scitex 2.0.0__py2.py3-none-any.whl → 2.1.0__py2.py3-none-any.whl

scitex/logging/_handlers.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""Custom handlers for SciTeX logging."""
+
+import logging
+import logging.handlers
+import os
+from datetime import datetime
+from pathlib import Path
+
+from ._formatters import SciTeXConsoleFormatter, SciTeXFileFormatter
+
+
+def create_console_handler(level=logging.INFO):
+    """Create a console handler with SciTeX formatting."""
+    handler = logging.StreamHandler()
+    handler.setLevel(level)
+    handler.setFormatter(SciTeXConsoleFormatter())
+    return handler
+
+
+def create_file_handler(log_file_path, level=logging.INFO, max_bytes=10*1024*1024, backup_count=5):
+    """Create a rotating file handler for log files.
+    
+    Args:
+        log_file_path: Path to the log file
+        level: Log level for the handler
+        max_bytes: Maximum size of log file before rotation (default: 10MB)
+        backup_count: Number of backup files to keep (default: 5)
+    """
+    # Ensure the log directory exists
+    log_dir = Path(log_file_path).parent
+    log_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Use RotatingFileHandler to prevent log files from growing too large
+    handler = logging.handlers.RotatingFileHandler(
+        log_file_path,
+        maxBytes=max_bytes,
+        backupCount=backup_count,
+        encoding='utf-8'
+    )
+    handler.setLevel(level)
+    handler.setFormatter(SciTeXFileFormatter())
+    return handler
+
+
+def get_default_log_path():
+    """Get the default log file path for SciTeX."""
+    # Use ~/.scitex/logs/ directory
+    scitex_dir = Path.home() / '.scitex'
+    logs_dir = scitex_dir / 'logs'
+    
+    # Create timestamped log file
+    timestamp = datetime.now().strftime("%Y-%m-%d")
+    log_file = logs_dir / f'scitex-{timestamp}.log'
+    
+    return str(log_file)
+
+
+__all__ = [
+    'create_console_handler',
+    'create_file_handler', 
+    'get_default_log_path'
+]

scitex/logging/_levels.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""Custom log levels for SciTeX."""
+
+import logging
+
+# Custom log levels for success/fail
+SUCCESS = 31  # Between WARNING (30) and ERROR (40)
+FAIL = 35     # Between WARNING (30) and ERROR (40)
+
+# Add custom levels to logging module with 4-character abbreviations
+logging.addLevelName(SUCCESS, 'SUCC')
+logging.addLevelName(FAIL, 'FAIL')
+logging.addLevelName(logging.DEBUG, 'DEBU')
+logging.addLevelName(logging.INFO, 'INFO')
+logging.addLevelName(logging.WARNING, 'WARN')
+logging.addLevelName(logging.ERROR, 'ERRO')
+logging.addLevelName(logging.CRITICAL, 'CRIT')
+
+# Standard levels for convenience
+DEBUG = logging.DEBUG
+INFO = logging.INFO
+WARNING = logging.WARNING
+ERROR = logging.ERROR
+CRITICAL = logging.CRITICAL
+
+__all__ = [
+    'SUCCESS',
+    'FAIL',
+    'DEBUG',
+    'INFO',
+    'WARNING', 
+    'ERROR',
+    'CRITICAL'
+]

scitex/logging/_logger.py

@@ -0,0 +1,163 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-10-17 15:03:33 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/logging/_logger.py
+# ----------------------------------------
+from __future__ import annotations
+import os
+__FILE__ = (
+    "./src/scitex/logging/_logger.py"
+)
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
+__FILE__ = __file__
+
+"""Enhanced logger class for SciTeX."""
+
+import logging
+
+from ._levels import FAIL, SUCCESS
+
+
+class SciTeXLogger(logging.Logger):
+    """Enhanced logger with success/fail methods, indent, separator, and color support."""
+
+    def _log_with_indent(
+        self,
+        level,
+        message,
+        indent=0,
+        sep=None,
+        n_sep=40,
+        c=None,
+        *args,
+        **kwargs,
+    ):
+        """Internal method to log with indent, separator, and color support."""
+        # Add separator lines if requested
+        if sep is not None:
+            separator = sep * n_sep
+            message = f"\n{separator}\n{message}\n{separator}"
+
+        # Add indent and color info to extra
+        if indent > 0 or sep is not None or c is not None:
+            extra = kwargs.get("extra", {})
+            extra["indent"] = indent
+            if c is not None:
+                extra["color"] = c
+            kwargs["extra"] = extra
+
+        self._log(level, message, args, **kwargs)
+
+    def debug(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log a debug message with optional indent, separator, and color."""
+        if self.isEnabledFor(logging.DEBUG):
+            self._log_with_indent(
+                logging.DEBUG, message, indent, sep, n_sep, c, *args, **kwargs
+            )
+
+    def info(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log an info message with optional indent, separator, and color."""
+        if self.isEnabledFor(logging.INFO):
+            self._log_with_indent(
+                logging.INFO, message, indent, sep, n_sep, c, *args, **kwargs
+            )
+
+    def warning(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log a warning message with optional indent, separator, and color."""
+        if self.isEnabledFor(logging.WARNING):
+            self._log_with_indent(
+                logging.WARNING,
+                message,
+                indent,
+                sep,
+                n_sep,
+                c,
+                *args,
+                **kwargs,
+            )
+
+    def error(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log an error message with optional indent, separator, and color."""
+        if self.isEnabledFor(logging.ERROR):
+            self._log_with_indent(
+                logging.ERROR, message, indent, sep, n_sep, c, *args, **kwargs
+            )
+
+    def critical(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log a critical message with optional indent, separator, and color."""
+        if self.isEnabledFor(logging.CRITICAL):
+            self._log_with_indent(
+                logging.CRITICAL,
+                message,
+                indent,
+                sep,
+                n_sep,
+                c,
+                *args,
+                **kwargs,
+            )
+
+    def success(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log a success message with optional indent, separator, and color."""
+        if self.isEnabledFor(SUCCESS):
+            self._log_with_indent(
+                SUCCESS, message, indent, sep, n_sep, c, *args, **kwargs
+            )
+
+    def fail(
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+    ):
+        """Log a failure message with optional indent, separator, and color."""
+        if self.isEnabledFor(FAIL):
+            self._log_with_indent(
+                FAIL, message, indent, sep, n_sep, c, *args, **kwargs
+            )
+
+    def to(self, file_path, level=None, mode="w"):
+        """Context manager to temporarily log to a specific file.
+
+        Usage:
+            logger = logging.getLogger(__name__)
+            with logger.to("/path/to/file.log"):
+                logger.info("This goes to both console and file.log")
+
+        Args:
+            file_path: Path to log file
+            level: Logging level (default: DEBUG)
+            mode: File mode ('w' for overwrite, 'a' for append)
+
+        Returns:
+            Context manager
+        """
+        from ._context import log_to_file
+
+        return log_to_file(file_path, level=level or logging.DEBUG, mode=mode)
+
+
+def setup_logger_class():
+    """Setup the custom logger class."""
+    # Set custom logger class before any logger creation
+    logging.setLoggerClass(SciTeXLogger)
+
+    # Force existing root logger to use custom class
+    root = logging.getLogger()
+    root.__class__ = SciTeXLogger
+
+
+__all__ = ["SciTeXLogger", "setup_logger_class"]
+
+# EOF

scitex/logging/_print_capture.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""Print capture system for SciTeX logging."""
+
+import sys
+import logging
+from typing import Optional
+from io import StringIO
+
+
+class PrintCapture:
+    """Capture print() output and redirect to logging system."""
+    
+    def __init__(self, logger_name: str = "scitex.print_capture"):
+        self.logger = logging.getLogger(logger_name)
+        self.original_stdout = sys.stdout
+        self.original_stderr = sys.stderr
+        self.capturing = False
+        
+    def start_capture(self):
+        """Start capturing print output."""
+        if self.capturing:
+            return
+            
+        self.capturing = True
+        sys.stdout = self
+        
+    def stop_capture(self):
+        """Stop capturing print output."""
+        if not self.capturing:
+            return
+            
+        self.capturing = False
+        sys.stdout = self.original_stdout
+        
+    def write(self, text):
+        """Handle write calls from print()."""
+        # Also write to original stdout for real-time viewing
+        self.original_stdout.write(text)
+        self.original_stdout.flush()
+        
+        # Log the output (strip newlines for cleaner logs)
+        clean_text = text.rstrip('\n')
+        if clean_text:  # Only log non-empty text
+            self.logger.info(clean_text)
+            
+    def flush(self):
+        """Handle flush calls."""
+        self.original_stdout.flush()
+        
+    def isatty(self):
+        """Handle isatty calls."""
+        return self.original_stdout.isatty()
+        
+    def __enter__(self):
+        """Context manager entry."""
+        self.start_capture()
+        return self
+        
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Context manager exit."""
+        self.stop_capture()
+
+
+# Global print capture instance
+_print_capture = None
+
+
+def enable_print_capture(logger_name: str = "scitex.print_capture"):
+    """Enable automatic print capture globally."""
+    global _print_capture
+    if _print_capture is None:
+        _print_capture = PrintCapture(logger_name)
+    _print_capture.start_capture()
+
+
+def disable_print_capture():
+    """Disable automatic print capture globally."""
+    global _print_capture
+    if _print_capture is not None:
+        _print_capture.stop_capture()
+
+
+def is_print_capture_enabled():
+    """Check if print capture is currently enabled."""
+    global _print_capture
+    return _print_capture is not None and _print_capture.capturing
+
+
+__all__ = [
+    'PrintCapture',
+    'enable_print_capture', 
+    'disable_print_capture',
+    'is_print_capture_enabled'
+]

scitex/ml/__init__.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-07-19 10:50:54 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/ai/__init__.py
+# ----------------------------------------
+import os
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+"""Scitex AI module for machine learning and artificial intelligence utilities."""
+
+# Lazy imports to avoid loading heavy dependencies eagerly
+from .classification import ClassificationReporter
+from .training._LearningCurveLogger import LearningCurveLogger
+from .training._EarlyStopping import EarlyStopping
+from .loss import MultiTaskLoss
+from .classification import Classifier
+from .optim import get_optimizer, set_optimizer
+
+# Import submodules to make them accessible
+from . import activation
+from . import classification
+from . import clustering
+from . import feature_extraction
+# from . import layer
+from . import loss
+from . import metrics
+from . import optim
+from . import plt
+from . import sampling
+from . import sklearn
+from . import training
+from . import utils
+
+# Lazy import for GenAI (heavy anthropic dependency)
+def __getattr__(name):
+    if name == "GenAI":
+        from ._gen_ai import GenAI
+        return GenAI
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+__all__ = [
+    # "Classifiers",  # Moved to .old directory
+    "LearningCurveLogger",
+    "ClassificationReporter",
+    "EarlyStopping",
+    "MultiTaskLoss",
+    "GenAI",  # Lazy loaded
+    "Classifier",
+    "get_optimizer",
+    "set_optimizer",
+    # Submodules
+    "activation",
+    "classification",
+    "clustering",
+    "feature_extraction",
+    # "genai",
+    # "layer",
+    "loss",
+    "metrics",
+    "optim",
+    "plt",
+    "sampling",
+    "sklearn",
+    "training",
+    "utils",
+]
+
+# EOF

scitex/{ai/genai/anthropic.py → ml/_gen_ai/_Anthropic.py}

@@ -1,15 +1,12 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Timestamp: "2025-02-26 09:02:48 (ywatanabe)"
-# File: ./src/scitex/ai/_gen_ai/_Anthropic.py
-
-THIS_FILE = "/home/ywatanabe/proj/scitex_repo/src/scitex/ai/_gen_ai/_Anthropic.py"
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Time-stamp: "2025-02-26 09:02:48 (ywatanabe)"
-# File: ./scitex_repo/src/scitex/ai/_gen_ai/_Anthropic.py
-
-THIS_FILE = "/home/ywatanabe/proj/scitex_repo/src/scitex/ai/_gen_ai/_Anthropic.py"
+# Timestamp: "2025-06-24 19:20:24 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/ai/_gen_ai/_Anthropic.py
+# ----------------------------------------
+import os
+__FILE__ = __file__
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
 
 """
 Functionality:
@@ -27,20 +24,15 @@ Prerequisites:
 """
 
 """Imports"""
-import os
 import sys
-from typing import Any, Dict, Generator, List, Optional, Union
+from typing import Dict, Generator, List, Optional
 
 import anthropic
 import matplotlib.pyplot as plt
 
-from .base_genai import BaseGenAI
-import re
-
+from ._BaseGenAI import BaseGenAI
 
 """Functions & Classes"""
-
-
 class Anthropic(BaseGenAI):
     def __init__(
         self,
@@ -164,9 +156,11 @@ def main() -> None:
 if __name__ == "__main__":
     import scitex
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
+        sys, plt, verbose=False
+    )
     main()
-    scitex.gen.close(CONFIG, verbose=False, notify=False)
+    scitex.session.close(CONFIG, verbose=False, notify=False)
 
 
 """

scitex/{ai/genai/base_genai.py → ml/_gen_ai/_BaseGenAI.py}

@@ -18,9 +18,9 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 from ...io._load import load
-from .calc_cost import calc_cost
-from .format_output_func import format_output_func
-from .params import MODELS
+from ._calc_cost import calc_cost
+from ._format_output_func import format_output_func
+from ._PARAMS import MODELS
 
 
 class BaseGenAI(ABC):
@@ -324,9 +324,9 @@ def main() -> None:
 if __name__ == "__main__":
     import scitex
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
     main()
-    scitex.gen.close(CONFIG, verbose=False, notify=False)
+    scitex.session.close(CONFIG, verbose=False, notify=False)
 
 """
 python src/scitex/ai/_gen_ai/_BaseGenAI.py

scitex/{ai/genai/deepseek.py → ml/_gen_ai/_DeepSeek.py}

@@ -13,9 +13,6 @@
 4. Prerequisites:
    - DEEPSEEK_API_KEY environment variable
    - requests library
-
-DEPRECATED: This module is deprecated. Please use deepseek_provider.py instead.
-The new provider-based architecture offers better modularity and maintainability.
 """
 
 """Imports"""
@@ -23,19 +20,11 @@ import json
 import os
 import sys
 from typing import Dict, Generator, List, Optional
-import warnings
 
 import scitex
 import requests
 
-from .base_genai import BaseGenAI
-
-warnings.warn(
-    "deepseek.py is deprecated. Please use deepseek_provider.py instead. "
-    "See PROVIDER_MIGRATION_GUIDE.md for migration instructions.",
-    DeprecationWarning,
-    stacklevel=2,
-)
+from ._BaseGenAI import BaseGenAI
 
 """Warnings"""
 # scitex.pd.ignore_SettingWithCopyWarning()
@@ -48,8 +37,6 @@ warnings.warn(
 # CONFIG = load_configs()
 
 """Functions & Classes"""
-"""Imports"""
-from .base_genai import BaseGenAI
 from openai import OpenAI as _OpenAI
 
 """Functions & Classes"""
@@ -152,7 +139,7 @@ if __name__ == "__main__":
     import matplotlib.pyplot as plt
 
     # Configurations
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
         sys,
         plt,
         verbose=False,
@@ -172,12 +159,20 @@ if __name__ == "__main__":
     # -----------------------------------
     # Main
     # -----------------------------------
+    def main():
+        # Example usage
+        client = DeepSeek()
+        prompt = "Hello, how can I help you?"
+        response = client.complete(prompt)
+        print(response)
+        return 0
+    
     exit_status = main()
 
     # -----------------------------------
     # Cleanup scitex format
     # -----------------------------------
-    scitex.gen.close(
+    scitex.session.close(
         CONFIG,
         verbose=False,
         notify=False,

scitex/{ai/genai/google.py → ml/_gen_ai/_Google.py}

@@ -19,9 +19,6 @@ Output:
 Prerequisites:
     - Google API key (GOOGLE_API_KEY environment variable)
     - google.generativeai package
-
-DEPRECATED: This module is deprecated. Please use google_provider.py instead.
-The new provider-based architecture offers better modularity and maintainability.
 """
 
 """Imports"""
@@ -29,21 +26,16 @@ import os
 import sys
 from pprint import pprint
 from typing import Any, Dict, Generator, List, Optional
-import warnings
 
 import matplotlib.pyplot as plt
 import scitex
 
-from google import genai
-
-from .base_genai import BaseGenAI
+try:
+    from google import genai
+except ImportError:
+    genai = None
 
-warnings.warn(
-    "google.py is deprecated. Please use google_provider.py instead. "
-    "See PROVIDER_MIGRATION_GUIDE.md for migration instructions.",
-    DeprecationWarning,
-    stacklevel=2,
-)
+from ._BaseGenAI import BaseGenAI
 
 """Functions & Classes"""
 
@@ -155,9 +147,9 @@ def main() -> None:
 
 
 if __name__ == "__main__":
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
     main()
-    scitex.gen.close(CONFIG, verbose=False, notify=False)
+    scitex.session.close(CONFIG, verbose=False, notify=False)
 
 
 """

scitex/{ai/genai/groq.py → ml/_gen_ai/_Groq.py}

@@ -23,13 +23,12 @@ Prerequisites:
 """Imports"""
 import os
 import sys
-import warnings
 from typing import Any, Dict, Generator, List, Optional, Union
 
 from groq import Groq as _Groq
 import matplotlib.pyplot as plt
 
-from .base_genai import BaseGenAI
+from ._BaseGenAI import BaseGenAI
 
 """Functions & Classes"""
 
@@ -47,12 +46,6 @@ class Groq(BaseGenAI):
         chat_history: Optional[List[Dict[str, str]]] = None,
         max_tokens: int = 8000,
     ) -> None:
-        warnings.warn(
-            "Groq class is deprecated. Use GenAI(provider='groq') instead. "
-            "Example: from scitex.ai.genai import GenAI; ai = GenAI(provider='groq', model='llama3-8b-8192')",
-            DeprecationWarning,
-            stacklevel=2,
-        )
         max_tokens = min(max_tokens, 8000)
         if not api_key:
             raise ValueError("GROQ_API_KEY environment variable not set")