scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/repro/_RandomStateManager.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Timestamp: "2025-09-14 11:00:03 (ywatanabe)"
-# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/rng/_RandomStateManager.py
+# Timestamp: "2025-12-09 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/repro/_RandomStateManager.py
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -25,6 +26,8 @@ from contextlib import contextmanager
 from pathlib import Path
 from typing import Any
 
+from scitex.config import get_paths
+
 # Global singleton instance
 _GLOBAL_INSTANCE = None
 
@@ -54,7 +57,7 @@ class RandomStateManager:
         self.seed = seed
         self.verbose = verbose
         self._generators = {}
-        self._cache_dir = Path.home() / ".scitex" / "rng"
+        self._cache_dir = get_paths().rng
         self._cache_dir.mkdir(parents=True, exist_ok=True)
         self._jax_key = None  # Initialize to None, will be set if jax is available
 
@@ -168,28 +171,30 @@ class RandomStateManager:
             self._generators[name] = self._np.random.default_rng(seed)
 
         return self._generators[name]
-    
+
     def __call__(self, name: str, verbose: bool = None):
         """
         Get or create a named NumPy random generator.
-        
+
         This is a backward compatibility wrapper for get_np_generator().
         Consider using get_np_generator() directly for clarity.
-        
+
         Parameters
         ----------
         name : str
             Generator name
         verbose : bool, optional
             Whether to show deprecation warning
-        
+
         Returns
         -------
         numpy.random.Generator
             NumPy random generator with deterministic seed
         """
         if verbose:
-            print(f"Note: rng('{name}') is deprecated. Use rng.get_np_generator('{name}') instead.")
+            print(
+                f"Note: rng('{name}') is deprecated. Use rng.get_np_generator('{name}') instead."
+            )
         return self.get_np_generator(name)
 
     def verify(self, obj: Any, name: str = None, verbose: bool = True) -> bool:
@@ -232,9 +237,7 @@ class RandomStateManager:
             name = f"{filename}_L{lineno}"
 
         # Sanitize name
-        safe_name = "".join(
-            c if c.isalnum() or c in "-_" else "_" for c in name
-        )
+        safe_name = "".join(c if c.isalnum() or c in "-_" else "_" for c in name)
         cache_file = self._cache_dir / f"{safe_name}.json"
 
         # Compute hash based on object type
@@ -254,9 +257,7 @@ class RandomStateManager:
                 print(f"⚠️  Reproducibility broken for '{name}'!")
                 print(f"   Expected: {cached['hash'][:16]}...")
                 print(f"   Got:      {obj_hash[:16]}...")
-                raise ValueError(
-                    f"Reproducibility verification failed for '{name}'"
-                )
+                raise ValueError(f"Reproducibility verification failed for '{name}'")
             elif matches and verbose:
                 print(f"✓ Reproducibility verified for '{name}'")
 
@@ -264,9 +265,7 @@ class RandomStateManager:
         else:
             # First call - cache it
             with open(cache_file, "w") as f:
-                json.dump(
-                    {"name": name, "hash": obj_hash, "seed": self.seed}, f
-                )
+                json.dump({"name": name, "hash": obj_hash, "seed": self.seed}, f)
             return True
 
     def _compute_hash(self, obj: Any) -> str:
@@ -477,11 +476,11 @@ class RandomStateManager:
     def get_generator(self, name: str):
         """Alias for get_np_generator for compatibility."""
         return self.get_np_generator(name)
-    
+
     def clear_cache(self, patterns: str | list[str] = None) -> int:
         """
         Clear verification cache files.
-        
+
         Parameters
         ----------
         patterns : str or list of str, optional
@@ -491,12 +490,12 @@ class RandomStateManager:
             - List of names: ["data1", "data2"]
             - Glob pattern: "experiment_*"
             - None: clear all cache files
-        
+
         Returns
         -------
         int
             Number of cache files removed
-        
+
         Examples
         --------
         >>> rng_manager = RandomStateManager(42)
@@ -506,12 +505,12 @@ class RandomStateManager:
         >>> rng.clear_cache("experiment_*")  # Clear pattern
         """
         import glob
-        
+
         if not self._cache_dir.exists():
             return 0
-        
+
         removed_count = 0
-        
+
         if patterns is None:
             # Clear all .json files
             cache_files = list(self._cache_dir.glob("*.json"))
@@ -522,7 +521,7 @@ class RandomStateManager:
             # Ensure patterns is a list
             if isinstance(patterns, str):
                 patterns = [patterns]
-            
+
             for pattern in patterns:
                 # Handle glob patterns
                 if "*" in pattern or "?" in pattern:
@@ -531,11 +530,11 @@ class RandomStateManager:
                     # Exact match
                     cache_file = self._cache_dir / f"{pattern}.json"
                     cache_files = [cache_file] if cache_file.exists() else []
-                
+
                 for cache_file in cache_files:
                     cache_file.unlink()
                     removed_count += 1
-        
+
         return removed_count
 
 
@@ -599,14 +598,10 @@ def reset(seed: int = 42, verbose: bool = False) -> RandomStateManager:
 def parse_args():
     """Parse command line arguments."""
     import argparse
-    parser = argparse.ArgumentParser(
-        description="Demonstrate RandomStateManager usage"
-    )
+
+    parser = argparse.ArgumentParser(description="Demonstrate RandomStateManager usage")
     parser.add_argument(
-        "--seed",
-        type=int,
-        default=42,
-        help="Random seed (default: 42)"
+        "--seed", type=int, default=42, help="Random seed (default: 42)"
     )
     return parser.parse_args()
 
@@ -622,9 +617,9 @@ def main(args):
     import numpy as np
 
     # Create RandomStateManager (already created by session.start)
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("RandomStateManager Demo")
-    print(f"{'='*60}")
+    print(f"{'=' * 60}")
     print(f"Seed: {args.seed}")
 
     # Get named generators
@@ -646,9 +641,9 @@ def main(args):
     rng_manager.verify(data, "demo_data")
     print("✓ Data reproducibility verified")
 
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Demo completed successfully!")
-    print(f"{'='*60}\n")
+    print(f"{'=' * 60}\n")
 
     return 0
 

scitex/repro/__init__.py

@@ -19,39 +19,48 @@ from ._hash_array import hash_array
 # Random state management (moved from scitex.rng)
 from ._RandomStateManager import RandomStateManager, get, reset
 
+
 # Legacy function for backward compatibility
-def fix_seeds(seed=42, os=True, random=True, np=True, torch=True,
-              tf=False, jax=False, verbose=False, **kwargs):
+def fix_seeds(
+    seed=42,
+    os=True,
+    random=True,
+    np=True,
+    torch=True,
+    tf=False,
+    jax=False,
+    verbose=False,
+    **kwargs,
+):
     """
     Deprecated: Use stx.repro.RandomStateManager instead.
 
     This function maintains backward compatibility with the old fix_seeds API.
     """
     import warnings
+
     warnings.warn(
         "fix_seeds is deprecated. Use stx.repro.RandomStateManager instead.",
         DeprecationWarning,
-        stacklevel=2
+        stacklevel=2,
     )
     # Create RandomStateManager with seed and verbose
     # It automatically handles all available modules
     return RandomStateManager(seed=seed, verbose=verbose)
 
+
 __all__ = [
     # ID and timestamp utilities
     "gen_ID",
     "gen_id",
     "gen_timestamp",
     "timestamp",
-
     # Hash utilities
     "hash_array",
-
     # Random state management
     "RandomStateManager",
     "get",
     "reset",
-
     # Legacy (deprecated)
     "fix_seeds",
-]
+]

scitex/repro/_gen_ID.py

@@ -59,18 +59,16 @@ gen_ID = gen_id  # Deprecated: use gen_id instead
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser(description="Demonstrate ID generation")
     parser.add_argument(
         "--format",
         type=str,
         default="%YY-%mM-%dD-%Hh%Mm%Ss",
-        help="Time format (default: %%YY-%%mM-%%dD-%%Hh%%Mm%%Ss)"
+        help="Time format (default: %%YY-%%mM-%%dD-%%Hh%%Mm%%Ss)",
     )
     parser.add_argument(
-        "--length",
-        type=int,
-        default=8,
-        help="Random string length (default: 8)"
+        "--length", type=int, default=8, help="Random string length (default: 8)"
     )
     return parser.parse_args()
 
@@ -80,9 +78,9 @@ def main(args):
 
     Demonstrates ID generation with different formats.
     """
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("ID Generation Demo")
-    print(f"{'='*60}")
+    print(f"{'=' * 60}")
 
     # Generate with default format
     print(f"\n{'Default Format':-^60}")
@@ -102,9 +100,9 @@ def main(args):
     for i, id_str in enumerate(ids, 1):
         print(f"{i}. {id_str}")
 
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Demo completed successfully!")
-    print(f"{'='*60}\n")
+    print(f"{'=' * 60}\n")
 
     return 0
 

scitex/repro/_gen_timestamp.py

@@ -39,12 +39,13 @@ timestamp = gen_timestamp
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser(description="Demonstrate timestamp generation")
     parser.add_argument(
         "--count",
         type=int,
         default=5,
-        help="Number of timestamps to generate (default: 5)"
+        help="Number of timestamps to generate (default: 5)",
     )
     return parser.parse_args()
 
@@ -56,9 +57,9 @@ def main(args):
     """
     import time
 
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Timestamp Generation Demo")
-    print(f"{'='*60}")
+    print(f"{'=' * 60}")
 
     # Generate single timestamp
     print(f"\n{'Single Timestamp':-^60}")
@@ -73,12 +74,12 @@ def main(args):
     for i in range(args.count):
         ts = gen_timestamp()
         timestamps.append(ts)
-        print(f"{i+1}. {ts}")
+        print(f"{i + 1}. {ts}")
         time.sleep(0.5)  # Small delay to show time progression
 
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Demo completed successfully!")
-    print(f"{'='*60}\n")
+    print(f"{'=' * 60}\n")
 
     return 0
 

scitex/repro/_hash_array.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -49,18 +50,13 @@ def hash_array(array_data: np.ndarray) -> str:
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser(description="Demonstrate array hashing")
     parser.add_argument(
-        "--size",
-        type=int,
-        default=100,
-        help="Array size (default: 100)"
+        "--size", type=int, default=100, help="Array size (default: 100)"
     )
     parser.add_argument(
-        "--seed",
-        type=int,
-        default=42,
-        help="Random seed (default: 42)"
+        "--seed", type=int, default=42, help="Random seed (default: 42)"
     )
     return parser.parse_args()
 
@@ -70,9 +66,9 @@ def main(args):
 
     Demonstrates array hashing for reproducibility verification.
     """
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Array Hashing Demo")
-    print(f"{'='*60}")
+    print(f"{'=' * 60}")
     print(f"Array size: {args.size}")
     print(f"Seed: {args.seed}")
 
@@ -105,9 +101,9 @@ def main(args):
     print(f"Array 3 hash (reproduced): {hash3}")
     print(f"Reproduces original: {hash1 == hash3}")
 
-    print(f"\n{'='*60}")
+    print(f"\n{'=' * 60}")
     print("Demo completed successfully!")
-    print(f"{'='*60}\n")
+    print(f"{'=' * 60}\n")
 
     return 0
 

scitex/reproduce/__init__.py

@@ -19,7 +19,7 @@ warnings.warn(
     "'scitex.reproduce'. This compatibility layer will be removed in a "
     "future version.",
     DeprecationWarning,
-    stacklevel=2
+    stacklevel=2,
 )
 
 # Import everything from the new module for backward compatibility

scitex/resource/_get_processor_usages.py

@@ -165,7 +165,9 @@ def _get_gpu_usage(n_round: int = 1) -> Tuple[float, float]:
 if __name__ == "__main__":
     import scitex
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
+        sys, plt, verbose=False
+    )
 
     usage = scitex.resource.get_processor_usages()
     scitex.io.save(usage, "usage.csv")

scitex/resource/_log_processor_usages.py

@@ -181,7 +181,9 @@ def _ensure_log_file(path: str, init: bool) -> None:
 main = log_processor_usages
 
 if __name__ == "__main__":
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
+        sys, plt, verbose=False
+    )
     main()
     scitex.session.close(CONFIG, verbose=False, notify=False)
 

scitex/rng/__init__.py

@@ -19,7 +19,7 @@ warnings.warn(
     "'scitex.rng'. This compatibility layer will be removed in a "
     "future version.",
     DeprecationWarning,
-    stacklevel=2
+    stacklevel=2,
 )
 
 # Import everything from the new module for backward compatibility

scitex/schema/README.md

@@ -0,0 +1,178 @@
+<!-- ---
+!-- Timestamp: 2025-12-09 20:40:40
+!-- Author: ywatanabe
+!-- File: /home/ywatanabe/proj/scitex-code/src/scitex/schema/README.md
+!-- --- -->
+
+# SciTeX Schema Module
+
+Central source of truth for cross-module data structures and JSON schemas.
+
+## Overview
+
+This module defines standardized schemas for data that:
+- Crosses module boundaries (vis, plt, stats, io, cloud)
+- Is serialized to JSON/disk
+- Needs version tracking for compatibility
+
+## Schema Types
+
+| Schema                     | Version | Module                                  | Purpose                               |
+|----------------------------|---------|-----------------------------------------|---------------------------------------|
+| `scitex.schema.canvas`     | 0.1.0   | `_canvas.py`                            | Multi-panel figure composition        |
+| `scitex.schema.stats`      | 0.1.0   | `_stats.py`                             | Statistical test results              |
+| `scitex.schema.figure`     | 0.1.0   | `__init__.py`                           | Figure specifications (via vis.model) |
+| `scitex.plt.figure`        | 0.1.0   | `plt/utils/_collect_figure_metadata.py` | plt module figure metadata            |
+
+## JSON Schema Identifiers
+
+All SciTeX JSON files should include schema identification:
+
+```json
+{
+  "scitex_schema": "scitex.schema.canvas",
+  "scitex_schema_version": "0.1.0",
+  ...
+}
+```
+
+### Schema Naming Convention
+
+- **Field name**: `scitex_schema` (identifies the schema type)
+- **Version field**: `scitex_schema_version` (semantic versioning)
+- **Format**: `scitex.schema.<type>` where type is one of:
+  - `canvas` - Canvas/multi-panel layouts
+  - `stats` - Statistical results
+  - `figure` - Figure specifications
+  - `plt.figure` - plt module figure metadata
+
+## Module Structure
+
+```
+scitex/schema/
+├── __init__.py      # Public API, re-exports, SCHEMA_VERSION
+├── _canvas.py       # Canvas/panel specifications
+├── _stats.py        # Statistical result schemas
+├── _validation.py   # Validation functions
+└── README.md        # This file
+```
+
+## Usage
+
+### Import from Central Location
+
+```python
+# Recommended: Import from scitex.schema
+from scitex.schema import (
+    # Figure specs (from vis.model)
+    FigureSpec, AxesSpec, PlotSpec,
+
+    # Statistical results
+    StatResult, create_stat_result,
+
+    # Canvas specs
+    CanvasSpec, PanelSpec,
+
+    # Validation
+    validate_figure, validate_stat_result,
+)
+```
+
+### Creating Statistical Results
+
+```python
+from scitex.schema import StatResult, create_stat_result
+
+# Quick creation
+result = create_stat_result(
+    test_type="pearson",
+    statistic_name="r",
+    statistic_value=0.85,
+    p_value=0.001
+)
+
+# Full specification
+result = StatResult(
+    test_type="t-test",
+    test_category="parametric",
+    statistic={"name": "t", "value": 3.45},
+    p_value=0.002,
+    stars="**",
+    effect_size={"name": "cohens_d", "value": 0.85}
+)
+
+# Format for display
+print(result.format_text("publication"))  # (t = 3.45, p < 0.01)
+print(result.format_text("compact"))      # t = 3.450**
+```
+
+### Creating Canvas Specifications
+
+```python
+from scitex.schema import CanvasSpec, PanelSpec
+
+canvas = CanvasSpec(
+    canvas_name="figure1",
+    size=CanvasSizeSpec(width_mm=180, height_mm=120)
+)
+
+panel = PanelSpec(
+    name="a",
+    type="scitex",
+    source="plot_a.png"
+)
+canvas.panels.append(panel)
+
+# Serialize
+json_dict = canvas.to_dict()
+```
+
+## Design Principles
+
+1. **Single Source of Truth**: Schema definitions live here, not in consuming modules
+2. **Backward Compatibility**: Version fields enable migration
+3. **JSON-First**: All schemas are JSON-serializable
+4. **GUI Integration**: Schemas support scitex-cloud GUI requirements
+5. **Type Safety**: Full type hints and dataclass validation
+
+## Schema Version History
+
+### Canvas Schema (`scitex.schema.canvas`)
+- **0.1.0**: Initial release with panel/annotation support
+
+### Stats Schema (`scitex.schema.stats`)
+- **0.1.0**: Initial release with GUI positioning support
+
+### Figure Schema (`scitex.schema.figure`)
+- **0.1.0**: Re-exports from vis.model
+
+### plt.figure Schema (`scitex.plt.figure`)
+- **0.1.0**: Figure metadata with traces, axes, dimensions
+
+## Validation
+
+```python
+from scitex.schema import validate_figure, validate_stat_result, ValidationError
+
+try:
+    validate_stat_result(result)
+except ValidationError as e:
+    print(f"Invalid: {e}")
+```
+
+## Integration Points
+
+| Consumer Module | Schema Used        | Purpose                 |
+|-----------------|--------------------|-------------------------|
+| `scitex.plt`    | `plt.figure`       | Figure metadata in JSON |
+| `scitex.vis`    | `canvas`, `figure` | Canvas composition      |
+| `scitex.stats`  | `stats`            | Test result output      |
+| `scitex-cloud`  | All                | GUI rendering           |
+| `scitex.bridge` | All                | Cross-module adapters   |
+
+## Related Documentation
+
+- `src/scitex/plt/docs/FIGURE_ARCHITECTURE.md` - plt module figure format
+- `src/scitex/vis/docs/CANVAS_ARCHITECTURE.md` - Canvas architecture
+
+<!-- EOF -->