Merge pull request #34 from lanl/sammy_param_user

Add parser for user defined function card

src/pleiades/core/data_manager.py

@@ -73,9 +73,7 @@ def get_file_path(self, category: DataCategory, filename: str) -> Path:
 
         file_path = Path(filename)
         if file_path.suffix not in self._VALID_EXTENSIONS[category]:
-            raise ValueError(
-                f"Invalid file extension for {category}. " f"Allowed extensions: {self._VALID_EXTENSIONS[category]}"
-            )
+            raise ValueError(f"Invalid file extension for {category}. " f"Allowed extensions: {self._VALID_EXTENSIONS[category]}")
 
         try:
             with resources.path(f"pleiades.data.{self._get_category_path(category)}", filename) as path:

src/pleiades/core/models.py

@@ -231,9 +231,7 @@ def areal_density(self) -> float:
         if self.thickness_unit == "mm":
             thickness_cm /= 10.0
 
-        return (
-            thickness_cm * self.density * CONSTANTS.avogadro_number / self.atomic_mass.value / 1e24
-        )  # Convert to atoms/barn
+        return thickness_cm * self.density * CONSTANTS.avogadro_number / self.atomic_mass.value / 1e24  # Convert to atoms/barn
 
 
 # Unit conversion functions

src/pleiades/sammy/backends/docker.py

@@ -48,9 +48,7 @@ def prepare_environment(self, files: SammyFiles) -> None:
                 raise EnvironmentPreparationError("Docker not found in PATH")
 
             # Verify docker image exists
-            result = subprocess.run(
-                ["docker", "image", "inspect", self.config.image_name], capture_output=True, text=True
-            )
+            result = subprocess.run(["docker", "image", "inspect", self.config.image_name], capture_output=True, text=True)
             if result.returncode != 0:
                 raise EnvironmentPreparationError(f"Docker image not found: {self.config.image_name}")
 

src/pleiades/sammy/backends/local.py

@@ -81,10 +81,7 @@ def execute_sammy(self, files: SammyFiles) -> SammyExecutionResult:
 
             if not success:
                 logger.error(f"SAMMY execution failed for {execution_id}")
-                error_message = (
-                    f"SAMMY execution failed with return code {process.returncode}. "
-                    "Check console output for details."
-                )
+                error_message = f"SAMMY execution failed with return code {process.returncode}. " "Check console output for details."
             else:
                 logger.info(f"SAMMY execution completed successfully for {execution_id}")
                 error_message = None

src/pleiades/sammy/factory.py

@@ -105,9 +105,7 @@ def list_available_backends() -> Dict[BackendType, bool]:
         return available
 
     @classmethod
-    def create_runner(
-        cls, backend_type: str, working_dir: Path, output_dir: Optional[Path] = None, **kwargs
-    ) -> SammyRunner:
+    def create_runner(cls, backend_type: str, working_dir: Path, output_dir: Optional[Path] = None, **kwargs) -> SammyRunner:
         """
         Create a SAMMY runner with the specified backend and configuration.
 
@@ -295,9 +293,7 @@ def process_config(cfg):
             backend_config = config.get(backend_type, {})
 
             # Create runner using create_runner
-            return cls.create_runner(
-                backend_type=backend_type, working_dir=working_dir, output_dir=output_dir, **backend_config
-            )
+            return cls.create_runner(backend_type=backend_type, working_dir=working_dir, output_dir=output_dir, **backend_config)
 
         except Exception as e:
             if not isinstance(e, (ConfigurationError, BackendNotAvailableError)):
@@ -347,9 +343,7 @@ def auto_select(
                 preferred = BackendType(preferred_backend.lower())
                 if available[preferred]:
                     logger.info(f"Using preferred backend: {preferred.value}")
-                    return cls.create_runner(
-                        backend_type=preferred.value, working_dir=working_dir, output_dir=output_dir, **kwargs
-                    )
+                    return cls.create_runner(backend_type=preferred.value, working_dir=working_dir, output_dir=output_dir, **kwargs)
                 else:
                     logger.warning(f"Preferred backend {preferred.value} not available, " "trying alternatives")
             except ValueError:
@@ -367,9 +361,7 @@ def auto_select(
             if available[backend]:
                 try:
                     logger.info(f"Attempting to use {backend.value} backend")
-                    return cls.create_runner(
-                        backend_type=backend.value, working_dir=working_dir, output_dir=output_dir, **kwargs
-                    )
+                    return cls.create_runner(backend_type=backend.value, working_dir=working_dir, output_dir=output_dir, **kwargs)
                 except Exception as e:
                     logger.warning(f"Failed to configure {backend.value} backend: {str(e)}")
                     errors.append(f"{backend.value}: {str(e)}")

src/pleiades/sammy/parameters/__init__.py

@@ -1,8 +1,11 @@
 from pleiades.sammy.parameters.broadening import BroadeningParameterCard  # noqa: F401
 from pleiades.sammy.parameters.data_reduction import DataReductionCard  # noqa: F401
 from pleiades.sammy.parameters.external_r import ExternalREntry  # noqa: F401
+from pleiades.sammy.parameters.isotope import IsotopeCard  # noqa: F401
 from pleiades.sammy.parameters.normalization import NormalizationBackgroundCard  # noqa: F401
 from pleiades.sammy.parameters.orres import ORRESCard  # noqa: F401
+from pleiades.sammy.parameters.paramagnetic import ParamagneticParameters  # noqa: F401
 from pleiades.sammy.parameters.radius import RadiusCard  # noqa: F401
 from pleiades.sammy.parameters.resonance import ResonanceEntry  # noqa: F401
 from pleiades.sammy.parameters.unused_var import UnusedCorrelatedCard  # noqa: F401
+from pleiades.sammy.parameters.user_resolution import UserResolutionParameters  # noqa: F401

src/pleiades/sammy/parameters/background.py

@@ -1,5 +1,74 @@
 #!/usr/bin/env python
-"""Background function card for SAMMY.
+"""Parsers and containers for SAMMY's Card Set 13 background function parameters.
 
-TODO: This card will be implemented in the future.
+This module implements parsers and containers for Card Set 13 background parameters
+which can appear in either the PARameter or INPut file.
+
+Format specification from Table VI B.2:
+Card Set 13 contains background function parameters with distinct formats:
+1. CONST - Constant background
+2. EXPON - Exponential background
+3. POWER - Power law background
+4. EXPLN - Exponential with logarithmic terms
+5. T-PNT - Point-wise linear function of time
+6. E-PNT - Point-wise linear function of energy
+7. TFILE - File-based time function
+8. EFILE - File-based energy function
+9. AETOB - Power of energy
+
+Currently unimplemented - placeholder for future development.
 """
+
+from enum import Enum
+from typing import List
+
+from pydantic import BaseModel, Field
+
+
+class BackgroundType(str, Enum):
+    """Types of background functions available."""
+
+    CONST = "CONST"  # Constant background
+    EXPON = "EXPON"  # Exponential background
+    POWER = "POWER"  # Power law background
+    EXPLN = "EXPLN"  # Exponential with logarithmic terms
+    T_PNT = "T-PNT"  # Point-wise linear in time
+    E_PNT = "E-PNT"  # Point-wise linear in energy
+    TFILE = "TFILE"  # Time function from file
+    EFILE = "EFILE"  # Energy function from file
+    AETOB = "AETOB"  # Power of energy
+
+
+class BackgroundParameters(BaseModel):
+    """Container for Card Set 13 background function parameters.
+
+    Currently unimplemented - placeholder for future development.
+
+    Format specification from Table VI B.2:
+    Cols    Format  Variable    Description
+    1-80    A       WHAT        "BACKGround functions"
+
+    Followed by one or more background function definitions.
+    """
+
+    type: BackgroundType = Field(..., description="Type of background function")
+
+    @classmethod
+    def from_lines(cls, lines: List[str]) -> "BackgroundParameters":
+        """Parse background parameters from fixed-width format lines.
+
+        Args:
+            lines: List of input lines for background parameters
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 13 background parameter parsing is not yet implemented")
+
+    def to_lines(self) -> List[str]:
+        """Convert parameters to fixed-width format lines.
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 13 background parameter formatting is not yet implemented")

src/pleiades/sammy/parameters/det_efficiency.py

@@ -1,5 +1,68 @@
 #!/usr/bin/env python
-"""Detector efficiency function card for SAMMY.
+"""Parsers and containers for SAMMY's Card Set 15 detector efficiency parameters.
 
-TODO: This card will be implemented in the future.
+This module implements parsers and containers for Card Set 15 detector efficiency parameters
+which can appear in either the PARameter or INPut file.
+
+Format specification from Table VI B.2:
+Card Set 15 contains detector efficiency parameters for specific spin groups.
+Each efficiency value can be assigned to multiple spin groups, with any unassigned
+groups taking the final efficiency in the list.
+
+Currently unimplemented - placeholder for future development.
 """
+
+from typing import List
+
+from pydantic import BaseModel
+
+
+class DetectorEfficiencyParameters(BaseModel):
+    """Container for Card Set 15 detector efficiency parameters.
+
+    Currently unimplemented - placeholder for future development.
+
+    Format specification from Table VI B.2:
+    Cols    Format  Variable    Description
+    1-80    A       WHAT        "DETECtor efficiencies"
+
+    Followed by one or more efficiency definitions:
+    1-10    F       PARDET      Detector efficiency
+    11-20   F       DELDET      Uncertainty on efficiency
+    21-22   I       IFLDET      Flag to vary efficiency
+    23-24   I       IGRDET      First spin group number
+    25-26   I       IGRDET      Second spin group number
+    ...etc.
+
+    Notes:
+    - If more than 29 spin groups needed, insert "-1" in cols 79-80
+      and continue on next line
+    - When more than 99 spin groups total, use 5 columns per group number
+    - Any spin groups not included use the final efficiency in the list
+
+    Attributes:
+        efficiencies: List of efficiency values
+        uncertainties: List of uncertainty values
+        flags: List of vary flags
+        group_assignments: List of lists containing group numbers for each efficiency
+    """
+
+    @classmethod
+    def from_lines(cls, lines: List[str]) -> "DetectorEfficiencyParameters":
+        """Parse detector efficiency parameters from fixed-width format lines.
+
+        Args:
+            lines: List of input lines for efficiency parameters
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 15 detector efficiency parameter parsing is not yet implemented")
+
+    def to_lines(self) -> List[str]:
+        """Convert parameters to fixed-width format lines.
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 15 detector efficiency parameter formatting is not yet implemented")

src/pleiades/sammy/parameters/resolution.py

@@ -1,5 +1,134 @@
 #!/usr/bin/env python
-"""Resolution function card for SAMMY.
+"""Parsers and containers for SAMMY's Card Set 14 resolution function parameters.
 
-TODO: This module will be implemented in the future.
+This module implements parsers and containers for Card Set 14 resolution parameters
+which can appear in either the PARameter or INPut file.
+
+Format specification from Table VI B.2:
+Card Set 14 contains resolution function parameters with distinct formats:
+1. RPI Resolution function
+2. GEEL resolution function
+3. GELINA resolution function
+4. NTOF resolution function
+5. User-defined resolution function
+
+Each type has its own multi-line parameter structure.
+Currently unimplemented - placeholder for future development.
 """
+
+from enum import Enum
+from typing import List
+
+from pydantic import BaseModel, Field
+
+
+class ResolutionType(str, Enum):
+    """Types of resolution functions available."""
+
+    RPI = "RPI Resolution"
+    GEEL = "GEEL resolution"
+    GELINA = "GELINa resolution"
+    NTOF = "NTOF resolution"
+    USER = "USER-Defined resolution function"
+
+
+class ResolutionParameters(BaseModel):
+    """Container for Card Set 14 resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+
+    Format specification from Table VI B.2:
+    Different resolution types have different parameter structures:
+
+    RPI Resolution:
+    - Optional burst width
+    - Optional tau parameters
+    - Optional lambda parameters
+    - Optional A1 parameters
+    - Optional exponential parameters
+    - Optional channel parameters
+
+    GEEL Resolution:
+    - Similar structure with different defaults
+
+    GELINA Resolution:
+    - Similar structure with different defaults
+
+    NTOF Resolution:
+    - Similar structure with different defaults
+
+    User-Defined Resolution:
+    - Custom file-based definition
+    """
+
+    type: ResolutionType = Field(..., description="Type of resolution function")
+
+    @classmethod
+    def from_lines(cls, lines: List[str]) -> "ResolutionParameters":
+        """Parse resolution parameters from fixed-width format lines.
+
+        Args:
+            lines: List of input lines for resolution parameters
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 14 resolution parameter parsing is not yet implemented")
+
+    def to_lines(self) -> List[str]:
+        """Convert parameters to fixed-width format lines.
+
+        Raises:
+            NotImplementedError: This class is not yet implemented
+        """
+        raise NotImplementedError("Card Set 14 resolution parameter formatting is not yet implemented")
+
+
+class RPIResolutionParameters(ResolutionParameters):
+    """Container for RPI resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+    Format includes burst width, tau, lambda, A1, exponential and channel parameters.
+    """
+
+    type: ResolutionType = ResolutionType.RPI
+
+
+class GEELResolutionParameters(ResolutionParameters):
+    """Container for GEEL resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+    Similar format to RPI with different defaults.
+    """
+
+    type: ResolutionType = ResolutionType.GEEL
+
+
+class GELINAResolutionParameters(ResolutionParameters):
+    """Container for GELINA resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+    Similar format to RPI with different defaults.
+    """
+
+    type: ResolutionType = ResolutionType.GELINA
+
+
+class NTOFResolutionParameters(ResolutionParameters):
+    """Container for NTOF resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+    Similar format to RPI with different defaults.
+    """
+
+    type: ResolutionType = ResolutionType.NTOF
+
+
+class UserResolutionParameters(ResolutionParameters):
+    """Container for user-defined resolution function parameters.
+
+    Currently unimplemented - placeholder for future development.
+    Includes file-based definition capability.
+    """
+
+    type: ResolutionType = ResolutionType.USER