Update posterior predictive sampling and notebook (#5268)

* improve idata-sample_posterior_predictive integration and add thinning example to docstring
* remove plot_posterior_predictive_glm (arviz.plot_lm should be used now)

Co-authored-by: Michael Osthege <michael.osthege@outlook.com>

.github/workflows/pytest.yml

@@ -46,7 +46,6 @@ jobs:
             --ignore=pymc/tests/test_dist_math.py
             --ignore=pymc/tests/test_minibatches.py
             --ignore=pymc/tests/test_pickling.py
-            --ignore=pymc/tests/test_plots.py
             --ignore=pymc/tests/test_updates.py
             --ignore=pymc/tests/test_gp.py
             --ignore=pymc/tests/test_model.py
@@ -68,7 +67,6 @@ jobs:
             pymc/tests/test_dist_math.py
             pymc/tests/test_minibatches.py
             pymc/tests/test_pickling.py
-            pymc/tests/test_plots.py
             pymc/tests/test_updates.py
             pymc/tests/test_transforms.py
 

pymc/backends/arviz.py

@@ -138,7 +138,6 @@ def __init__(
         dims: Optional[DimSpec] = None,
         model=None,
         save_warmup: Optional[bool] = None,
-        density_dist_obs: bool = True,
     ):
 
         self.save_warmup = rcParams["data.save_warmup"] if save_warmup is None else save_warmup
@@ -175,29 +174,11 @@ def __init__(
         self.log_likelihood = log_likelihood
         self.predictions = predictions
 
-        def arbitrary_element(dct: Dict[Any, np.ndarray]) -> np.ndarray:
-            return next(iter(dct.values()))
-
-        if trace is None:
-            # if you have a posterior_predictive built with keep_dims,
-            # you'll lose here, but there's nothing I can do about that.
-            self.nchains = 1
-            get_from = None
-            if predictions is not None:
-                get_from = predictions
-            elif posterior_predictive is not None:
-                get_from = posterior_predictive
-            elif prior is not None:
-                get_from = prior
-            if get_from is None:
-                # pylint: disable=line-too-long
-                raise ValueError(
-                    "When constructing InferenceData must have at least"
-                    " one of trace, prior, posterior_predictive or predictions."
-                )
-
-            aelem = arbitrary_element(get_from)
-            self.ndraws = aelem.shape[0]
+        if all(elem is None for elem in (trace, predictions, posterior_predictive, prior)):
+            raise ValueError(
+                "When constructing InferenceData you must pass at least"
+                " one of trace, prior, posterior_predictive or predictions."
+            )
 
         self.coords = {**self.model.coords, **(coords or {})}
         self.coords = {
@@ -214,7 +195,6 @@ def arbitrary_element(dct: Dict[Any, np.ndarray]) -> np.ndarray:
             }
             self.dims = {**model_dims, **self.dims}
 
-        self.density_dist_obs = density_dist_obs
         self.observations = find_observations(self.model)
 
     def split_trace(self) -> Tuple[Union[None, "MultiTrace"], Union[None, "MultiTrace"]]:
@@ -396,34 +376,35 @@ def log_likelihood_to_xarray(self):
             ),
         )
 
-    def translate_posterior_predictive_dict_to_xarray(self, dct) -> xr.Dataset:
+    def translate_posterior_predictive_dict_to_xarray(self, dct, kind) -> xr.Dataset:
         """Take Dict of variables to numpy ndarrays (samples) and translate into dataset."""
         data = {}
+        warning_vars = []
         for k, ary in dct.items():
-            shape = ary.shape
-            if shape[0] == self.nchains and shape[1] == self.ndraws:
+            if (ary.shape[0] == self.nchains) and (ary.shape[1] == self.ndraws):
                 data[k] = ary
-            elif shape[0] == self.nchains * self.ndraws:
-                data[k] = ary.reshape((self.nchains, self.ndraws, *shape[1:]))
             else:
                 data[k] = np.expand_dims(ary, 0)
-                # pylint: disable=line-too-long
-                _log.warning(
-                    "posterior predictive variable %s's shape not compatible with number of chains and draws. "
-                    "This can mean that some draws or even whole chains are not represented.",
-                    k,
-                )
+                warning_vars.append(k)
+        warnings.warn(
+            f"The shape of variables {', '.join(warning_vars)} in {kind} group is not compatible "
+            "with number of chains and draws. The automatic dimension naming might not have worked. "
+            "This can also mean that some draws or even whole chains are not represented.",
+            UserWarning,
+        )
         return dict_to_dataset(data, library=pymc, coords=self.coords, dims=self.dims)
 
     @requires(["posterior_predictive"])
     def posterior_predictive_to_xarray(self):
         """Convert posterior_predictive samples to xarray."""
-        return self.translate_posterior_predictive_dict_to_xarray(self.posterior_predictive)
+        return self.translate_posterior_predictive_dict_to_xarray(
+            self.posterior_predictive, "posterior_predictive"
+        )
 
     @requires(["predictions"])
     def predictions_to_xarray(self):
         """Convert predictions (out of sample predictions) to xarray."""
-        return self.translate_posterior_predictive_dict_to_xarray(self.predictions)
+        return self.translate_posterior_predictive_dict_to_xarray(self.predictions, "predictions")
 
     def priors_to_xarray(self):
         """Convert prior samples (and if possible prior predictive too) to xarray."""
@@ -545,7 +526,6 @@ def to_inference_data(
     dims: Optional[DimSpec] = None,
     model: Optional["Model"] = None,
     save_warmup: Optional[bool] = None,
-    density_dist_obs: bool = True,
 ) -> InferenceData:
     """Convert pymc data into an InferenceData object.
 
@@ -578,9 +558,6 @@ def to_inference_data(
     save_warmup : bool, optional
         Save warmup iterations InferenceData object. If not defined, use default
         defined by the rcParams.
-    density_dist_obs : bool, default True
-        Store variables passed with ``observed`` arg to
-        :class:`~pymc.distributions.DensityDist` in the generated InferenceData.
 
     Returns
     -------
@@ -598,7 +575,6 @@ def to_inference_data(
         dims=dims,
         model=model,
         save_warmup=save_warmup,
-        density_dist_obs=density_dist_obs,
     ).to_inference_data()
 
 
@@ -620,6 +596,7 @@ def predictions_to_inference_data(
     predictions: Dict[str, np.ndarray]
         The predictions are the return value of :func:`~pymc.sample_posterior_predictive`,
         a dictionary of strings (variable names) to numpy ndarrays (draws).
+        Requires the arrays to follow the convention ``chain, draw, *shape``.
     posterior_trace: MultiTrace
         This should be a trace that has been thinned appropriately for
         ``pymc.sample_posterior_predictive``. Specifically, any variable whose shape is
@@ -648,14 +625,21 @@ def predictions_to_inference_data(
         raise ValueError(
             "Do not pass True for inplace unless passing" "an existing InferenceData as idata_orig"
         )
-    new_idata = InferenceDataConverter(
+    converter = InferenceDataConverter(
         trace=posterior_trace,
         predictions=predictions,
         model=model,
         coords=coords,
         dims=dims,
         log_likelihood=False,
-    ).to_inference_data()
+    )
+    if hasattr(idata_orig, "posterior"):
+        converter.nchains = idata_orig.posterior.dims["chain"]
+        converter.ndraws = idata_orig.posterior.dims["draw"]
+    else:
+        aelem = next(iter(predictions.values()))
+        converter.nchains, converter.ndraws = aelem.shape[:2]
+    new_idata = converter.to_inference_data()
     if idata_orig is None:
         return new_idata
     elif inplace:

pymc/plots/__init__.py

@@ -56,8 +56,6 @@ def wrapped(*args, **kwargs):
 compareplot = alias_deprecation(az.plot_compare, alias="compareplot")
 
 
-from pymc.plots.posteriorplot import plot_posterior_predictive_glm
-
 __all__ = tuple(az.plots.__all__) + (
     "autocorrplot",
     "compareplot",
@@ -67,5 +65,4 @@ def wrapped(*args, **kwargs):
     "energyplot",
     "densityplot",
     "pairplot",
-    "plot_posterior_predictive_glm",
 )