Remove t suffix from Model methods (#5863)

* Future warning for logpt

* Future warning for dlogpt and d2logpt

* Updated references to logpt, and updated varlogpt, datalogpt, joint_logpt

* Fix issue with d2logpt

* Added tests

* Fix typo

* Updated release notes for 4.0

* Added potentiallogpt test

* Updated developer guide

* Update pymc/distributions/logprob.py

Co-authored-by: Ricardo Vieira <[email protected]>

* Removed t from varlogp_nojact

* Revert Release Notes

* Revert changes to developer guide

* Future warning for logpt

* Future warning for dlogpt and d2logpt

* Updated references to logpt, and updated varlogpt, datalogpt, joint_logpt

* Fix issue with d2logpt

* Added tests

* Fix typo

* Updated release notes for 4.0

* Added potentiallogpt test

* Update pymc/distributions/logprob.py

Co-authored-by: Ricardo Vieira <[email protected]>

* Removed t from varlogp_nojact

* Revert Release Notes

* Updated release notes for 4.0

* Revert Release Notes

* Added deprecation of functions/properties ending with t to release notes

* Update RELEASE-NOTES.md

Co-authored-by: Ricardo Vieira <[email protected]>
Co-authored-by: Thomas Wiecki <[email protected]>

Author: 3 people

RELEASE-NOTES.md

@@ -4,6 +4,16 @@
 + Fixed an incorrect entry in `pm.Metropolis.stats_dtypes` (see #5582).
 + Added a check in `Empirical` approximation which does not yet support `InferenceData` inputs (see #5874, #5884).
 + Fixed bug when sampling discrete variables with SMC (see #5887).
++ Removed trailing `t` (for tensor) in functions and properties from the model class and from `jointlogpt` (see #5859).
+  + `Model.logpt` → `Model.logp`
+  + `Model.dlogpt` → `Model.dlogp`
+  + `Model.d2logpt` → `Model.d2logp`
+  + `Model.datalogpt` → `Model.datalogp`
+  + `Model.varlogpt` → `Model.varlogp`
+  + `Model.observedlogpt` → `Model.observedlogp`
+  + `Model.potentiallogpt` → `Model.potentiallogp`
+  + `Model.varlogp_nojact` → `Model.varlogp_nojac`
+  + `logprob.joint_logpt` → `logprob.joint_logp`
 
 ## PyMC 4.0.0 (2022-06-03)
 

docs/source/learn/core_notebooks/pymc_aesara.ipynb

@@ -1844,7 +1844,7 @@
     }
    },
    "source": [
-    "`pymc` models provide some helpful routines to facilitating the conversion of `RandomVariable`s to probability functions. {meth}`~pymc.Model.logpt`, for instance can be used to extract the joint probability of all variables in the model:"
+    "`pymc` models provide some helpful routines to facilitating the conversion of `RandomVariable`s to probability functions. {meth}`~pymc.Model.logp`, for instance can be used to extract the joint probability of all variables in the model:"
    ]
   },
   {
@@ -1902,7 +1902,7 @@
     }
    ],
    "source": [
-    "aesara.dprint(model.logpt(sum=False))"
+    "aesara.dprint(model.logp(sum=False))"
    ]
   },
   {
@@ -2213,7 +2213,7 @@
     "sigma_log_value = model_2.rvs_to_values[sigma]\n",
     "x_value = model_2.rvs_to_values[x]\n",
     "# element-wise log-probability of the model (we do not take te sum)\n",
-    "logp_graph = at.stack(model_2.logpt(sum=False))\n",
+    "logp_graph = at.stack(model_2.logp(sum=False))\n",
     "# evaluate by passing concrete values\n",
     "logp_graph.eval({mu_value: 0, sigma_log_value: -10, x_value:0})"
    ]
@@ -2314,7 +2314,7 @@
     }
    },
    "source": [
-    "The {class}`~pymc.Model` class also has methods to extract the gradient ({meth}`~pymc.Model.dlogpt`) and the hessian ({meth}`~pymc.Model.d2logpt`) of the logp."
+    "The {class}`~pymc.Model` class also has methods to extract the gradient ({meth}`~pymc.Model.dlogp`) and the hessian ({meth}`~pymc.Model.d2logp`) of the logp."
    ]
   },
   {

pymc/backends/arviz.py

@@ -251,7 +251,7 @@ def _extract_log_likelihood(self, trace):
                 (
                     var,
                     self.model.compile_fn(
-                        self.model.logpt(var, sum=False)[0],
+                        self.model.logp(var, sum=False)[0],
                         inputs=self.model.value_vars,
                         on_unused_input="ignore",
                     ),
@@ -263,7 +263,7 @@ def _extract_log_likelihood(self, trace):
                 (
                     var,
                     self.model.compile_fn(
-                        self.model.logpt(var, sum=False)[0],
+                        self.model.logp(var, sum=False)[0],
                         inputs=self.model.value_vars,
                         on_unused_input="ignore",
                     ),

pymc/distributions/__init__.py

@@ -15,6 +15,7 @@
 from pymc.distributions.logprob import (  # isort:skip
     logcdf,
     logp,
+    joint_logp,
     joint_logpt,
 )
 
@@ -191,6 +192,7 @@
     "CAR",
     "PolyaGamma",
     "joint_logpt",
+    "joint_logp",
     "logp",
     "logcdf",
 ]

pymc/distributions/continuous.py

@@ -2558,7 +2558,7 @@ def logcdf(value, nu):
         return logcdf(Gamma.dist(alpha=nu / 2, beta=0.5), value)
 
 
-# TODO: Remove this once logpt for multiplication is working!
+# TODO: Remove this once logp for multiplication is working!
 class WeibullBetaRV(WeibullRV):
     ndims_params = [0, 0]
 

pymc/distributions/logprob.py

@@ -11,6 +11,7 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+import warnings
 
 from collections.abc import Mapping
 from typing import Dict, List, Optional, Sequence, Union
@@ -119,7 +120,15 @@ def _get_scaling(
 )
 
 
-def joint_logpt(
+def joint_logpt(*args, **kwargs):
+    warnings.warn(
+        "joint_logpt has been deprecated. Use joint_logp instead.",
+        FutureWarning,
+    )
+    return joint_logp(*args, **kwargs)
+
+
+def joint_logp(
     var: Union[TensorVariable, List[TensorVariable]],
     rv_values: Optional[Union[TensorVariable, Dict[TensorVariable, TensorVariable]]] = None,
     *,
@@ -159,14 +168,14 @@ def joint_logpt(
 
     """
     # TODO: In future when we drop support for tag.value_var most of the following
-    # logic can be removed and logpt can just be a wrapper function that calls aeppl's
+    # logic can be removed and logp can just be a wrapper function that calls aeppl's
     # joint_logprob directly.
 
     # If var is not a list make it one.
     if not isinstance(var, (list, tuple)):
         var = [var]
 
-    # If logpt isn't provided values it is assumed that the tagged value var or
+    # If logp isn't provided values it is assumed that the tagged value var or
     # observation is the value variable for that particular RV.
     if rv_values is None:
         rv_values = {}
@@ -251,7 +260,7 @@ def joint_logpt(
             "reference nonlocal variables."
         )
 
-    # aeppl returns the logpt for every single value term we provided to it. This includes
+    # aeppl returns the logp for every single value term we provided to it. This includes
     # the extra values we plugged in above, so we filter those we actually wanted in the
     # same order they were given in.
     logp_var_dict = {}

pymc/model.py

@@ -57,7 +57,7 @@
 )
 from pymc.blocking import DictToArrayBijection, RaveledVars
 from pymc.data import GenTensorVariable, Minibatch
-from pymc.distributions import joint_logpt
+from pymc.distributions import joint_logp
 from pymc.distributions.logprob import _get_scaling
 from pymc.distributions.transforms import _default_transform
 from pymc.exceptions import ImputationWarning, SamplingError, ShapeError, ShapeWarning
@@ -623,9 +623,9 @@ def logp_dlogp_function(self, grad_vars=None, tempered=False, **kwargs):
                     raise ValueError(f"Can only compute the gradient of continuous types: {var}")
 
         if tempered:
-            costs = [self.varlogpt, self.datalogpt]
+            costs = [self.varlogp, self.datalogp]
         else:
-            costs = [self.logpt()]
+            costs = [self.logp()]
 
         input_vars = {i for i in graph_inputs(costs) if not isinstance(i, Constant)}
         extra_vars = [self.rvs_to_values.get(var, var) for var in self.free_RVs]
@@ -654,7 +654,7 @@ def compile_logp(
             Whether to sum all logp terms or return elemwise logp for each variable.
             Defaults to True.
         """
-        return self.model.compile_fn(self.logpt(vars=vars, jacobian=jacobian, sum=sum))
+        return self.model.compile_fn(self.logp(vars=vars, jacobian=jacobian, sum=sum))
 
     def compile_dlogp(
         self,
@@ -671,7 +671,7 @@ def compile_dlogp(
         jacobian:
             Whether to include jacobian terms in logprob graph. Defaults to True.
         """
-        return self.model.compile_fn(self.dlogpt(vars=vars, jacobian=jacobian))
+        return self.model.compile_fn(self.dlogp(vars=vars, jacobian=jacobian))
 
     def compile_d2logp(
         self,
@@ -688,9 +688,16 @@ def compile_d2logp(
         jacobian:
             Whether to include jacobian terms in logprob graph. Defaults to True.
         """
-        return self.model.compile_fn(self.d2logpt(vars=vars, jacobian=jacobian))
+        return self.model.compile_fn(self.d2logp(vars=vars, jacobian=jacobian))
 
-    def logpt(
+    def logpt(self, *args, **kwargs):
+        warnings.warn(
+            "Model.logpt has been deprecated. Use Model.logp instead.",
+            FutureWarning,
+        )
+        return self.logp(*args, **kwargs)
+
+    def logp(
         self,
         vars: Optional[Union[Variable, Sequence[Variable]]] = None,
         jacobian: bool = True,
@@ -742,7 +749,7 @@ def logpt(
 
         rv_logps: List[TensorVariable] = []
         if rv_values:
-            rv_logps = joint_logpt(list(rv_values.keys()), rv_values, sum=False, jacobian=jacobian)
+            rv_logps = joint_logp(list(rv_values.keys()), rv_values, sum=False, jacobian=jacobian)
             assert isinstance(rv_logps, list)
 
         # Replace random variables by their value variables in potential terms
@@ -764,7 +771,14 @@ def logpt(
         logp_scalar.name = logp_scalar_name
         return logp_scalar
 
-    def dlogpt(
+    def dlogpt(self, *args, **kwargs):
+        warnings.warn(
+            "Model.dlogpt has been deprecated. Use Model.dlogp instead.",
+            FutureWarning,
+        )
+        return self.dlogp(*args, **kwargs)
+
+    def dlogp(
         self,
         vars: Optional[Union[Variable, Sequence[Variable]]] = None,
         jacobian: bool = True,
@@ -799,10 +813,17 @@ def dlogpt(
                         f"Requested variable {var} not found among the model variables"
                     )
 
-        cost = self.logpt(jacobian=jacobian)
+        cost = self.logp(jacobian=jacobian)
         return gradient(cost, value_vars)
 
-    def d2logpt(
+    def d2logpt(self, *args, **kwargs):
+        warnings.warn(
+            "Model.d2logpt has been deprecated. Use Model.d2logp instead.",
+            FutureWarning,
+        )
+        return self.d2logp(*args, **kwargs)
+
+    def d2logp(
         self,
         vars: Optional[Union[Variable, Sequence[Variable]]] = None,
         jacobian: bool = True,
@@ -837,34 +858,74 @@ def d2logpt(
                         f"Requested variable {var} not found among the model variables"
                     )
 
-        cost = self.logpt(jacobian=jacobian)
+        cost = self.logp(jacobian=jacobian)
         return hessian(cost, value_vars)
 
     @property
-    def datalogpt(self) -> Variable:
+    def datalogpt(self):
+        warnings.warn(
+            "Model.datalogpt has been deprecated. Use Model.datalogp instead.",
+            FutureWarning,
+        )
+        return self.datalogp
+
+    @property
+    def datalogp(self) -> Variable:
         """Aesara scalar of log-probability of the observed variables and
         potential terms"""
-        return self.observedlogpt + self.potentiallogpt
+        return self.observedlogp + self.potentiallogp
 
     @property
-    def varlogpt(self) -> Variable:
+    def varlogpt(self):
+        warnings.warn(
+            "Model.varlogpt has been deprecated. Use Model.varlogp instead.",
+            FutureWarning,
+        )
+        return self.varlogp
+
+    @property
+    def varlogp(self) -> Variable:
         """Aesara scalar of log-probability of the unobserved random variables
         (excluding deterministic)."""
-        return self.logpt(vars=self.free_RVs)
+        return self.logp(vars=self.free_RVs)
 
     @property
-    def varlogp_nojact(self) -> Variable:
+    def varlogp_nojact(self):
+        warnings.warn(
+            "Model.varlogp_nojact has been deprecated. Use Model.varlogp_nojac instead.",
+            FutureWarning,
+        )
+        return self.varlogp_nojac
+
+    @property
+    def varlogp_nojac(self) -> Variable:
         """Aesara scalar of log-probability of the unobserved random variables
         (excluding deterministic) without jacobian term."""
-        return self.logpt(vars=self.free_RVs, jacobian=False)
+        return self.logp(vars=self.free_RVs, jacobian=False)
+
+    @property
+    def observedlogpt(self):
+        warnings.warn(
+            "Model.observedlogpt has been deprecated. Use Model.observedlogp instead.",
+            FutureWarning,
+        )
+        return self.observedlogp
 
     @property
-    def observedlogpt(self) -> Variable:
+    def observedlogp(self) -> Variable:
         """Aesara scalar of log-probability of the observed variables"""
-        return self.logpt(vars=self.observed_RVs)
+        return self.logp(vars=self.observed_RVs)
+
+    @property
+    def potentiallogpt(self):
+        warnings.warn(
+            "Model.potentiallogpt has been deprecated. Use Model.potentiallogp instead.",
+            FutureWarning,
+        )
+        return self.potentiallogp
 
     @property
-    def potentiallogpt(self) -> Variable:
+    def potentiallogp(self) -> Variable:
         """Aesara scalar of log-probability of the Potential terms"""
         # Convert random variables in Potential expression into their log-likelihood
         # inputs and apply their transforms, if any
@@ -1755,7 +1816,7 @@ def point_logps(self, point=None, round_vals=2):
             point = self.initial_point()
 
         factors = self.basic_RVs + self.potentials
-        factor_logps_fn = [at.sum(factor) for factor in self.logpt(factors, sum=False)]
+        factor_logps_fn = [at.sum(factor) for factor in self.logp(factors, sum=False)]
         return {
             factor.name: np.round(np.asarray(factor_logp), round_vals)
             for factor, factor_logp in zip(

pymc/sampling.py

@@ -204,15 +204,15 @@ def assign_step_methods(model, step=None, methods=None, step_kwargs=None):
     # Use competence classmethods to select step methods for remaining
     # variables
     selected_steps = defaultdict(list)
-    model_logpt = model.logpt()
+    model_logp = model.logp()
 
     for var in model.value_vars:
         if var not in assigned_vars:
             # determine if a gradient can be computed
             has_gradient = var.dtype not in discrete_types
             if has_gradient:
                 try:
-                    tg.grad(model_logpt, var)
+                    tg.grad(model_logp, var)
                 except (NotImplementedError, tg.NullTypeGradError):
                     has_gradient = False
 

pymc/sampling_jax.py

@@ -100,10 +100,10 @@ def get_jaxified_graph(
 
 
 def get_jaxified_logp(model: Model, negative_logp=True) -> Callable:
-    model_logpt = model.logpt()
+    model_logp = model.logp()
     if not negative_logp:
-        model_logpt = -model_logpt
-    logp_fn = get_jaxified_graph(inputs=model.value_vars, outputs=[model_logpt])
+        model_logp = -model_logp
+    logp_fn = get_jaxified_graph(inputs=model.value_vars, outputs=[model_logp])
 
     def logp_fn_wrap(x):
         return logp_fn(*x)[0]
@@ -136,8 +136,8 @@ def _get_log_likelihood(model: Model, samples, backend=None) -> Dict:
     """Compute log-likelihood for all observations"""
     data = {}
     for v in model.observed_RVs:
-        v_elemwise_logpt = model.logpt(v, sum=False)
-        jax_fn = get_jaxified_graph(inputs=model.value_vars, outputs=v_elemwise_logpt)
+        v_elemwise_logp = model.logp(v, sum=False)
+        jax_fn = get_jaxified_graph(inputs=model.value_vars, outputs=v_elemwise_logp)
         result = jax.jit(jax.vmap(jax.vmap(jax_fn)), backend=backend)(*samples)[0]
         data[v.name] = result
     return data

pymc/smc/smc.py

@@ -219,10 +219,10 @@ def _initialize_kernel(self):
         shared = make_shared_replacements(initial_point, self.variables, self.model)
 
         self.prior_logp_func = _logp_forw(
-            initial_point, [self.model.varlogpt], self.variables, shared
+            initial_point, [self.model.varlogp], self.variables, shared
         )
         self.likelihood_logp_func = _logp_forw(
-            initial_point, [self.model.datalogpt], self.variables, shared
+            initial_point, [self.model.datalogp], self.variables, shared
         )
 
         priors = [self.prior_logp_func(sample) for sample in self.tempered_posterior]