Implement default_transform and transform argument for distributions

pymc/distributions/distribution.py

@@ -333,6 +333,7 @@ def __new__(
         observed=None,
         total_size=None,
         transform=UNSET,
+        default_transform=UNSET,
         **kwargs,
     ) -> TensorVariable:
         """Adds a tensor variable corresponding to a PyMC distribution to the current model.
@@ -414,10 +415,11 @@ def __new__(
         rv_out = model.register_rv(
             rv_out,
             name,
-            observed,
-            total_size,
+            observed=observed,
+            total_size=total_size,
             dims=dims,
             transform=transform,
+            default_transform=default_transform,
             initval=initval,
         )
 

pymc/model/core.py

@@ -22,7 +22,6 @@
 from sys import modules
 from typing import (
     TYPE_CHECKING,
-    Any,
     Literal,
     Optional,
     TypeVar,
@@ -48,7 +47,7 @@
 
 from pymc.blocking import DictToArrayBijection, RaveledVars
 from pymc.data import GenTensorVariable, is_minibatch
-from pymc.distributions.transforms import _default_transform
+from pymc.distributions.transforms import ChainedTransform, _default_transform
 from pymc.exceptions import (
     BlockModelAccessError,
     ImputationWarning,
@@ -58,6 +57,7 @@
 )
 from pymc.initial_point import make_initial_point_fn
 from pymc.logprob.basic import transformed_conditional_logp
+from pymc.logprob.transforms import Transform
 from pymc.logprob.utils import ParameterValueError, replace_rvs_by_values
 from pymc.model_graph import model_to_graphviz
 from pymc.pytensorf import (
@@ -1214,7 +1214,16 @@ def set_data(
         shared_object.set_value(values)
 
     def register_rv(
-        self, rv_var, name, observed=None, total_size=None, dims=None, transform=UNSET, initval=None
+        self,
+        rv_var,
+        name,
+        *,
+        observed=None,
+        total_size=None,
+        dims=None,
+        default_transform=UNSET,
+        transform=UNSET,
+        initval=None,
     ):
         """Register an (un)observed random variable with the model.
 
@@ -1229,8 +1238,10 @@ def register_rv(
             upscales logp of variable with ``coef = total_size/var.shape[0]``
         dims : tuple
             Dimension names for the variable.
+        default_transform
+            A default transform for the random variable in log-likelihood space.
         transform
-            A transform for the random variable in log-likelihood space.
+            Additional transform which may be applied after default transform.
         initval
             The initial value of the random variable.
 
@@ -1255,7 +1266,7 @@ def register_rv(
             if total_size is not None:
                 raise ValueError("total_size can only be passed to observed RVs")
             self.free_RVs.append(rv_var)
-            self.create_value_var(rv_var, transform)
+            self.create_value_var(rv_var, transform=transform, default_transform=default_transform)
             self.add_named_variable(rv_var, dims)
             self.set_initval(rv_var, initval)
         else:
@@ -1278,7 +1289,9 @@ def register_rv(
 
             # `rv_var` is potentially changed by `make_obs_var`,
             # for example into a new graph for imputation of missing data.
-            rv_var = self.make_obs_var(rv_var, observed, dims, transform, total_size)
+            rv_var = self.make_obs_var(
+                rv_var, observed, dims, default_transform, transform, total_size
+            )
 
         return rv_var
 
@@ -1287,7 +1300,8 @@ def make_obs_var(
         rv_var: TensorVariable,
         data: np.ndarray,
         dims,
-        transform: Any | None,
+        default_transform: Transform | None,
+        transform: Transform | None,
         total_size: int | None,
     ) -> TensorVariable:
         """Create a `TensorVariable` for an observed random variable.
@@ -1301,8 +1315,10 @@ def make_obs_var(
             The observed data.
         dims : tuple
             Dimension names for the variable.
-        transform : int, optional
+        default_transform
             A transform for the random variable in log-likelihood space.
+        transform
+            Additional transform which may be applied after default transform.
 
         Returns
         -------
@@ -1339,12 +1355,19 @@ def make_obs_var(
 
             # Register ObservedRV corresponding to observed component
             observed_rv.name = f"{name}_observed"
-            self.create_value_var(observed_rv, transform=None, value_var=observed_data)
+            self.create_value_var(
+                observed_rv, transform=transform, default_transform=None, value_var=observed_data
+            )
             self.add_named_variable(observed_rv)
             self.observed_RVs.append(observed_rv)
 
             # Register FreeRV corresponding to unobserved components
-            self.register_rv(unobserved_rv, f"{name}_unobserved", transform=transform)
+            self.register_rv(
+                unobserved_rv,
+                f"{name}_unobserved",
+                transform=transform,
+                default_transform=default_transform,
+            )
 
             # Register Deterministic that combines observed and missing
             # Note: This can widely increase memory consumption during sampling for large datasets
@@ -1363,14 +1386,21 @@ def make_obs_var(
                 rv_var.name = name
 
             rv_var.tag.observations = data
-            self.create_value_var(rv_var, transform=None, value_var=data)
+            self.create_value_var(
+                rv_var, transform=transform, default_transform=None, value_var=data
+            )
             self.add_named_variable(rv_var, dims)
             self.observed_RVs.append(rv_var)
 
         return rv_var
 
     def create_value_var(
-        self, rv_var: TensorVariable, transform: Any, value_var: Variable | None = None
+        self,
+        rv_var: TensorVariable,
+        *,
+        default_transform: Transform,
+        transform: Transform,
+        value_var: Variable | None = None,
     ) -> TensorVariable:
         """Create a ``TensorVariable`` that will be used as the random
         variable's "value" in log-likelihood graphs.
@@ -1385,7 +1415,11 @@ def create_value_var(
         ----------
         rv_var : TensorVariable
 
-        transform : Any
+        default_transform: Transform
+            A transform for the random variable in log-likelihood space.
+
+        transform: Transform
+            Additional transform which may be applied after default transform.
 
         value_var : Variable, optional
 
@@ -1396,11 +1430,25 @@ def create_value_var(
 
         # Make the value variable a transformed value variable,
         # if there's an applicable transform
-        if transform is UNSET:
+        if transform is None and default_transform is UNSET:
+            default_transform = None
+            warnings.warn(
+                "To disable default transform, please use default_transform=None"
+                " instead of transform=None. Setting transform to None will"
+                " not have any effect in future.",
+                UserWarning,
+            )
+
+        if default_transform is UNSET:
             if rv_var.owner is None:
-                transform = None
+                default_transform = None
             else:
-                transform = _default_transform(rv_var.owner.op, rv_var)
+                default_transform = _default_transform(rv_var.owner.op, rv_var)
+
+        if transform is UNSET:
+            transform = default_transform
+        elif transform is not None and default_transform is not None:
+            transform = ChainedTransform([default_transform, transform])
 
         if value_var is None:
             if transform is None:

pymc/model/fgraph.py

@@ -320,12 +320,14 @@ def first_non_model_var(var):
             var, value, *dims = model_var.owner.inputs
             transform = model_var.owner.op.transform
             model.free_RVs.append(var)
-            model.create_value_var(var, transform=transform, value_var=value)
+            model.create_value_var(
+                var, transform=transform, default_transform=None, value_var=value
+            )
             model.set_initval(var, initval=None)
         elif isinstance(model_var.owner.op, ModelObservedRV):
             var, value, *dims = model_var.owner.inputs
             model.observed_RVs.append(var)
-            model.create_value_var(var, transform=None, value_var=value)
+            model.create_value_var(var, transform=None, default_transform=None, value_var=value)
         elif isinstance(model_var.owner.op, ModelPotential):
             var, *dims = model_var.owner.inputs
             model.potentials.append(var)

tests/distributions/test_mixture.py

@@ -1359,17 +1359,17 @@ def test_warning(self):
 
             with warnings.catch_warnings():
                 warnings.simplefilter("error")
-                Mixture("mix4", w=[0.5, 0.5], comp_dists=comp_dists, transform=None)
+                Mixture("mix4", w=[0.5, 0.5], comp_dists=comp_dists, default_transform=None)
 
             with warnings.catch_warnings():
                 warnings.simplefilter("error")
-                Mixture("mix5", w=[0.5, 0.5], comp_dists=comp_dists, observed=1)
+                Mixture("mix6", w=[0.5, 0.5], comp_dists=comp_dists, observed=1)
 
             # Case where the appropriate default transform is None
             comp_dists = [Normal.dist(), Normal.dist()]
             with warnings.catch_warnings():
                 warnings.simplefilter("error")
-                Mixture("mix6", w=[0.5, 0.5], comp_dists=comp_dists)
+                Mixture("mix7", w=[0.5, 0.5], comp_dists=comp_dists)
 
 
 class TestZeroInflatedMixture:

tests/distributions/test_transform.py

@@ -619,7 +619,7 @@ def test_transform_univariate_dist_logp_shape():
 
 def test_univariate_transform_multivariate_dist_raises():
     with pm.Model() as m:
-        pm.Dirichlet("x", [1, 1, 1], transform=tr.log)
+        pm.Dirichlet("x", [1, 1, 1], default_transform=tr.log)
 
     for jacobian_val in (True, False):
         with pytest.raises(
@@ -645,7 +645,7 @@ def log_jac_det(self, value, *inputs):
     buggy_transform = BuggyTransform()
 
     with pm.Model() as m:
-        pm.Uniform("x", shape=(4, 3), transform=buggy_transform)
+        pm.Uniform("x", shape=(4, 3), default_transform=buggy_transform)
 
     for jacobian_val in (True, False):
         with pytest.raises(

tests/logprob/test_utils.py

@@ -218,11 +218,11 @@ def test_interdependent_transformed_rvs(self, reversed):
             transform = pm.distributions.transforms.Interval(
                 bounds_fn=lambda *inputs: (inputs[-2], inputs[-1])
             )
-            x = pm.Uniform("x", lower=0, upper=1, transform=transform)
+            x = pm.Uniform("x", lower=0, upper=1, default_transform=transform)
             # Operation between the variables provides a regression test for #7054
-            y = pm.Uniform("y", lower=0, upper=pt.exp(x), transform=transform)
-            z = pm.Uniform("z", lower=0, upper=y, transform=transform)
-            w = pm.Uniform("w", lower=0, upper=pt.square(z), transform=transform)
+            y = pm.Uniform("y", lower=0, upper=pt.exp(x), default_transform=transform)
+            z = pm.Uniform("z", lower=0, upper=y, default_transform=transform)
+            w = pm.Uniform("w", lower=0, upper=pt.square(z), default_transform=transform)
 
         rvs = [x, y, z, w]
         if reversed:

tests/model/test_core.py

@@ -42,7 +42,14 @@
 from pymc.blocking import DictToArrayBijection, RaveledVars
 from pymc.distributions import Normal, transforms
 from pymc.distributions.distribution import PartialObservedRV
-from pymc.distributions.transforms import log, simplex
+from pymc.distributions.transforms import (
+    ChainedTransform,
+    Interval,
+    LogTransform,
+    log,
+    ordered,
+    simplex,
+)
 from pymc.exceptions import ImputationWarning, ShapeError, ShapeWarning
 from pymc.logprob.basic import transformed_conditional_logp
 from pymc.logprob.transforms import IntervalTransform
@@ -527,6 +534,35 @@ def test_model_var_maps():
     assert model.rvs_to_transforms[x] is None
 
 
+class TestTransformArgs:
+    def test_transform_warning(self):
+        with pm.Model():
+            with pytest.warns(
+                UserWarning,
+                match="To disable default transform,"
+                " please use default_transform=None"
+                " instead of transform=None. Setting transform to"
+                " None will not have any effect in future.",
+            ):
+                a = pm.Normal("a", transform=None)
+
+    def test_transform_order(self):
+        with pm.Model() as model:
+            x = pm.Normal("x", transform=Interval(0, 1), default_transform=log)
+        transform = model.rvs_to_transforms[x]
+        assert isinstance(transform, ChainedTransform)
+        assert isinstance(transform.transform_list[0], LogTransform)
+        assert isinstance(transform.transform_list[1], Interval)
+
+    def test_default_transform_is_applied(self):
+        with pm.Model() as model1:
+            x1 = pm.LogNormal("x1", [0, 0], [1, 1], transform=ordered, default_transform=None)
+        with pm.Model() as model2:
+            x2 = pm.LogNormal("x2", [0, 0], [1, 1], transform=ordered)
+        assert np.isinf(model1.compile_logp()({"x1_ordered__": (-1, -1)}))
+        assert np.isfinite(model2.compile_logp()({"x2_chain__": (-1, -1)}))
+
+
 def test_make_obs_var():
     """
     Check returned values for `data` given known inputs to `as_tensor()`.
@@ -549,26 +585,26 @@ def test_make_obs_var():
 
     # The function requires data and RV dimensionality to be compatible
     with pytest.raises(ShapeError, match="Dimensionality of data and RV don't match."):
-        fake_model.make_obs_var(fake_distribution, np.ones((3, 3, 1)), None, None, None)
+        fake_model.make_obs_var(fake_distribution, np.ones((3, 3, 1)), None, None, None, None)
 
     # Check function behavior using the various inputs
     # dense, sparse: Ensure that the missing values are appropriately set to None
     # masked: a deterministic variable is returned
 
-    dense_output = fake_model.make_obs_var(fake_distribution, dense_input, None, None, None)
+    dense_output = fake_model.make_obs_var(fake_distribution, dense_input, None, None, None, None)
     assert dense_output == fake_distribution
     assert isinstance(fake_model.rvs_to_values[dense_output], TensorConstant)
     del fake_model.named_vars[fake_distribution.name]
 
-    sparse_output = fake_model.make_obs_var(fake_distribution, sparse_input, None, None, None)
+    sparse_output = fake_model.make_obs_var(fake_distribution, sparse_input, None, None, None, None)
     assert sparse_output == fake_distribution
     assert sparse.basic._is_sparse_variable(fake_model.rvs_to_values[sparse_output])
     del fake_model.named_vars[fake_distribution.name]
 
     # Here the RandomVariable is split into observed/imputed and a Deterministic is returned
     with pytest.warns(ImputationWarning):
         masked_output = fake_model.make_obs_var(
-            fake_distribution, masked_array_input, None, None, None
+            fake_distribution, masked_array_input, None, None, None, None
         )
     assert masked_output != fake_distribution
     assert not isinstance(masked_output, RandomVariable)
@@ -581,7 +617,7 @@ def test_make_obs_var():
 
     # Test that setting total_size returns a MinibatchRandomVariable
     scaled_outputs = fake_model.make_obs_var(
-        fake_distribution, dense_input, None, None, total_size=100
+        fake_distribution, dense_input, None, None, None, total_size=100
     )
     assert scaled_outputs != fake_distribution
     assert isinstance(scaled_outputs.owner.op, MinibatchRandomVariable)

tests/model/transform/test_conditioning.py

@@ -286,8 +286,8 @@ def test_change_value_transforms_error():
 
 def test_remove_value_transforms():
     with pm.Model() as base_m:
-        p = pm.Uniform("p", transform=logodds)
-        q = pm.Uniform("q", transform=logodds)
+        p = pm.Uniform("p", transform=logodds, default_transform=None)
+        q = pm.Uniform("q", transform=logodds, default_transform=None)
 
     new_m = remove_value_transforms(base_m)
     new_p = new_m["p"]

tests/sampling/test_mcmc.py

@@ -303,7 +303,7 @@ def test_transform_with_rv_dependency(self, symbolic_rv):
             transform = pm.distributions.transforms.Interval(
                 bounds_fn=lambda *inputs: (inputs[-2], inputs[-1])
             )
-            y = pm.Uniform("y", lower=0, upper=x, transform=transform)
+            y = pm.Uniform("y", lower=0, upper=x, transform=transform, default_transform=None)
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", ".*number of samples.*", UserWarning)
                 trace = pm.sample(tune=10, draws=50, return_inferencedata=False, random_seed=336)