Make VI default

biocore · Sep 18, 2023 · 752109e · 752109e
1 parent d4fd94a
commit 752109e
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/birdman/model_base.py b/birdman/model_base.py
@@ -114,7 +114,7 @@ def add_parameters(self, param_dict: dict = None):
 
     def fit_model(
         self,
-        method: str = "mcmc",
+        method: str = "vi",
         num_draws: int = 500,
         mcmc_warmup: int = None,
         mcmc_chains: int = 4,

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -47,7 +47,7 @@ def model():
         metadata=md,
     )
     nb.compile_model()
-    nb.fit_model(mcmc_chains=4, num_draws=100)
+    nb.fit_model(method="mcmc", mcmc_chains=4, num_draws=100)
     return nb
 
 
@@ -76,7 +76,7 @@ def single_feat_model():
     )
 
     nb.compile_model()
-    nb.fit_model(mcmc_chains=4, num_draws=100)
+    nb.fit_model(method="mcmc", mcmc_chains=4, num_draws=100)
 
     return nb
 

diff --git a/tests/test_custom_model.py b/tests/test_custom_model.py
@@ -40,7 +40,7 @@ def test_custom_model(table_biom, metadata):
         },
     )
     custom_model.compile_model()
-    custom_model.fit_model(num_draws=100, mcmc_chains=4, seed=42)
+    custom_model.fit_model(method="mcmc", num_draws=100, mcmc_chains=4, seed=42)
     inference = custom_model.to_inference()
 
     assert set(inference.groups()) == {"posterior"}

diff --git a/tests/test_model.py b/tests/test_model.py
@@ -49,7 +49,7 @@ def test_nb_lme(self, table_biom, metadata):
             metadata=md,
         )
         nb_lme.compile_model()
-        nb_lme.fit_model(num_draws=100)
+        nb_lme.fit_model(method="mcmc", num_draws=100)
 
         inf = nb_lme.to_inference()
         post = inf.posterior
@@ -68,7 +68,7 @@ def test_single_feat(self, table_biom, metadata):
                 metadata=md,
             )
             nb.compile_model()
-            nb.fit_model(num_draws=100)
+            nb.fit_model(method="mcmc", num_draws=100)
 
 
 class TestToInference:
@@ -159,5 +159,5 @@ def test_iteration_fit(self, table_biom, metadata):
 
         for fit, model in model_iterator:
             model.compile_model()
-            model.fit_model(num_draws=100, mcmc_chains=4, seed=42)
+            model.fit_model(method="mcmc", num_draws=100, mcmc_chains=4, seed=42)
             _ = model.to_inference()