Merge branch '39-v20-examples' of github.com:lanl/PLEIADES into 39-v2…

…0-examples

docs/repo.map

@@ -29,7 +29,7 @@ PLEIADES
 |           ├── __init__.py
 |           ├── factory.py
 |           ├── parfile.py
-|           ├── backends/  
+|           ├── backends/
 |           │   ├── nova_ornl.py
 |           │   ├── __init__.py
 |           │   ├── local.py
@@ -65,7 +65,7 @@ PLEIADES
 │   │   └── conftest.py
 │   └── data/
 │       ├── config
-│       └── ex012 
+│       └── ex012
 └── notebook/
     ├── sammy.param/
     │   └── example.ipynb
@@ -74,4 +74,4 @@ PLEIADES
         │   ├── ex012.ipynb
         │   └── ex012a.par
         └── ex027/
-            └── ex027a.endf
+            └── ex027a.endf

notebook/samexm/ex012/ex012a.ipynb

@@ -13,9 +13,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pathlib  # Importing pathlib to work with file system paths\n",
-    "import tempfile # Importing tempfile to create temporary files and directories\n",
-    "\n",
     "# Importing specific classes from the pleiades.sammy module\n",
     "from pleiades.sammy.parfile import SammyParameterFile"
    ]

notebook/samexm/ex012/ex012a.par

@@ -160,16 +160,16 @@
 10934820.00 1.2000E+03 2.7611E+05                       0 0 0    23
 15050371.00 1.2000E+03 6.3499E+05                       0 0 0    23
 25004488.00 1.2000E+03 6.9186E+03                       0 0 0    23
- 
+
 0.1
- 
+
 RADIUS PARAMETERS FOLLOW
    4.13642   4.13642 0-1 1 4 5
    4.94372   4.94372 0-1 2 3 6 7
    4.40000   4.40000 0-1 8 91011121314151617
    4.20000   4.20000 0-11819202122
    4.20000   4.20000 0-123242526272829
- 
+
 ISOTOPIC MASSES AND ABUNDANCES FOLLOW
  27.976929 1.0000000  .9200    1 1 2 3 4 5 6 7
  28.976496  .0467000  .0500    1 8 91011121314151617

src/pleiades/sammy/notes/parfile_notes.md

@@ -57,7 +57,7 @@
             - Parameters:
                 - header: str
             - Returns: Type[BaseModel]
-        - from_string 
+        - from_string
             @classmethod
             - Parameters:
                 - data: str
@@ -72,7 +72,7 @@
             - Parameters:
                 - card_name: str
             - Returns: Type[BaseModel]
-        - from_file 
+        - from_file
             @classmethod
             - Parameters:
                 - file_path: Union[str, pathlib.Path]
@@ -85,4 +85,4 @@
                 - None
 
 ## Main Function
-- Example usage
+- Example usage

src/pleiades/sammy/parameters/isotope.py

@@ -45,6 +45,7 @@
 - Masses must be > 0
 - Spin groups must be valid for the model
 """
+
 import os
 from typing import List, Optional
 
@@ -54,25 +55,25 @@
 from pleiades.utils.logger import Logger, _log_and_raise_error
 
 # Initialize logger with file logging
-log_file_path = os.path.join(os.getcwd(), 'pleiades-par.log')
+log_file_path = os.path.join(os.getcwd(), "pleiades-par.log")
 logger = Logger(__name__, log_file=log_file_path)
 
 # Format definitions for standard format (<99 spin groups)
 # Each numeric field has specific width requirements
 FORMAT_STANDARD = {
-    "mass": slice(0, 10),           # AMUISO: Atomic mass (amu)
-    "abundance": slice(10, 20),     # PARISO: Fractional abundance
-    "uncertainty": slice(20, 30),   # DELISO: Uncertainty on abundance
-    "flag": slice(30, 32),          # IFLISO: Treatment flag
+    "mass": slice(0, 10),  # AMUISO: Atomic mass (amu)
+    "abundance": slice(10, 20),  # PARISO: Fractional abundance
+    "uncertainty": slice(20, 30),  # DELISO: Uncertainty on abundance
+    "flag": slice(30, 32),  # IFLISO: Treatment flag
 }
 
 # Spin group number positions
 # Standard format: 2 columns per group starting at col 33
 SPIN_GROUP_STANDARD = {
-    "width": 2,                     # Character width of each group number
-    "start": 32,                    # Start of first group
-    "per_line": 24,                 # Max groups per line
-    "cont_marker": slice(78, 80),   # "-1" indicates continuation
+    "width": 2,  # Character width of each group number
+    "start": 32,  # Start of first group
+    "per_line": 24,  # Max groups per line
+    "cont_marker": slice(78, 80),  # "-1" indicates continuation
 }
 
 # Format for extended format (>99 spin groups)
@@ -140,7 +141,7 @@ def validate_groups(self) -> "IsotopeParameters":
 
         for group in self.spin_groups:
             if group == 0:
-                _log_and_raise_error(logger, f"Spin group number cannot be 0",ValueError)
+                _log_and_raise_error(logger, "Spin group number cannot be 0", ValueError)
 
             # Check if we need extended format
             if abs(group) > max_standard:
@@ -179,8 +180,8 @@ def from_lines(cls, lines: List[str], extended: bool = False) -> "IsotopeParamet
         if not lines or not lines[0].strip():
             _log_and_raise_error(logger, "No valid parameter line provided", ValueError)
 
-        # Set format to standard. 
-        format_dict = FORMAT_STANDARD # NOTE: EXTENDED format is currently not supported.
+        # Set format to standard.
+        format_dict = FORMAT_STANDARD  # NOTE: EXTENDED format is currently not supported.
 
         main_line = f"{lines[0]:<80}"  # Pad to full width
 
@@ -207,7 +208,7 @@ def from_lines(cls, lines: List[str], extended: bool = False) -> "IsotopeParamet
 
         # Parse spin groups
         spin_groups = []
-        group_format = SPIN_GROUP_STANDARD #NOTE: EXTENDED format is currently not supported.
+        group_format = SPIN_GROUP_STANDARD  # NOTE: EXTENDED format is currently not supported.
 
         # Helper function to parse groups from a line
         def parse_groups(line: str, start_pos: int = None, continuation: bool = False) -> List[int]:
@@ -253,7 +254,7 @@ def parse_groups(line: str, start_pos: int = None, continuation: bool = False) -
             spin_groups.extend(parse_groups(line, start_pos=0, continuation=True))
 
         params["spin_groups"] = spin_groups
-        
+
         return cls(**params)
 
     def to_lines(self, extended: bool = False) -> List[str]:
@@ -321,7 +322,7 @@ class IsotopeCard(BaseModel):
         isotopes (List[IsotopeParameters]): List of isotope parameter sets
         extended (bool): Whether to use extended format for >99 spin groups
 
-    NOTE:   Fixed formats for both standard and extended are defined in the 
+    NOTE:   Fixed formats for both standard and extended are defined in the
             IsotopeParameters class. But only using the standard format for now.
     """
 
@@ -378,12 +379,12 @@ def from_lines(cls, lines: List[str]) -> "IsotopeCard":
         current_lines = []
 
         for line in content_lines:
-
             current_lines.append(line)
-            
+
             # check if characters 79-80 is a "-1". this means that there are more spin groups in the next line.
-            if line[78:80] == "-1": continue
-
+            if line[78:80] == "-1":
+                continue
+
             # Otherwise the are no more lines for spin groups, so process the current lines.
             else:
                 isotopes.append(IsotopeParameters.from_lines(current_lines, extended=extended))

src/pleiades/sammy/parameters/notes/isotope_notes.md

@@ -48,4 +48,4 @@
         - to_lines
 
 ## Main Function
-- Example usage
+- Example usage

src/pleiades/sammy/parameters/notes/radius_notes.md

@@ -100,4 +100,4 @@
     - from_values
 
 ## Main Function
-- Example usage
+- Example usage

src/pleiades/sammy/parameters/radius.py

@@ -5,7 +5,8 @@
 for radius parameters in SAMMY parameter files.
 """
 
-import re, os
+import os
+import re
 from enum import Enum
 from typing import List, Optional, Tuple, Union
 
@@ -15,7 +16,7 @@
 from pleiades.utils.logger import Logger, _log_and_raise_error
 
 # Initialize logger with file logging
-log_file_path = os.path.join(os.getcwd(), 'pleiades-par.log')
+log_file_path = os.path.join(os.getcwd(), "pleiades-par.log")
 logger = Logger(__name__, log_file=log_file_path)
 
 ####################################################################################################
@@ -47,6 +48,7 @@
     # After IX=0 marker, channel numbers use 5 cols each
 }
 
+
 class RadiusFormat(Enum):
     """Supported formats for radius parameter cards."""
 
@@ -314,7 +316,7 @@ def _parse_spin_groups_and_channels(cls, line: str) -> Tuple[List[int], Optional
         """
         where_am_i = "RadiusCardDefault._parse_spin_groups_and_channels()"
         logger.info(f"{where_am_i}: Parsing spin groups and channels from line: {line}")
-        
+
         spin_groups = []
         channels = None
 
@@ -416,7 +418,7 @@ def from_lines(cls, lines: List[str]) -> "RadiusCardDefault":
                 raise ValueError(f"Invalid parameter values: {e}")
 
         logger.info(f"{where_am_i}: Successfully parsed radius parameters")
-        
+
         return cls(parameters=radius_parameters_list)
 
     def to_lines(self) -> List[str]:
@@ -426,7 +428,7 @@ def to_lines(self) -> List[str]:
             List[str]: Lines including header
         """
         where_am_i = "RadiusCardDefault.to_lines()"
-       
+
         logger.info(f"{where_am_i}: Converting radius parameters to lines")
         lines = []
 
@@ -928,16 +930,16 @@ def is_header_line(cls, line: str) -> bool:
         """
         # set location for logger
         where_am_i = "RadiusCard.is_header_line()"
-        
+
         line_upper = line.strip().upper()
 
         logger.info(f"{where_am_i}: {line_upper}")
 
         # Check all valid header formats
         valid_headers = [
-            "RADIUS PARAMETERS FOLLOW",         # Standard/Alternate fixed width
-            "RADII ARE IN KEY-WORD FORMAT",     # Keyword format
-            "CHANNEL RADIUS PARAMETERS FOLLOW", # Alternative keyword format
+            "RADIUS PARAMETERS FOLLOW",  # Standard/Alternate fixed width
+            "RADII ARE IN KEY-WORD FORMAT",  # Keyword format
+            "CHANNEL RADIUS PARAMETERS FOLLOW",  # Alternative keyword format
         ]
 
         return any(header in line_upper for header in valid_headers)
@@ -959,17 +961,17 @@ def detect_format(cls, lines: List[str]) -> RadiusFormat:
         if "KEY-WORD" in header:
             logger.info(f"{where_am_i}: Detected keyword format!")
             return RadiusFormat.KEYWORD
-        
+
         # If DEFAULT or ALTERNATE card formats then "RADIUS" should be in the header
         elif "RADIU" in header:
             # Check format by examining spin group columns
             content_line = next((l for l in lines[1:] if l.strip()), "")  # noqa: E741
-            
+
             # Check for alternate format (5-column integer values)
             if len(content_line) >= 35 and content_line[25:30].strip():  # 5-col format
                 logger.info(f"{where_am_i}: Detected ALTERNATE format based on {content_line}")
                 return RadiusFormat.ALTERNATE
-            
+
             logger.info(f"{where_am_i}: Detected DEFAULT format based on {content_line}")
             return RadiusFormat.DEFAULT
 
@@ -983,7 +985,7 @@ def from_lines(cls, lines: List[str]) -> "RadiusCard":
         logger.info(f"{where_am_i}: Attempting to parse radius card from lines")
         format_type = cls.detect_format(lines)
 
-        # Try reading in the radius card based on the determined format 
+        # Try reading in the radius card based on the determined format
         try:
             if format_type == RadiusFormat.KEYWORD:
                 keyword_card = RadiusCardKeyword.from_lines(lines)
@@ -1003,7 +1005,7 @@ def from_lines(cls, lines: List[str]) -> "RadiusCard":
                 radius_card = cls(parameters=RadiusCardDefault.from_lines(lines).parameters)
                 logger.info(f"{where_am_i}: Successfully parsed radius card from lines in default format")
                 return radius_card
-            
+
         except Exception as e:
             logger.error(f"{where_am_i}Failed to parse radius card: {str(e)}\nLines: {lines}")
             raise ValueError(f"Failed to parse radius card: {str(e)}\nLines: {lines}")
@@ -1017,13 +1019,15 @@ def to_lines(self, radius_format: RadiusFormat = RadiusFormat.DEFAULT) -> List[s
             if radius_format == RadiusFormat.KEYWORD:
                 lines = [CARD_7A_HEADER]
                 for param in self.parameters:
-                    lines.extend(RadiusCardKeyword(
-                        parameters=param,
-                        particle_pair=self.particle_pair,
-                        orbital_momentum=self.orbital_momentum,
-                        relative_uncertainty=self.relative_uncertainty,
-                        absolute_uncertainty=self.absolute_uncertainty,
-                    ).to_lines())
+                    lines.extend(
+                        RadiusCardKeyword(
+                            parameters=param,
+                            particle_pair=self.particle_pair,
+                            orbital_momentum=self.orbital_momentum,
+                            relative_uncertainty=self.relative_uncertainty,
+                            absolute_uncertainty=self.absolute_uncertainty,
+                        ).to_lines()
+                    )
             elif radius_format == RadiusFormat.ALTERNATE:
                 lines = [CARD_7_ALT_HEADER]
                 for param in self.parameters:
@@ -1032,13 +1036,13 @@ def to_lines(self, radius_format: RadiusFormat = RadiusFormat.DEFAULT) -> List[s
                 lines = [CARD_7_HEADER]
                 for param in self.parameters:
                     lines.extend(RadiusCardDefault(parameters=[param]).to_lines())
-            
+
             # Add trailing blank line
             lines.append("")
-            
+
             logger.info(f"{where_am_i}: Successfully wrote radius card")
             return lines
-        
+
         except Exception as e:
             logger.error(f"{where_am_i}: Failed to write radius card: {str(e)}")
             raise ValueError(f"Failed to write radius card: {str(e)}")

src/pleiades/sammy/parameters/resonance.py

@@ -37,32 +37,32 @@ class UnsupportedFormatError(ValueError):
 
 class ResonanceEntry(BaseModel):
     """This class handles the parameters for a single resonance entry in Card Set 1 of a SAMMY parameter file.
-    
+
     Single resonance entry for SAMMY parameter file (strict format)
-    
+
     Attributes:
         resonance_energy: Resonance energy Eλ (eV)
         capture_width: Capture width Γγ (milli-eV)
 
         channel1_width: Particle width for channel 1 (milli-eV)
         channel2_width: Particle width for channel 2 (milli-eV)
         channel3_width: Particle width for channel 3 (milli-eV)
-        NOTE:   If any particle width Γ is negative, SAMMY uses abs(Γ) 
+        NOTE:   If any particle width Γ is negative, SAMMY uses abs(Γ)
                 for the width and set the associated amplitude γ to be negative.
 
-        vary_energy:    Flag indicating if resonance energy is varied 
+        vary_energy:    Flag indicating if resonance energy is varied
         vary_capture_width: Flag indicating if capture width is varied
         vary_channel1: Flag indicating if channel 1 width is varied
         vary_channel2: Flag indicating if channel 2 width is varied
         vary_channel3: Flag indicating if channel 3 width is varied
         NOTE:   0 = no, 1 = yes, 3 = PUP (PUP = Partially Unknown Parameter)
 
         igroup: Quantum numbers group number (or spin_groups)
-        NOTE:   If IGROUP is negative or greater than 50, this resonance will be 
+        NOTE:   If IGROUP is negative or greater than 50, this resonance will be
                 omitted from the calculation.
-        
+
         x_value: Special value used to detect multi-line entries (unsupported)
-    
+
     """
 
     resonance_energy: float = Field(description="Resonance energy Eλ (eV)")