Adds code to construct inputs for the compiled code (#25)

* Tidies up configs for pydantic models

* Moves enums into "utils/enums.py"

* First draft of "inputs.py" code to construct inputs for compiled code

* Renames enums

* Moves definition of dataclasses to "utils/dataclasses.py"

* Tidies up "inputs" module with "make_problem"2" and "make_cells" routines

* Adds offset to the "index" routine in "classList.py"

* Adds "NaNList" class to "tests/utils.py"

* Adds "test_inputs.py", and corrects code in "inputs.py"

* Adjusts tests to fit with pybind example

* Updates code to ensure tests pass

* Renames parameters to match matlab updates

* Converts "inputs.py" to use C++ objects directly.

* Renames "misc.py" as "wrappers.py" and "Calc" enum as "Calculations"

* Adds background actions to the contrast model

* Adds file wrappers to "make"cells"

* Adds additional examples to "test_inputs.py" to improve test coverage"

* Adds code to support recording custom files in "make_cells"

* Updates submodule and tidying up

* Updates requirements

* . . .and "pyproject.toml"

* Fixes pydantic to version 2.6.4

* . . . and "setup.py"

* Sort out version requirements

* Addresses review comments and import statements

* Changes parameters from optional to compulsory in "Layer" and "AbsorptionLayer" models

* Enables optional hydration in layer models

CONTRIBUTING.md

@@ -16,6 +16,10 @@ And finally create a separate branch to begin work
 
     git checkout -b new-feature
 
+If there are updates to the C++ RAT submodule, run the following command to update the local branch
+
+    git submodule update --remote
+
 Once complete submit a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork) via GitHub. 
 Ensure to rebase your branch to include the latest changes on your branch and resolve possible merge conflicts.
 

RAT/__init__.py

@@ -1,9 +1,8 @@
 import os
 from RAT.classlist import ClassList
 from RAT.project import Project
-import RAT.controls
+from RAT.controls import set_controls
 import RAT.models
 
-
 dir_path = os.path.dirname(os.path.realpath(__file__))
 os.environ["RAT_PATH"] = os.path.join(dir_path, '')

RAT/classlist.py

@@ -63,11 +63,11 @@ def __repr__(self):
                 output = repr(self.data)
         return output
 
-    def __setitem__(self, index: int, item: 'RAT.models') -> None:
+    def __setitem__(self, index: int, item: object) -> None:
         """Replace the object at an existing index of the ClassList."""
         self._setitem(index, item)
 
-    def _setitem(self, index: int, item: 'RAT.models') -> None:
+    def _setitem(self, index: int, item: object) -> None:
         """Auxiliary routine of "__setitem__" used to enable wrapping."""
         self._check_classes(self + [item])
         self._check_unique_name_fields(self + [item])
@@ -171,7 +171,7 @@ def insert(self, index: int, obj: object = None, **kwargs) -> None:
             inserted into the ClassList and the keyword arguments are discarded.
         """
         if obj and kwargs:
-            warnings.warn('ClassList.insert() called with both object and keyword arguments. '
+            warnings.warn('ClassList.insert() called with both an object and keyword arguments. '
                           'The keyword arguments will be ignored.', SyntaxWarning)
         if obj:
             if not hasattr(self, '_class_handle'):
@@ -193,15 +193,17 @@ def remove(self, item: Union[object, str]) -> None:
 
     def count(self, item: Union[object, str]) -> int:
         """Return the number of times an object appears in the ClassList using either the object itself or its
-        name_field value."""
+        name_field value.
+        """
         item = self._get_item_from_name_field(item)
         return self.data.count(item)
 
-    def index(self, item: Union[object, str], *args) -> int:
+    def index(self, item: Union[object, str], offset: bool = False, *args) -> int:
         """Return the index of a particular object in the ClassList using either the object itself or its
-        name_field value."""
+        name_field value. If offset is specified, add one to the index. This is used to account for one-based indexing.
+        """
         item = self._get_item_from_name_field(item)
-        return self.data.index(item, *args)
+        return self.data.index(item, *args) + int(offset)
 
     def extend(self, other: Sequence[object]) -> None:
         """Extend the ClassList by adding another sequence."""

RAT/controls.py

@@ -1,27 +1,65 @@
+from dataclasses import dataclass, field
 import prettytable
 from pydantic import BaseModel, Field, field_validator, ValidationError
 from typing import Literal, Union
 
-from RAT.utils.enums import ParallelOptions, Procedures, DisplayOptions, BoundHandlingOptions, StrategyOptions
+from RAT.utils.enums import Parallel, Procedures, Display, BoundHandling, Strategies
 from RAT.utils.custom_errors import custom_pydantic_validation_error
 
 
+@dataclass(frozen=True)
+class Controls:
+    """The full set of controls parameters required for the compiled RAT code."""
+    # All Procedures
+    procedure: Procedures = Procedures.Calculate
+    parallel: Parallel = Parallel.Single
+    calcSldDuringFit: bool = False
+    resampleParams: list[float] = field(default_factory=list[0.9, 50.0])
+    display: Display = Display.Iter
+    # Simplex
+    xTolerance: float = 1.0e-6
+    funcTolerance: float = 1.0e-6
+    maxFuncEvals: int = 10000
+    maxIterations: int = 1000
+    updateFreq: int = -1
+    updatePlotFreq: int = 1
+    # DE
+    populationSize: int = 20
+    fWeight: float = 0.5
+    crossoverProbability: float = 0.8
+    strategy: Strategies = Strategies.RandomWithPerVectorDither.value
+    targetValue: float = 1.0
+    numGenerations: int = 500
+    # NS
+    nLive: int = 150
+    nMCMC: float = 0.0
+    propScale: float = 0.1
+    nsTolerance: float = 0.1
+    # Dream
+    nSamples: int = 50000
+    nChains: int = 10
+    jumpProbability: float = 0.5
+    pUnitGamma: float = 0.2
+    boundHandling: BoundHandling = BoundHandling.Fold
+    adaptPCR: bool = False
+
+
 class Calculate(BaseModel, validate_assignment=True, extra='forbid'):
     """Defines the class for the calculate procedure, which includes the properties used in all five procedures."""
     procedure: Literal[Procedures.Calculate] = Procedures.Calculate
-    parallel: ParallelOptions = ParallelOptions.Single
+    parallel: Parallel = Parallel.Single
     calcSldDuringFit: bool = False
-    resamPars: list[float] = Field([0.9, 50], min_length=2, max_length=2)
-    display: DisplayOptions = DisplayOptions.Iter
+    resampleParams: list[float] = Field([0.9, 50], min_length=2, max_length=2)
+    display: Display = Display.Iter
 
-    @field_validator("resamPars")
+    @field_validator("resampleParams")
     @classmethod
-    def check_resamPars(cls, resamPars):
-        if not 0 < resamPars[0] < 1:
-            raise ValueError('resamPars[0] must be between 0 and 1')
-        if resamPars[1] < 0:
-            raise ValueError('resamPars[1] must be greater than or equal to 0')
-        return resamPars
+    def check_resample_params(cls, resampleParams):
+        if not 0 < resampleParams[0] < 1:
+            raise ValueError('resampleParams[0] must be between 0 and 1')
+        if resampleParams[1] < 0:
+            raise ValueError('resampleParams[1] must be greater than or equal to 0')
+        return resampleParams
 
     def __repr__(self) -> str:
         table = prettytable.PrettyTable()
@@ -30,45 +68,46 @@ def __repr__(self) -> str:
         return table.get_string()
 
 
-class Simplex(Calculate, validate_assignment=True, extra='forbid'):
+class Simplex(Calculate):
     """Defines the additional fields for the simplex procedure."""
     procedure: Literal[Procedures.Simplex] = Procedures.Simplex
-    tolX: float = Field(1.0e-6, gt=0.0)
-    tolFun: float = Field(1.0e-6, gt=0.0)
-    maxFunEvals: int = Field(10000, gt=0)
-    maxIter: int = Field(1000, gt=0)
+    xTolerance: float = Field(1.0e-6, gt=0.0)
+    funcTolerance: float = Field(1.0e-6, gt=0.0)
+    maxFuncEvals: int = Field(10000, gt=0)
+    maxIterations: int = Field(1000, gt=0)
     updateFreq: int = -1
-    updatePlotFreq: int = -1
+    updatePlotFreq: int = 1
 
 
-class DE(Calculate, validate_assignment=True, extra='forbid'):
+class DE(Calculate):
     """Defines the additional fields for the Differential Evolution procedure."""
     procedure: Literal[Procedures.DE] = Procedures.DE
     populationSize: int = Field(20, ge=1)
     fWeight: float = 0.5
     crossoverProbability: float = Field(0.8, gt=0.0, lt=1.0)
-    strategy: StrategyOptions = StrategyOptions.RandomWithPerVectorDither
+    strategy: Strategies = Strategies.RandomWithPerVectorDither
     targetValue: float = Field(1.0, ge=1.0)
     numGenerations: int = Field(500, ge=1)
 
 
-class NS(Calculate, validate_assignment=True, extra='forbid'):
+class NS(Calculate):
     """Defines the additional fields for the Nested Sampler procedure."""
     procedure: Literal[Procedures.NS] = Procedures.NS
-    Nlive: int = Field(150, ge=1)
-    Nmcmc: float = Field(0.0, ge=0.0)
+    nLive: int = Field(150, ge=1)
+    nMCMC: float = Field(0.0, ge=0.0)
     propScale: float = Field(0.1, gt=0.0, lt=1.0)
     nsTolerance: float = Field(0.1, ge=0.0)
 
 
-class Dream(Calculate, validate_assignment=True, extra='forbid'):
+class Dream(Calculate):
     """Defines the additional fields for the Dream procedure."""
     procedure: Literal[Procedures.Dream] = Procedures.Dream
     nSamples: int = Field(50000, ge=0)
     nChains: int = Field(10, gt=0)
-    jumpProb: float = Field(0.5, gt=0.0, lt=1.0)
+    jumpProbability: float = Field(0.5, gt=0.0, lt=1.0)
     pUnitGamma: float = Field(0.2, gt=0.0, lt=1.0)
-    boundHandling: BoundHandlingOptions = BoundHandlingOptions.Fold
+    boundHandling: BoundHandling = BoundHandling.Fold
+    adaptPCR: bool = False
 
 
 def set_controls(procedure: Procedures = Procedures.Calculate, **properties)\

RAT/events.py

@@ -1,6 +1,5 @@
 from typing import Callable, Union, List
-import RAT.rat_core
-from RAT.rat_core import EventTypes, PlotEventData, ProgressEventData
+from RAT.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
 
 
 def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEventData]) -> None:
@@ -18,6 +17,7 @@ def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEvent
     for callback in callbacks:
         callback(data)
 
+
 def get_event_callback(event_type: EventTypes) -> List[Callable[[Union[str, PlotEventData, ProgressEventData]], None]]:
     """Returns all callbacks registered for the given event type.
 
@@ -59,5 +59,5 @@ def clear() -> None:
         __event_callbacks[key] = set()
 
 
-__event_impl = RAT.rat_core.EventBridge(notify)
+__event_impl = EventBridge(notify)
 __event_callbacks = {EventTypes.Message: set(), EventTypes.Plot: set(), EventTypes.Progress: set()}