Sphinx documentation for 4a92743

emdgroup · Oct 9, 2024 · 44664e5 · 44664e5
1 parent 371086c
commit 44664e5
Show file tree

Hide file tree

Showing 32 changed files with 615 additions and 603 deletions.
diff --git a/latest/_sources/examples/Backtesting/full_lookup.md.txt b/latest/_sources/examples/Backtesting/full_lookup.md.txt
@@ -231,7 +231,7 @@ C)=CC=C2OC)C4=CC(C(F)(F)F)=CC(C(F)(F)F)=C4)=CC(C(F)(F)F)=C1')
 C)=C1)C')
 
 
-    _______________________________________smiles_to_mordred_features - 0.2s, 0.0min
+    _______________________________________smiles_to_mordred_features - 0.3s, 0.0min
 
 
     ________________________________________________________________________________
@@ -252,68 +252,68 @@ C)=C1)C')
     _______________________________________smiles_to_mordred_features - 0.1s, 0.0min
 
 
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-
-
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
-    [14:35:34] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:57] DEPRECATION WARNING: please use MorganGenerator
+
+
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
+    [14:59:58] DEPRECATION WARNING: please use MorganGenerator
 
 
 Now we create another campaign that treats the substances as simple one-hot encoded

diff --git a/latest/_sources/examples/Backtesting/multi_target.md.txt b/latest/_sources/examples/Backtesting/multi_target.md.txt
@@ -165,20 +165,20 @@ print(results)
 ```
 
       Scenario  Monte_Carlo_Run  Iteration  Num_Experiments Target_1_Measurements  \
-    0    BayBE                0          0                1                [16.0]   
+    0    BayBE                0          0                1                [12.0]   
     1    BayBE                0          1                2                [16.0]   
-    2    BayBE                1          0                1                [16.0]   
+    2    BayBE                1          0                1                 [4.0]   
     3    BayBE                1          1                2                [16.0]   
 
       Target_2_Measurements  Target_1_IterBest  Target_1_CumBest  \
-    0               [511.0]               16.0              16.0   
+    0               [287.0]               12.0              12.0   
     1               [511.0]               16.0              16.0   
-    2               [511.0]               16.0              16.0   
+    2                [31.0]                4.0               4.0   
     3               [511.0]               16.0              16.0   
 
        Target_2_IterBest  Target_2_CumBest  
-    0              511.0             511.0  
-    1              511.0             511.0  
-    2              511.0             511.0  
-    3              511.0             511.0  
+    0              287.0             287.0  
+    1              511.0             287.0  
+    2               31.0              31.0  
+    3              511.0              31.0  
 
diff --git a/latest/_sources/examples/Basics/campaign.md.txt b/latest/_sources/examples/Basics/campaign.md.txt
@@ -119,13 +119,13 @@ print(recommendation)
 
 
     Recommended measurements with batch_size = 2: 
-               Solvent               Base                        Ligand  \
-    230  Butyornitrile  Potassium acetate                     BrettPhos   
-    313           DMAc     Cesium acetate  Di-tert-butylphenylphosphine   
+          Solvent             Base                        Ligand  Temperature  \
+    358  p-Xylene  Cesium pivalate  Di-tert-butylphenylphosphine        120.0   
+    214  p-Xylene  Cesium pivalate                     BrettPhos        120.0   
 
-         Temperature  Concentration  
-    230        105.0          0.153  
-    313        120.0          0.100  
+         Concentration  
+    358            0.1  
+    214            0.1  
 
 
 Adding target values is done by creating a new column in the `recommendation`
@@ -143,13 +143,13 @@ print(recommendation)
 
 
     Recommended experiments with fake measured values: 
-               Solvent               Base                        Ligand  \
-    230  Butyornitrile  Potassium acetate                     BrettPhos   
-    313           DMAc     Cesium acetate  Di-tert-butylphenylphosphine   
+          Solvent             Base                        Ligand  Temperature  \
+    358  p-Xylene  Cesium pivalate  Di-tert-butylphenylphosphine        120.0   
+    214  p-Xylene  Cesium pivalate                     BrettPhos        120.0   
 
-         Temperature  Concentration      yield  
-    230        105.0          0.153  25.504824  
-    313        120.0          0.100  11.184203  
+         Concentration      yield  
+    358            0.1  23.416661  
+    214            0.1  27.810909  
 
 
 

diff --git a/latest/_sources/examples/Basics/recommenders.md.txt b/latest/_sources/examples/Basics/recommenders.md.txt
@@ -266,10 +266,15 @@ print(recommendation)
 
 
     Recommended experiments: 
-               Solvent                Base     Ligand  Temperature  Concentration
-    286       p-Xylene  Potassium pivalate  BrettPhos        120.0          0.100
-    171       p-Xylene      Cesium acetate  BrettPhos         90.0          0.057
-    226  Butyornitrile   Potassium acetate  BrettPhos         90.0          0.100
+               Solvent                Base         Ligand  Temperature  \
+    196  Butyornitrile     Cesium pivalate      BrettPhos        120.0   
+    81   Butyornitrile   Potassium acetate  (t-Bu)PhCPhos         90.0   
+    283       p-Xylene  Potassium pivalate      BrettPhos        105.0   
+
+         Concentration  
+    196          0.100  
+    81           0.057  
+    283          0.100  
 
 
 
@@ -282,15 +287,15 @@ print(recommendation)
 
 
     Recommended experiments with fake measured values: 
-               Solvent                Base     Ligand  Temperature  Concentration  \
-    286       p-Xylene  Potassium pivalate  BrettPhos        120.0          0.100   
-    171       p-Xylene      Cesium acetate  BrettPhos         90.0          0.057   
-    226  Butyornitrile   Potassium acetate  BrettPhos         90.0          0.100   
+               Solvent                Base         Ligand  Temperature  \
+    196  Butyornitrile     Cesium pivalate      BrettPhos        120.0   
+    81   Butyornitrile   Potassium acetate  (t-Bu)PhCPhos         90.0   
+    283       p-Xylene  Potassium pivalate      BrettPhos        105.0   
 
-             yield  
-    286  14.181010  
-    171   6.181388  
-    226   6.446978  
+         Concentration      yield  
+    196          0.100   2.524372  
+    81           0.057  19.714731  
+    283          0.100  32.259344  
 
 
 

diff --git a/latest/_sources/examples/Constraints_Discrete/custom_constraints.md.txt b/latest/_sources/examples/Constraints_Discrete/custom_constraints.md.txt
@@ -129,30 +129,30 @@ constraint = DiscreteCustomConstraint(
 searchspace = SearchSpace.from_product(parameters=parameters, constraints=[constraint])
 ```
 
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:26] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:08] DEPRECATION WARNING: please use MorganGenerator
 
 
 

diff --git a/latest/_sources/examples/Constraints_Discrete/exclusion_constraints.md.txt b/latest/_sources/examples/Constraints_Discrete/exclusion_constraints.md.txt
@@ -127,30 +127,30 @@ searchspace = SearchSpace.from_product(
 )
 ```
 
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:38] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
-    [14:32:39] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator
+    [14:57:19] DEPRECATION WARNING: please use MorganGenerator