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

scitex/__init__.py

@@ -1,38 +1,52 @@
 #!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-07-14 15:28:49 (ywatanabe)"
+# File: /ssh:ywatanabe@sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/__init__.py
+# ----------------------------------------
+import os
+
+__FILE__ = "./src/scitex/__init__.py"
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+
 """
 Minimal scitex initialization.
 Modules are imported on-demand to avoid circular dependencies.
 """
 
-import os
 import warnings
-
-# Configure warnings
+# Always show our own deprecation warnings first
+warnings.filterwarnings(
+    "always", category=DeprecationWarning, module="scitex.*"
+)
+# Then ignore others
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 # Version
-try:
-    from .__version__ import __version__
-except ImportError:
-    __version__ = "unknown"
+from .__version__ import __version__
 
 # Lazy loading for all modules
 class _LazyModule:
     def __init__(self, name):
         self._name = name
         self._module = None
-    
+
     def __getattr__(self, attr):
         if self._module is None:
             import importlib
-            self._module = importlib.import_module(f".{self._name}", package="scitex")
+
+            self._module = importlib.import_module(
+                f".{self._name}", package="scitex"
+            )
         return getattr(self._module, attr)
 
+
 # Create lazy modules
 io = _LazyModule("io")
 gen = _LazyModule("gen")
 plt = _LazyModule("plt")
 ai = _LazyModule("ai")
+ml = _LazyModule("ai")  # Alias for machine learning - same as ai
 pd = _LazyModule("pd")
 str = _LazyModule("str")
 stats = _LazyModule("stats")
@@ -44,7 +58,9 @@ nn = _LazyModule("nn")
 torch = _LazyModule("torch")
 web = _LazyModule("web")
 db = _LazyModule("db")
+repro = _LazyModule("repro")
 reproduce = _LazyModule("reproduce")
+rng = _LazyModule("rng")
 scholar = _LazyModule("scholar")
 resource = _LazyModule("resource")
 tex = _LazyModule("tex")
@@ -57,6 +73,12 @@ etc = _LazyModule("etc")
 context = _LazyModule("context")
 dev = _LazyModule("dev")
 gists = _LazyModule("gists")
+errors = _LazyModule("errors")
+units = _LazyModule("units")
+logging = _LazyModule("logging")
+# log = _LazyModule("log")
+session = _LazyModule("session")
+capture = _LazyModule("capture")
 
 # Import sh function directly as it's commonly used
 try:
@@ -64,10 +86,26 @@ try:
 except ImportError:
     sh = None
 
-# Common function that's often needed
-def start(*args, **kwargs):
-    """Convenience function to access gen.start"""
-    return gen.start(*args, **kwargs)
+__all__ = [
+    "io",
+    "gen",
+    "plt",
+    "ai",
+    "ml",
+    "pd",
+    "str",
+    "stats",
+    "path",
+    "dict",
+    "decorators",
+    "__version__",
+    "sh",
+    "errors",
+    "units",
+    "logging",
+    "session",
+    "rng",
+    "capture",
+]
 
-__all__ = ["io", "gen", "plt", "ai", "pd", "str", "stats", "path", 
-           "dict", "decorators", "start", "__version__", "sh"]
+# EOF

scitex/__main__.py

@@ -1,5 +1,32 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+"""
+SciTeX Package Entry Point
+
+Allows running: python -m scitex [command]
+"""
+
+import sys
+
+
+def main():
+    """Main entry point for scitex CLI"""
+    try:
+        from scitex.cli.main import cli
+        cli()
+    except ImportError:
+        # CLI not available (click not installed)
+        print("SciTeX CLI requires 'click' package")
+        print("Install: pip install click")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()
+
+# Original content preserved below:
+# #!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 # Time-stamp: "2024-10-13 18:56:15 (ywatanabe)"
 # /home/yusukew/proj/scitex_repo/src/scitex/__main__.py
 
@@ -20,44 +47,31 @@ import warnings
 warnings.filterwarnings("ignore")
 
 import sys
-from typing import List
-from .gen._print_config import print_config_main
-
-
-def main(args: List[str] = None) -> None:
-    """
-    Main function to handle command-line arguments and execute appropriate submodules.
-
-    Parameters
-    ----------
-    args : List[str], optional
-        Command-line arguments. If None, sys.argv[1:] will be used.
-
-    Returns
-    -------
-    None
-
-    Example
-    -------
-    >>> import scitex.__main__ as main_module
-    >>> main_module.main(['print_config', 'SOME_KEY'])
-    """
-
-
 from .gen._print_config import print_config_main
+from .template.create_research import main as create_research_main
+from .template.create_pip_project import main as create_pip_project_main
+from .template.create_singularity import main as create_singularity_main
 
 
 def main():
     """Main entry point for SciTeX command-line interface.
 
-    Provides command-line access to various SciTeX utilities. Currently
-    supports configuration printing functionality.
+    Provides command-line access to various SciTeX utilities.
 
     Commands
     --------
     print_config : Print configuration values
         Usage: python -m scitex print_config [key]
 
+    create_research_project : Create a new research project from template
+        Usage: python -m scitex create_research_project <project-name> [target-dir]
+
+    create_pip_project : Create a new pip project from template
+        Usage: python -m scitex create_pip_project <project-name> [target-dir]
+
+    create_singularity_project : Create a new singularity project from template
+        Usage: python -m scitex create_singularity_project <project-name> [target-dir]
+
     Examples
     --------
     >>> # Print all configuration
@@ -66,6 +80,18 @@ def main():
     >>> # Print specific configuration key
     >>> python -m scitex print_config DATABASE_URL
 
+    >>> # Create a new research project
+    >>> python -m scitex create_research_project my_research_project
+
+    >>> # Create a new pip project
+    >>> python -m scitex create_pip_project my_pip_project
+
+    >>> # Create a new singularity project
+    >>> python -m scitex create_singularity_project my_singularity_project
+
+    >>> # Create in a specific directory
+    >>> python -m scitex create_research_project my_project ~/projects
+
     Raises
     ------
     SystemExit
@@ -73,6 +99,14 @@ def main():
     """
     if len(sys.argv) < 2:
         print("Usage: python -m scitex <command> [args]")
+        print("")
+        print("Available commands:")
+        print("  print_config          Print configuration values")
+        print("  create_research_project       Create a new research project")
+        print("  create_pip_project    Create a new pip project")
+        print("  create_singularity_project    Create a new singularity project")
+        print("")
+        print("Use 'python -m scitex <command> --help' for more information on a command.")
         sys.exit(1)
 
     command = sys.argv[1]
@@ -80,8 +114,20 @@ def main():
 
     if command == "print_config":
         print_config_main(args)
+    elif command == "create_research_project":
+        create_research_main(args)
+    elif command == "create_pip_project":
+        create_pip_project_main(args)
+    elif command == "create_singularity_project":
+        create_singularity_main(args)
     else:
         print(f"Unknown command: {command}")
+        print("")
+        print("Available commands:")
+        print("  print_config          Print configuration values")
+        print("  create_research_project       Create a new research project")
+        print("  create_pip_project    Create a new pip project")
+        print("  create_singularity_project    Create a new singularity project")
         sys.exit(1)
 
 

scitex/__version__.py

@@ -9,6 +9,6 @@ __FILE__ = "./src/scitex/__version__.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
-__version__ = "2.0.0"
+__version__ = "2.1.0"
 
 # EOF

scitex/_sh.py

@@ -1,47 +1,147 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Timestamp: "2025-06-13 22:51:08 (ywatanabe)"
-# File: /ssh:sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/_sh.py
+# Timestamp: "2025-09-14 11:29:19 (ywatanabe)"
+# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/_sh.py
 # ----------------------------------------
+from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/_sh.py"
-)
+__FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
-# Time-stamp: "2024-11-03 02:23:16 (ywatanabe)"
 
 import subprocess
+from typing import Union, List, Dict, Literal
 
 import scitex
 
 
-def sh(command_str, verbose=True):
+def sh(
+    command_str_or_list: Union[str, List[str]], 
+    verbose: bool = True, 
+    return_as: Literal["dict", "str"] = "dict"
+) -> Union[str, Dict[str, Union[str, int, bool]]]:
     """
     Executes a shell command from Python.
 
     Parameters:
-    - command_str (str): The command string to execute.
+    - command_str_or_list (str or list): Command to execute. 
+        - str: Shell command string (uses shell=True)
+        - list: Command and arguments (safer, uses shell=False)
+    - verbose (bool): Whether to print command and output.
+    - return_as ("dict" or "str"): Return format.
+        - "dict": Returns dict with stdout, stderr, exit_code
+        - "str": Returns string output for backward compatibility
 
     Returns:
-    - output (str): The standard output from the executed command.
+    - If return_as="str": output (str) - stdout if success, stderr if failure
+    - If return_as="dict": dict with keys:
+        - 'stdout' (str): Standard output
+        - 'stderr' (str): Standard error
+        - 'exit_code' (int): Exit code (0 for success)
+        - 'success' (bool): True if exit_code == 0
+        
+    Examples:
+    --------
+    >>> # String command (uses shell)
+    >>> sh("ls -la | grep .py")
+    
+    >>> # List command (safer, no shell)
+    >>> sh(["ls", "-la", "/home"])
+    
+    >>> # Command with environment variable expansion
+    >>> sh(["echo", "$HOME"])  # Won't expand $HOME
+    >>> sh("echo $HOME")  # Will expand $HOME
     """
+    # Display command
     if verbose:
-        print(scitex.str.color_text(f"{command_str}", "yellow"))
+        if isinstance(command_str_or_list, list):
+            cmd_display = " ".join(command_str_or_list)
+        else:
+            cmd_display = command_str_or_list
+        print(scitex.str.color_text(f"{cmd_display}", "yellow"))
 
-    process = subprocess.Popen(
-        command_str, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
-    )
-    output, error = process.communicate()
-    if process.returncode == 0:
-        out = output.decode("utf-8").strip()
+    # Execute based on command type
+    if isinstance(command_str_or_list, list):
+        # List mode: safer, no shell injection
+        process = subprocess.Popen(
+            command_str_or_list, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
     else:
-        out = error.decode("utf-8").strip()
+        # String mode: uses shell, supports pipes and redirects
+        process = subprocess.Popen(
+            command_str_or_list, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
+    
+    stdout_bytes, stderr_bytes = process.communicate()
 
-    if verbose:
-        print(out)
+    # Decode outputs
+    stdout = stdout_bytes.decode("utf-8").strip()
+    stderr = stderr_bytes.decode("utf-8").strip()
+    exit_code = process.returncode
+
+    if return_as == "dict":
+        result = {
+            "stdout": stdout,
+            "stderr": stderr,
+            "exit_code": exit_code,
+            "success": exit_code == 0,
+        }
+
+        if verbose:
+            if stdout:
+                print(stdout)
+            if stderr:
+                print(scitex.str.color_text(stderr, "red"))
+
+        return result
+    else:
+        # Backward compatibility mode
+        if exit_code == 0:
+            out = stdout
+        else:
+            out = stderr
+
+        if verbose:
+            print(out)
 
-    return out
+        return out
+
+
+def sh_run(command, verbose=True):
+    """
+    Executes a shell command and returns detailed results.
+    
+    This is a convenience function that always returns a dictionary
+    with complete execution information.
+    
+    Parameters:
+    - command (str or list): Command to execute.
+        - str: Shell command string (uses shell=True)
+        - list: Command and arguments (safer, uses shell=False)
+    - verbose (bool): Whether to print command and output.
+    
+    Returns:
+    - dict with keys:
+        - 'stdout' (str): Standard output
+        - 'stderr' (str): Standard error  
+        - 'exit_code' (int): Exit code (0 for success)
+        - 'success' (bool): True if exit_code == 0
+    
+    Examples:
+    --------
+    >>> # String command with pipe
+    >>> result = sh_run("ls -la | grep .py")
+    >>> if result['success']:
+    ...     print(result['stdout'])
+    
+    >>> # List command (safer)
+    >>> result = sh_run(["ls", "-la", "/home"])
+    >>> print(f"Exit code: {result['exit_code']}")
+    
+    >>> # Command with spaces in arguments
+    >>> result = sh_run(["mkdir", "-p", "/tmp/my folder"])  # Handles spaces correctly
+    """
+    return sh(command, verbose=verbose, return_dict=True)
 
 
 if __name__ == "__main__":
@@ -50,10 +150,32 @@ if __name__ == "__main__":
     import matplotlib.pyplot as plt
     import scitex
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
         sys, plt, verbose=False
     )
-    sh("ls")
-    scitex.gen.close(CONFIG, verbose=False, notify=False)
+    
+    # Test backward compatibility
+    print("Test 1: Backward compatibility mode")
+    output = sh("echo 'Hello World'", verbose=True)
+    print(f"Output: {output}\n")
+    
+    # Test new dict mode
+    print("Test 2: Dictionary return mode")
+    result = sh("echo 'Hello' && echo 'Error message' >&2", verbose=True, return_dict=True)
+    print(f"Result dict: {result}\n")
+    
+    # Test sh_run convenience function
+    print("Test 3: sh_run convenience function")
+    result = sh_run("ls -la | head -5")
+    print(f"Success: {result['success']}, Exit code: {result['exit_code']}\n")
+    
+    # Test error handling
+    print("Test 4: Error handling")
+    result = sh_run("cat /nonexistent/file", verbose=False)
+    print(f"Success: {result['success']}")
+    print(f"Exit code: {result['exit_code']}")
+    print(f"Stderr: {result['stderr']}\n")
+    
+    scitex.session.close(CONFIG, verbose=False, notify=False)
 
 # EOF

scitex/ai/__init__.py

@@ -1,22 +1,28 @@
 #!/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."""
 
-from ._LearningCurveLogger import LearningCurveLogger
-from .__Classifiers import Classifiers
-from .classification_reporter import ClassificationReporter, MultiClassificationReporter
-from .early_stopping import EarlyStopping
+# 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 .genai import GenAI
-from .classification import ClassifierServer
+from .classification import Classifier
 from .optim import get_optimizer, set_optimizer
 
 # Import submodules to make them accessible
-from . import act
+from . import activation
 from . import classification
 from . import clustering
 from . import feature_extraction
-from . import genai
-from . import layer
+# from . import layer
 from . import loss
 from . import metrics
 from . import optim
@@ -26,24 +32,30 @@ 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",
+    # "Classifiers",  # Moved to .old directory
     "LearningCurveLogger",
     "ClassificationReporter",
-    "MultiClassificationReporter",
     "EarlyStopping",
     "MultiTaskLoss",
-    "GenAI",
-    "ClassifierServer",
+    "GenAI",  # Lazy loaded
+    "Classifier",
     "get_optimizer",
     "set_optimizer",
     # Submodules
-    "act",
+    "activation",
     "classification",
     "clustering",
     "feature_extraction",
-    "genai",
-    "layer",
+    # "genai",
+    # "layer",
     "loss",
     "metrics",
     "optim",
@@ -53,3 +65,5 @@ __all__ = [
     "training",
     "utils",
 ]
+
+# EOF

scitex/ai/_gen_ai/_Anthropic.py

@@ -1,12 +1,10 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-# Timestamp: "2025-06-13 23:00:56 (ywatanabe)"
-# File: /ssh:sp:/home/ywatanabe/proj/SciTeX-Code/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__ = (
-    "./src/scitex/ai/_gen_ai/_Anthropic.py"
-)
+__FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -158,11 +156,11 @@ def main() -> None:
 if __name__ == "__main__":
     import scitex
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.gen.start(
+    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/_gen_ai/_BaseGenAI.py

@@ -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/_gen_ai/_DeepSeek.py

@@ -139,7 +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,
@@ -159,12 +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/_gen_ai/_Google.py

@@ -147,9 +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/_gen_ai/_Llama.py

@@ -135,8 +135,8 @@ def main():
 
 if __name__ == "__main__":
     # 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)
 
 # EOF

scitex/ai/_gen_ai/_OpenAI.py

@@ -218,9 +218,9 @@ if __name__ == "__main__":
     import matplotlib.pyplot as plt
     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)
 
 # EOF
 """