Merge pull request #87 from ChristopherMayes/pydantic_bugfix

Fix pydantic bug in tests/ add pinned version for botorch

docs/examples/bayes_opt/benchmarking.ipynb

@@ -826,4 +826,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - pydantic>=1.10.0
   - pyyaml
   - pytorch
-  - botorch>=0.6.5
+  - botorch==0.7.3
   - gpytorch
   - pandas
   - ipywidgets

requirements.txt

@@ -2,7 +2,7 @@ deap
 numpy
 pyyaml
 torch
-botorch>=0.6.5
+botorch==0.7.3
 gpytorch
 pandas
 pydantic>=1.10.0

tests/generators/bayesian/test_expected_improvement.py

@@ -6,23 +6,20 @@
 
 from xopt.evaluator import Evaluator
 from xopt.generators.bayesian.bayesian_exploration import BayesianExplorationOptions
-from xopt.generators.bayesian.expected_improvement import (
-    ExpectedImprovementGenerator,
-)
+from xopt.generators.bayesian.expected_improvement import ExpectedImprovementGenerator
 
 from xopt.resources.testing import TEST_VOCS_BASE, TEST_VOCS_DATA, xtest_callable
 
 
 class TestExpectedImprovement:
     def test_init(self):
-        ucb_gen = ExpectedImprovementGenerator(TEST_VOCS_BASE)
-        ucb_gen.options.dict()
-        ucb_gen.options.schema()
+        ei_gen = ExpectedImprovementGenerator(TEST_VOCS_BASE)
+        ei_gen.options.dict()
+        ei_gen.options.json()
+        # ei_gen.options.schema() wait till pydantic v2 for fix
 
         with pytest.raises(ValueError):
-            ExpectedImprovementGenerator(
-                TEST_VOCS_BASE, BayesianExplorationOptions()
-            )
+            ExpectedImprovementGenerator(TEST_VOCS_BASE, BayesianExplorationOptions())
 
     def test_generate(self):
         gen = ExpectedImprovementGenerator(

tests/generators/bayesian/test_upper_confidence_bound.py

@@ -19,12 +19,11 @@ class TestUpperConfidenceBoundGenerator:
     def test_init(self):
         ucb_gen = UpperConfidenceBoundGenerator(TEST_VOCS_BASE)
         ucb_gen.options.dict()
-        ucb_gen.options.schema()
+        ucb_gen.options.json()
+        # ucb_gen.options.schema() wait till pydantic v2 for fix
 
         with pytest.raises(ValueError):
-            UpperConfidenceBoundGenerator(
-                TEST_VOCS_BASE, BayesianExplorationOptions()
-            )
+            UpperConfidenceBoundGenerator(TEST_VOCS_BASE, BayesianExplorationOptions())
 
     def test_generate(self):
         gen = UpperConfidenceBoundGenerator(
@@ -96,10 +95,11 @@ def test_positivity(self):
         ucb_gen = UpperConfidenceBoundGenerator(
             TEST_VOCS_BASE,
         )
-        ucb_gen.add_data(pd.DataFrame({"x1": -1., "x2": -1., "y1": 100., "c1": -100},
-                                      index=[0]))
+        ucb_gen.add_data(
+            pd.DataFrame({"x1": -1.0, "x2": -1.0, "y1": 100.0, "c1": -100}, index=[0])
+        )
         ucb_gen.train_model()
         # evaluate acqf
         acqf = ucb_gen.get_acquisition(ucb_gen.model)
         with torch.no_grad():
-            assert acqf(torch.tensor((-1., -1.)).reshape(1, 1, 2)) >= 0.0
+            assert acqf(torch.tensor((-1.0, -1.0)).reshape(1, 1, 2)) >= 0.0

xopt/generators/bayesian/options.py

@@ -45,7 +45,7 @@ class OptimOptions(XoptBaseModel):
     )
 
 
-class ModelOptions(BaseModel):
+class ModelOptions(XoptBaseModel):
     """Options for defining the GP model in BO"""
 
     function: Callable