzRenderManifest
-from scitex.schema._plot import SelectableRegion as PltzSelectableRegion
-from scitex.schema._plot import SizeSpec as PltzSize
-from scitex.schema._plot import ThemeSpec as PltzTheme
-from scitex.schema._plot import TraceSpec as PltzTraceSpec
-from scitex.schema._plot import TraceStyleSpec as PltzTraceStyle
+from scitex.schema._stats import (
+    Position,
+    PositionMode,
+    StatPositioning,
+    StatResult,
+    StatStyling,
+    SymbolStyle,
+    UnitType,
+    create_stat_result,
+)
+
+# Theme schema
+from scitex.schema._theme import (
+    THEME_VERSION,
+    ColorScheme,
+    LegendStyle,
+    LineDefaults,
+    MarkerDefaults,
+    PlotTheme,
+)
+from scitex.schema._theme import TraceStyle as ThemeTraceStyle
+from scitex.schema._theme import Typography
 
 # Validation (temporarily keep here)
 from scitex.schema._validation import (
@@ -164,24 +160,24 @@ __all__ = [
     "LegendLocation",
     "BboxRatio",
     "BboxPx",
-    "PltzTraceSpec",
-    "PltzAxesLimits",
-    "PltzAxesLabels",
-    "PltzAxesItem",
-    "PltzDataSource",
-    "PltzSpec",
-    "PltzTraceStyle",
-    "PltzTheme",
-    "PltzFont",
-    "PltzSize",
-    "PltzLegendSpec",
-    "PltzStyle",
-    "PltzRenderedArtist",
-    "PltzRenderedAxes",
-    "PltzHitRegion",
-    "PltzSelectableRegion",
-    "PltzGeometry",
-    "PltzRenderManifest",
+    "TraceSpec",
+    "AxesLimits",
+    "AxesLabels",
+    "AxesSpecItem",
+    "DataSourceSpec",
+    "PlotSpec",
+    "TraceStyleSpec",
+    "ThemeSpec",
+    "FontSpec",
+    "SizeSpec",
+    "LegendSpec",
+    "PlotStyle",
+    "RenderedArtist",
+    "RenderedAxes",
+    "HitRegionEntry",
+    "SelectableRegion",
+    "PlotGeometry",
+    "RenderManifest",
     # Encoding
     "ENCODING_VERSION",
     "ChannelBinding",

scitex/schema/_canvas.py

@@ -327,7 +327,7 @@ class CanvasSpec:
     Complete specification for a SciTeX canvas.
 
     This is the wire format for canvas.json files.
-    The Canvas class in scitex.fig provides the OO interface.
+    The Canvas class in scitex.canvas provides the OO interface.
 
     Examples
     --------

scitex/schema/_stats.py

@@ -10,7 +10,7 @@ Statistical Result Schema - Central Source of Truth.
 This module defines the canonical schema for statistical test results
 that integrates with:
 - scitex.plt (TrackingMixin, metadata embedding)
-- scitex.fig (JSON serialization, FigureModel)
+- scitex.canvas (JSON serialization, FigureModel)
 - scitex-cloud GUI (Fabric.js canvas, properties panel, positioning)
 - scitex.bridge (cross-module adapters)
 
@@ -272,7 +272,7 @@ class StatResult:
 
     This is the central schema for statistical results that integrates with:
     - scitex.plt: Automatic annotation via TrackingMixin
-    - scitex.fig: JSON serialization for FigureModel
+    - scitex.canvas: JSON serialization for FigureModel
     - scitex-cloud GUI: Fabric.js canvas positioning and properties panel
     - scitex.bridge: Cross-module adapters
 

scitex/scholar/__main__.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # File: /home/ywatanabe/proj/scitex_repo/src/scitex/scholar/__main__.py
 
 """Scholar CLI entry point - Subcommand-based interface.
@@ -8,6 +7,7 @@ Clean interface routing to battle-tested pipeline implementations:
 - single: Process single paper (DOI or title)
 - parallel: Process multiple papers in parallel
 - bibtex: Process papers from BibTeX file
+- mcp: Start MCP server for LLM integration
 """
 
 from __future__ import annotations
@@ -33,6 +33,7 @@ Clean subcommand interface to battle-tested pipelines:
   single   - Process a single paper (DOI or title)
   parallel - Process multiple papers in parallel
   bibtex   - Process papers from BibTeX file
+  mcp      - Start MCP server for LLM integration
 
 STORAGE: ~/.scitex/scholar/library/
   MASTER/{8DIGITID}/  - Centralized storage (no duplicates)
@@ -193,6 +194,16 @@ STORAGE: ~/.scitex/scholar/library/
         help="Base Chrome profile to sync from (default: system)",
     )
 
+    # ========================================
+    # 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
 
 
@@ -220,7 +231,7 @@ async def run_single_pipeline(args):
         force=args.force,
     )
 
-    logger.success(f"Single paper pipeline completed")
+    logger.success("Single paper pipeline completed")
     return 0
 
 
@@ -288,6 +299,15 @@ async def run_bibtex_pipeline(args):
     return 0
 
 
+async def run_mcp_server():
+    """Run MCP server."""
+    from .mcp_server import main as mcp_main
+
+    logger.info("Starting Scholar MCP server...")
+    await mcp_main()
+    return 0
+
+
 async def main_async():
     """Main async entry point."""
     parser = create_parser()
@@ -300,6 +320,8 @@ async def main_async():
         return await run_parallel_pipeline(args)
     elif args.command == "bibtex":
         return await run_bibtex_pipeline(args)
+    elif args.command == "mcp":
+        return await run_mcp_server()
     else:
         logger.error(f"Unknown command: {args.command}")
         return 1