From b4aa877f4e12a62e4d2cce85e7ccab5d2e505638 Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Thu, 27 Jun 2024 10:36:02 +0100
Subject: [PATCH 1/2] Updates DREAM defaults

---
 RATpy/controls.py      | 12 ++++++------
 tests/test_controls.py | 14 ++++++++------
 tests/test_inputs.py   | 10 ++++++----
 3 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/RATpy/controls.py b/RATpy/controls.py
index be54ab89..64e94ca8 100644
--- a/RATpy/controls.py
+++ b/RATpy/controls.py
@@ -38,12 +38,12 @@ class Controls:
     propScale: float = 0.1
     nsTolerance: float = 0.1
     # Dream
-    nSamples: int = 50000
+    nSamples: int = 2000
     nChains: int = 10
     jumpProbability: float = 0.5
     pUnitGamma: float = 0.2
-    boundHandling: BoundHandling = BoundHandling.Fold
-    adaptPCR: bool = False
+    boundHandling: BoundHandling = BoundHandling.Reflect
+    adaptPCR: bool = True
 
 
 class Calculate(BaseModel, validate_assignment=True, extra="forbid"):
@@ -109,12 +109,12 @@ class Dream(Calculate):
     """Defines the additional fields for the Dream procedure."""
 
     procedure: Literal[Procedures.Dream] = Procedures.Dream
-    nSamples: int = Field(50000, ge=0)
+    nSamples: int = Field(2000, ge=0)
     nChains: int = Field(10, gt=0)
     jumpProbability: float = Field(0.5, gt=0.0, lt=1.0)
     pUnitGamma: float = Field(0.2, gt=0.0, lt=1.0)
-    boundHandling: BoundHandling = BoundHandling.Fold
-    adaptPCR: bool = False
+    boundHandling: BoundHandling = BoundHandling.Reflect
+    adaptPCR: bool = True
 
 
 def set_controls(
diff --git a/tests/test_controls.py b/tests/test_controls.py
index 0f806374..42783244 100644
--- a/tests/test_controls.py
+++ b/tests/test_controls.py
@@ -479,11 +479,12 @@ def setup_class(self):
             ("resampleParams", [0.9, 50]),
             ("display", Display.Iter),
             ("procedure", Procedures.Dream),
-            ("nSamples", 50000),
+            ("nSamples", 2000),
             ("nChains", 10),
             ("jumpProbability", 0.5),
             ("pUnitGamma", 0.2),
-            ("boundHandling", BoundHandling.Fold),
+            ("boundHandling", BoundHandling.Reflect),
+            ("adaptPCR", True),
         ],
     )
     def test_dream_property_values(self, control_property: str, value: Any) -> None:
@@ -501,7 +502,8 @@ def test_dream_property_values(self, control_property: str, value: Any) -> None:
             ("nChains", 1000),
             ("jumpProbability", 0.7),
             ("pUnitGamma", 0.3),
-            ("boundHandling", BoundHandling.Reflect),
+            ("boundHandling", BoundHandling.Fold),
+            ("adaptPCR", False),
         ],
     )
     def test_dream_property_setters(self, control_property: str, value: Any) -> None:
@@ -568,12 +570,12 @@ def test_control_class_dream_repr(self) -> None:
             "| calcSldDuringFit |   False   |\n"
             "|  resampleParams  | [0.9, 50] |\n"
             "|     display      |    iter   |\n"
-            "|     nSamples     |   50000   |\n"
+            "|     nSamples     |    2000   |\n"
             "|     nChains      |     10    |\n"
             "| jumpProbability  |    0.5    |\n"
             "|    pUnitGamma    |    0.2    |\n"
-            "|  boundHandling   |    fold   |\n"
-            "|     adaptPCR     |   False   |\n"
+            "|  boundHandling   |  reflect  |\n"
+            "|     adaptPCR     |    True   |\n"
             "+------------------+-----------+"
         )
 
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index 100af9a0..3f7117c6 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -488,11 +488,12 @@ def standard_layers_controls():
     controls.nMCMC = 0.0
     controls.propScale = 0.1
     controls.nsTolerance = 0.1
-    controls.nSamples = 50000
+    controls.nSamples = 2000
     controls.nChains = 10
     controls.jumpProbability = 0.5
     controls.pUnitGamma = 0.2
-    controls.boundHandling = BoundHandling.Fold
+    controls.boundHandling = BoundHandling.Reflect
+    controls.adaptPCR = True
     controls.checks.fitParam = [1, 0, 0, 0]
     controls.checks.fitBackgroundParam = [0]
     controls.checks.fitQzshift = []
@@ -532,11 +533,12 @@ def custom_xy_controls():
     controls.nMCMC = 0.0
     controls.propScale = 0.1
     controls.nsTolerance = 0.1
-    controls.nSamples = 50000
+    controls.nSamples = 2000
     controls.nChains = 10
     controls.jumpProbability = 0.5
     controls.pUnitGamma = 0.2
-    controls.boundHandling = BoundHandling.Fold
+    controls.boundHandling = BoundHandling.Reflect
+    controls.adaptPCR = True
     controls.checks.fitParam = [1, 0, 0, 0]
     controls.checks.fitBackgroundParam = [0]
     controls.checks.fitQzshift = []

From dc85a80874d049a35bbf7b5c82a4104c47d6d991 Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Thu, 27 Jun 2024 14:51:59 +0100
Subject: [PATCH 2/2] Corrects nSamples

---
 RATpy/controls.py      | 4 ++--
 tests/test_controls.py | 4 ++--
 tests/test_inputs.py   | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/RATpy/controls.py b/RATpy/controls.py
index 64e94ca8..d5785f6a 100644
--- a/RATpy/controls.py
+++ b/RATpy/controls.py
@@ -38,7 +38,7 @@ class Controls:
     propScale: float = 0.1
     nsTolerance: float = 0.1
     # Dream
-    nSamples: int = 2000
+    nSamples: int = 20000
     nChains: int = 10
     jumpProbability: float = 0.5
     pUnitGamma: float = 0.2
@@ -109,7 +109,7 @@ class Dream(Calculate):
     """Defines the additional fields for the Dream procedure."""
 
     procedure: Literal[Procedures.Dream] = Procedures.Dream
-    nSamples: int = Field(2000, ge=0)
+    nSamples: int = Field(20000, ge=0)
     nChains: int = Field(10, gt=0)
     jumpProbability: float = Field(0.5, gt=0.0, lt=1.0)
     pUnitGamma: float = Field(0.2, gt=0.0, lt=1.0)
diff --git a/tests/test_controls.py b/tests/test_controls.py
index 42783244..7a030985 100644
--- a/tests/test_controls.py
+++ b/tests/test_controls.py
@@ -479,7 +479,7 @@ def setup_class(self):
             ("resampleParams", [0.9, 50]),
             ("display", Display.Iter),
             ("procedure", Procedures.Dream),
-            ("nSamples", 2000),
+            ("nSamples", 20000),
             ("nChains", 10),
             ("jumpProbability", 0.5),
             ("pUnitGamma", 0.2),
@@ -570,7 +570,7 @@ def test_control_class_dream_repr(self) -> None:
             "| calcSldDuringFit |   False   |\n"
             "|  resampleParams  | [0.9, 50] |\n"
             "|     display      |    iter   |\n"
-            "|     nSamples     |    2000   |\n"
+            "|     nSamples     |   20000   |\n"
             "|     nChains      |     10    |\n"
             "| jumpProbability  |    0.5    |\n"
             "|    pUnitGamma    |    0.2    |\n"
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index 3f7117c6..dd415f26 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -488,7 +488,7 @@ def standard_layers_controls():
     controls.nMCMC = 0.0
     controls.propScale = 0.1
     controls.nsTolerance = 0.1
-    controls.nSamples = 2000
+    controls.nSamples = 20000
     controls.nChains = 10
     controls.jumpProbability = 0.5
     controls.pUnitGamma = 0.2
@@ -533,7 +533,7 @@ def custom_xy_controls():
     controls.nMCMC = 0.0
     controls.propScale = 0.1
     controls.nsTolerance = 0.1
-    controls.nSamples = 2000
+    controls.nSamples = 20000
     controls.nChains = 10
     controls.jumpProbability = 0.5
     controls.pUnitGamma = 0.2