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

scitex/template/create_singularity.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# File: /home/ywatanabe/proj/scitex_repo/src/scitex/template/create_singularity.py
+
+"""
+Create a new singularity project from the singularity_template.
+"""
+
+import sys
+from typing import Optional
+
+from ._create_project import create_project
+
+TEMPLATE_REPO_URL = "https://github.com/ywatanabe1989/singularity_template.git"
+
+
+def create_singularity(project_name: str, target_dir: Optional[str] = None) -> bool:
+    """
+    Create a new singularity project from the template repository.
+
+    Parameters
+    ----------
+    project_name : str
+        Name of the new singularity project
+    target_dir : str, optional
+        Directory where the project will be created. If None, uses current directory.
+
+    Returns
+    -------
+    bool
+        True if successful, False otherwise
+
+    Example
+    -------
+    >>> from scitex.template import create_singularity
+    >>> create_singularity("my_singularity_project")
+    """
+    return create_project(
+        project_name,
+        target_dir,
+        TEMPLATE_REPO_URL,
+        "singularity_template",
+    )
+
+
+def main(args: list = None) -> None:
+    """
+    Command-line interface for create_singularity.
+
+    Parameters
+    ----------
+    args : list, optional
+        Command-line arguments. If None, uses sys.argv[1:]
+    """
+    if args is None:
+        args = sys.argv[1:]
+
+    if len(args) < 1:
+        print("Usage: python -m scitex create_singularity_project <project-name> [target-dir]")
+        print("")
+        print("Arguments:")
+        print("  project-name  Name of the new singularity project")
+        print("  target-dir    Optional: Directory where project will be created (default: current directory)")
+        print("")
+        print("Example:")
+        print("  python -m scitex create_singularity_project my_singularity_project")
+        print("  python -m scitex create_singularity_project my_project ~/projects")
+        sys.exit(1)
+
+    project_name = args[0]
+    target_dir = args[1] if len(args) > 1 else None
+
+    success = create_singularity(project_name, target_dir)
+    sys.exit(0 if success else 1)
+
+
+if __name__ == "__main__":
+    main()
+
+# EOF

scitex/units.py

@@ -0,0 +1,291 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Unit Handling for Scientific Computing
+======================================
+
+This module provides unit handling capabilities for SciTeX, ensuring
+scientific validity in computations with physical quantities.
+
+Features:
+- Unit conversion and validation
+- Dimensional analysis
+- Unit-aware arithmetic operations
+- Common scientific unit presets
+
+Author: SciTeX Development Team
+Date: 2025-07-04
+"""
+
+from typing import Union, Optional, Dict, Any, Tuple
+import numpy as np
+from dataclasses import dataclass
+import warnings
+
+
+@dataclass
+class Unit:
+    """Represents a physical unit with dimensions."""
+    
+    name: str
+    symbol: str
+    dimensions: Dict[str, float]  # e.g., {'length': 1, 'time': -1} for m/s
+    scale: float = 1.0  # Conversion factor to SI base unit
+    
+    def __mul__(self, other: 'Unit') -> 'Unit':
+        """Multiply units."""
+        new_dims = self.dimensions.copy()
+        for dim, power in other.dimensions.items():
+            new_dims[dim] = new_dims.get(dim, 0) + power
+        
+        # Clean up zero dimensions
+        new_dims = {k: v for k, v in new_dims.items() if v != 0}
+        
+        return Unit(
+            name=f"{self.name}*{other.name}",
+            symbol=f"{self.symbol}·{other.symbol}",
+            dimensions=new_dims,
+            scale=self.scale * other.scale
+        )
+    
+    def __truediv__(self, other: 'Unit') -> 'Unit':
+        """Divide units."""
+        new_dims = self.dimensions.copy()
+        for dim, power in other.dimensions.items():
+            new_dims[dim] = new_dims.get(dim, 0) - power
+        
+        # Clean up zero dimensions
+        new_dims = {k: v for k, v in new_dims.items() if v != 0}
+        
+        return Unit(
+            name=f"{self.name}/{other.name}",
+            symbol=f"{self.symbol}/{other.symbol}",
+            dimensions=new_dims,
+            scale=self.scale / other.scale
+        )
+    
+    def __pow__(self, exponent: float) -> 'Unit':
+        """Raise unit to a power."""
+        new_dims = {k: v * exponent for k, v in self.dimensions.items()}
+        
+        return Unit(
+            name=f"{self.name}^{exponent}",
+            symbol=f"{self.symbol}^{exponent}",
+            dimensions=new_dims,
+            scale=self.scale ** exponent
+        )
+    
+    def is_compatible(self, other: 'Unit') -> bool:
+        """Check if units have same dimensions."""
+        return self.dimensions == other.dimensions
+
+
+class Quantity:
+    """A numeric value with associated units."""
+    
+    def __init__(self, value: Union[float, np.ndarray], unit: Unit):
+        self.value = np.asarray(value)
+        self.unit = unit
+    
+    def to(self, target_unit: Unit) -> 'Quantity':
+        """Convert to different unit."""
+        if not self.unit.is_compatible(target_unit):
+            raise ValueError(
+                f"Cannot convert {self.unit.symbol} to {target_unit.symbol}: "
+                f"incompatible dimensions"
+            )
+        
+        # Convert value
+        conversion_factor = self.unit.scale / target_unit.scale
+        new_value = self.value * conversion_factor
+        
+        return Quantity(new_value, target_unit)
+    
+    def __add__(self, other: 'Quantity') -> 'Quantity':
+        """Add quantities (must have compatible units)."""
+        if not isinstance(other, Quantity):
+            raise TypeError("Can only add Quantity to Quantity")
+        
+        if not self.unit.is_compatible(other.unit):
+            raise ValueError(
+                f"Cannot add {self.unit.symbol} and {other.unit.symbol}: "
+                f"incompatible units"
+            )
+        
+        # Convert other to self's units
+        other_converted = other.to(self.unit)
+        return Quantity(self.value + other_converted.value, self.unit)
+    
+    def __mul__(self, other: Union[float, 'Quantity']) -> 'Quantity':
+        """Multiply quantities or by scalar."""
+        if isinstance(other, Quantity):
+            return Quantity(
+                self.value * other.value,
+                self.unit * other.unit
+            )
+        else:
+            return Quantity(self.value * other, self.unit)
+    
+    def __truediv__(self, other: Union[float, 'Quantity']) -> 'Quantity':
+        """Divide quantities or by scalar."""
+        if isinstance(other, Quantity):
+            return Quantity(
+                self.value / other.value,
+                self.unit / other.unit
+            )
+        else:
+            return Quantity(self.value / other, self.unit)
+    
+    def __repr__(self) -> str:
+        return f"{self.value} {self.unit.symbol}"
+
+
+# Common unit definitions
+class Units:
+    """Common scientific units."""
+    
+    # Base SI units
+    meter = Unit("meter", "m", {"length": 1})
+    kilogram = Unit("kilogram", "kg", {"mass": 1})
+    second = Unit("second", "s", {"time": 1})
+    ampere = Unit("ampere", "A", {"current": 1})
+    kelvin = Unit("kelvin", "K", {"temperature": 1})
+    mole = Unit("mole", "mol", {"amount": 1})
+    
+    # Derived units
+    newton = Unit("newton", "N", {"mass": 1, "length": 1, "time": -2})
+    joule = Unit("joule", "J", {"mass": 1, "length": 2, "time": -2})
+    watt = Unit("watt", "W", {"mass": 1, "length": 2, "time": -3})
+    pascal = Unit("pascal", "Pa", {"mass": 1, "length": -1, "time": -2})
+    
+    # Length units
+    millimeter = Unit("millimeter", "mm", {"length": 1}, scale=0.001)
+    centimeter = Unit("centimeter", "cm", {"length": 1}, scale=0.01)
+    kilometer = Unit("kilometer", "km", {"length": 1}, scale=1000)
+    inch = Unit("inch", "in", {"length": 1}, scale=0.0254)
+    foot = Unit("foot", "ft", {"length": 1}, scale=0.3048)
+    mile = Unit("mile", "mi", {"length": 1}, scale=1609.344)
+    
+    # Time units
+    millisecond = Unit("millisecond", "ms", {"time": 1}, scale=0.001)
+    microsecond = Unit("microsecond", "μs", {"time": 1}, scale=1e-6)
+    minute = Unit("minute", "min", {"time": 1}, scale=60)
+    hour = Unit("hour", "h", {"time": 1}, scale=3600)
+    day = Unit("day", "d", {"time": 1}, scale=86400)
+    
+    # Mass units
+    gram = Unit("gram", "g", {"mass": 1}, scale=0.001)
+    milligram = Unit("milligram", "mg", {"mass": 1}, scale=1e-6)
+    pound = Unit("pound", "lb", {"mass": 1}, scale=0.453592)
+    
+    # Temperature (special handling needed for non-linear conversions)
+    celsius = Unit("celsius", "°C", {"temperature": 1})
+    fahrenheit = Unit("fahrenheit", "°F", {"temperature": 1})
+    
+    # Dimensionless
+    dimensionless = Unit("dimensionless", "", {})
+    percent = Unit("percent", "%", {}, scale=0.01)
+    
+    # Frequency
+    hertz = Unit("hertz", "Hz", {"time": -1})
+    kilohertz = Unit("kilohertz", "kHz", {"time": -1}, scale=1000)
+    megahertz = Unit("megahertz", "MHz", {"time": -1}, scale=1e6)
+    
+    # Electrical units
+    volt = Unit("volt", "V", {"mass": 1, "length": 2, "time": -3, "current": -1})
+    millivolt = Unit("millivolt", "mV", {"mass": 1, "length": 2, "time": -3, "current": -1}, scale=0.001)
+    microvolt = Unit("microvolt", "μV", {"mass": 1, "length": 2, "time": -3, "current": -1}, scale=1e-6)
+    kilovolt = Unit("kilovolt", "kV", {"mass": 1, "length": 2, "time": -3, "current": -1}, scale=1000)
+    
+    ohm = Unit("ohm", "Ω", {"mass": 1, "length": 2, "time": -3, "current": -2})
+    kiloohm = Unit("kiloohm", "kΩ", {"mass": 1, "length": 2, "time": -3, "current": -2}, scale=1000)
+    
+    farad = Unit("farad", "F", {"mass": -1, "length": -2, "time": 4, "current": 2})
+    microfarad = Unit("microfarad", "μF", {"mass": -1, "length": -2, "time": 4, "current": 2}, scale=1e-6)
+    nanofarad = Unit("nanofarad", "nF", {"mass": -1, "length": -2, "time": 4, "current": 2}, scale=1e-9)
+    picofarad = Unit("picofarad", "pF", {"mass": -1, "length": -2, "time": 4, "current": 2}, scale=1e-12)
+    
+    # Common abbreviations
+    s = second
+    ms = millisecond
+    Hz = hertz
+    V = volt
+    mV = millivolt
+    mA = Unit("milliampere", "mA", {"current": 1}, scale=0.001)
+
+
+def validate_units(func):
+    """Decorator to validate unit compatibility in operations."""
+    def wrapper(*args, **kwargs):
+        # Extract quantities from args
+        quantities = [arg for arg in args if isinstance(arg, Quantity)]
+        
+        # Check if all quantities have compatible units
+        if len(quantities) > 1:
+            base_unit = quantities[0].unit
+            for q in quantities[1:]:
+                if not base_unit.is_compatible(q.unit):
+                    warnings.warn(
+                        f"Unit mismatch: {base_unit.symbol} vs {q.unit.symbol}",
+                        UserWarning
+                    )
+        
+        return func(*args, **kwargs)
+    
+    return wrapper
+
+
+# Convenience functions
+def Q(value: Union[float, np.ndarray], unit: Unit) -> Quantity:
+    """Create a quantity (shorthand)."""
+    return Quantity(value, unit)
+
+
+def ensure_units(value: Union[float, np.ndarray, Quantity], 
+                default_unit: Unit) -> Quantity:
+    """Ensure value has units, applying default if needed."""
+    if isinstance(value, Quantity):
+        return value
+    else:
+        return Quantity(value, default_unit)
+
+
+def strip_units(quantity: Union[Quantity, float, np.ndarray]) -> np.ndarray:
+    """Extract numeric value, removing units if present."""
+    if isinstance(quantity, Quantity):
+        return quantity.value
+    else:
+        return np.asarray(quantity)
+
+
+# Example usage functions
+def convert_temperature(value: float, from_unit: str, to_unit: str) -> float:
+    """Convert temperature between units (handles non-linear conversions)."""
+    conversions = {
+        ('C', 'F'): lambda c: c * 9/5 + 32,
+        ('F', 'C'): lambda f: (f - 32) * 5/9,
+        ('C', 'K'): lambda c: c + 273.15,
+        ('K', 'C'): lambda k: k - 273.15,
+        ('F', 'K'): lambda f: (f - 32) * 5/9 + 273.15,
+        ('K', 'F'): lambda k: (k - 273.15) * 9/5 + 32
+    }
+    
+    from_unit = from_unit.upper()[0]
+    to_unit = to_unit.upper()[0]
+    
+    if from_unit == to_unit:
+        return value
+    
+    key = (from_unit, to_unit)
+    if key in conversions:
+        return conversions[key](value)
+    else:
+        raise ValueError(f"Unknown temperature conversion: {from_unit} to {to_unit}")
+
+
+# Export main components
+__all__ = [
+    'Unit', 'Quantity', 'Units', 'Q',
+    'validate_units', 'ensure_units', 'strip_units',
+    'convert_temperature'
+]

scitex/utils/_compress_hdf5.py

@@ -8,9 +8,9 @@ import os
 __FILE__ = "/ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/utils/_compress_hdf5.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
-import h5py
 import numpy as np
-from tqdm import tqdm
+
+# h5py and tqdm imported in functions that need them
 
 
 def compress_hdf5(input_file, output_file=None, compression_level=4):
@@ -26,6 +26,17 @@ def compress_hdf5(input_file, output_file=None, compression_level=4):
     compression_level : int, optional
         Compression level (1-9), higher means more compression but slower processing
     """
+    # Import h5py when actually needed
+    try:
+        import h5py
+    except ImportError:
+        raise ImportError("h5py is required for HDF5 compression but not installed")
+    
+    # Import tqdm if available
+    try:
+        from tqdm import tqdm
+    except ImportError:
+        tqdm = None
     if output_file is None:
         base, ext = os.path.splitext(input_file)
         output_file = f"{base}.compressed{ext}"
@@ -111,6 +122,6 @@ if __name__ == "__main__":
     )
 
     args = parser.parse_args()
-    compress_existing_h5(args.input_file, args.output_file, args.compression)
+    compress_hdf5(args.input_file, args.output_file, args.compression)
 
 # EOF

scitex/utils/_email.py

@@ -11,7 +11,7 @@ from email.mime.multipart import MIMEMultipart as _MIMEMultipart
 from email.mime.text import MIMEText as _MIMEText
 import mimetypes
 
-from ..reproduce._gen_ID import gen_ID
+from ..repro._gen_ID import gen_ID
 
 import re
 
@@ -29,7 +29,14 @@ def send_gmail(
     ID=None,
     attachment_paths=None,
     verbose=True,
+    smtp_server=None,
+    smtp_port=None,
 ):
+    """
+    Send email via SMTP. Despite the name, supports any SMTP server.
+    Uses mail1030.onamae.ne.jp by default (for scitex.ai emails).
+    Falls back to Gmail if sender email is @gmail.com.
+    """
     if ID == "auto":
         ID = gen_ID()
 
@@ -39,8 +46,20 @@ def send_gmail(
         else:
             subject = f"ID: {ID}"
 
+    # Auto-detect SMTP server based on sender email or use provided server
+    if smtp_server is None:
+        if '@gmail.com' in sender_gmail:
+            smtp_server = 'smtp.gmail.com'
+            smtp_port = smtp_port or 587
+        else:
+            # Use scitex.ai mail server for scitex.ai emails
+            smtp_server = os.getenv('SCITEX_SCHOLAR_FROM_EMAIL_SMTP_SERVER', 'mail1030.onamae.ne.jp')
+            smtp_port = smtp_port or int(os.getenv('SCITEX_SCHOLAR_FROM_EMAIL_SMTP_PORT', '587'))
+
+    smtp_port = smtp_port or 587
+
     try:
-        server = smtplib.SMTP("smtp.gmail.com", 587)
+        server = smtplib.SMTP(smtp_server, smtp_port)
         server.starttls()
         server.login(sender_gmail, sender_password)
 

scitex/utils/_grid.py

@@ -1,7 +1,7 @@
 #!./env/bin/python3
 # -*- coding: utf-8 -*-
 # Time-stamp: "2024-04-22 23:54:02"
-# Author: Yusuke Watanabe (ywata1989@gmail.com)
+# Author: Yusuke Watanabe (ywatanabe@scitex.ai)
 
 """
 This script defines scitex.ml.utils.grid_search
@@ -12,9 +12,10 @@ import itertools as _itertools
 import random as _random
 import sys as _sys
 
-import matplotlib.pyplot as _plt
 import scitex as _scitex
 
+# matplotlib imported in functions that need it
+
 
 # Functions
 def yield_grids(params_grid: dict, random=False):
@@ -108,9 +109,10 @@ def count_grids(params_grid):
 
 if __name__ == "__main__":
     import pandas as pd
+    import matplotlib.pyplot as _plt
 
     # Start
-    CONFIG, _sys.stdout, _sys.stderr, _plt, CC = _scitex.gen.start(
+    CONFIG, _sys.stdout, _sys.stderr, _plt, CC = _scitex.session.start(
         _sys, _plt, verbose=False
     )
 
@@ -139,7 +141,7 @@ if __name__ == "__main__":
         print(param_dict)
 
     # Close
-    _scitex.gen.close(CONFIG, verbose=False, notify=False)
+    _scitex.session.close(CONFIG, verbose=False, notify=False)
 
 # EOF
 

scitex/utils/_notify.py

@@ -4,9 +4,7 @@
 # File: /ssh:ywatanabe@sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/utils/_notify.py
 # ----------------------------------------
 import os
-__FILE__ = (
-    "./src/scitex/utils/_notify.py"
-)
+__FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 # Time-stamp: "2024-11-24 17:54:38 (ywatanabe)"
@@ -89,9 +87,10 @@ def notify(
         warnings.warn(str(e))
 
     FAKE_PYTHON_SCRIPT_NAME = "$ python -c ..."
-    sender_gmail = os.getenv("SCITEX_SENDER_GMAIL")
-    sender_password = os.getenv("SCITEX_SENDER_GMAIL_PASSWORD")
-    recipient_email = recipient_email or os.getenv("SCITEX_RECIPIENT_GMAIL")
+    # Use scitex.ai email addresses (not Gmail)
+    sender_gmail = os.getenv("SCITEX_SCHOLAR_FROM_EMAIL_ADDRESS", os.getenv("SCITEX_EMAIL_AGENT", "agent@scitex.ai"))
+    sender_password = os.getenv("SCITEX_SCHOLAR_FROM_EMAIL_PASSWORD", os.getenv("SCITEX_EMAIL_PASSWORD", ""))
+    recipient_email = recipient_email or os.getenv("SCITEX_SCHOLAR_TO_EMAIL_ADDRESS", "ywata1989@gmail.com")
 
     if file is not None:
         script_name = str(file)
@@ -123,9 +122,13 @@ def notify(
         print(
             f"""
         Please set environmental variables to use this function (f"{inspect.stack()[0][3]}"):\n\n
-        $ export SciTeX_SENDER_GMAIL="scitex.notification@gmail.com"
-        $ export SciTeX_SENDER_GMAIL_PASSWORD="YOUR_APP_PASSWORD"
-        $ export SciTeX_RECIPIENT_GMAIL="YOUR_GMAIL_ADDRESS"
+        $ export SCITEX_SCHOLAR_FROM_EMAIL_ADDRESS="agent@scitex.ai"
+        $ export SCITEX_SCHOLAR_FROM_EMAIL_PASSWORD="YOUR_EMAIL_PASSWORD"
+        $ export SCITEX_SCHOLAR_TO_EMAIL_ADDRESS="YOUR_EMAIL_ADDRESS"
+
+        Or alternatively:
+        $ export SCITEX_EMAIL_AGENT="agent@scitex.ai"
+        $ export SCITEX_EMAIL_PASSWORD="YOUR_EMAIL_PASSWORD"
         """
         )
 
@@ -152,7 +155,7 @@ if __name__ == "__main__":
 # # Example in shell
 # #!/bin/bash
 # # /home/ywatanabe/.dotfiles/.bin/notify
-# # Author: ywatanabe (ywatanabe@alumni.u-tokyo.ac.jp)
+# # Author: ywatanabe (ywatanabe@scitex.ai)
 # # Date: $(date +"%Y-%m-%d-%H-%M")
 
 # # LOG_FILE="${0%.sh}.log"