update model_comp examples and ppc_w to work with idata

RELEASE-NOTES.md

@@ -5,9 +5,12 @@
 ### Maintenance
 - Mentioned the way to do any random walk with `theano.tensor.cumsum()` in `GaussianRandomWalk` docstrings (see [#4048](https://github.com/pymc-devs/pymc3/pull/4048)).
 
+
 ### Documentation
 
 ### New features
+- `sample_posterior_predictive_w` can now feed on `xarray.Dataset` - e.g. from `InferenceData.posterior`. (see [#4042](https://github.com/pymc-devs/pymc3/pull/4042))
+
 
 ## PyMC3 3.9.3 (11 August 2020)
 
@@ -27,6 +30,7 @@
 
 _NB: The `docs/*` folder is still removed from the tarball due to an upload size limit on PyPi._
 
+
 ## PyMC3 3.9.2 (24 June 2020)
 ### Maintenance
 - Warning added in GP module when `input_dim` is lower than the number of columns in `X` to compute the covariance function (see [#3974](https://github.com/pymc-devs/pymc3/pull/3974)).

pymc3/sampling.py

@@ -226,9 +226,7 @@ def _print_step_hierarchy(s, level=0):
     else:
         varnames = ", ".join(
             [
-                get_untransformed_name(v.name)
-                if is_transformed_name(v.name)
-                else v.name
+                get_untransformed_name(v.name) if is_transformed_name(v.name) else v.name
                 for v in s.vars
             ]
         )
@@ -491,10 +489,7 @@ def sample(
                 start = start_
         except (AttributeError, NotImplementedError, tg.NullTypeGradError):
             # gradient computation failed
-            _log.info(
-                "Initializing NUTS failed. "
-                "Falling back to elementwise auto-assignment."
-            )
+            _log.info("Initializing NUTS failed. " "Falling back to elementwise auto-assignment.")
             _log.debug("Exception in init nuts", exec_info=True)
             step = assign_step_methods(model, step, step_kwargs=kwargs)
     else:
@@ -559,9 +554,7 @@ def sample(
             has_demcmc = np.any(
                 [
                     isinstance(m, DEMetropolis)
-                    for m in (
-                        step.methods if isinstance(step, CompoundStep) else [step]
-                    )
+                    for m in (step.methods if isinstance(step, CompoundStep) else [step])
                 ]
             )
             _log.info("Population sampling ({} chains)".format(chains))
@@ -625,9 +618,7 @@ def sample(
 
     if compute_convergence_checks:
         if draws - tune < 100:
-            warnings.warn(
-                "The number of samples is too small to check convergence reliably."
-            )
+            warnings.warn("The number of samples is too small to check convergence reliably.")
         else:
             trace.report._run_convergence_checks(idata, model)
     trace.report._log_summary()
@@ -664,14 +655,7 @@ def _check_start_shape(model, start):
 
 
 def _sample_many(
-    draws,
-    chain: int,
-    chains: int,
-    start: list,
-    random_seed: list,
-    step,
-    callback=None,
-    **kwargs,
+    draws, chain: int, chains: int, start: list, random_seed: list, step, callback=None, **kwargs,
 ):
     """Samples all chains sequentially.
 
@@ -833,9 +817,7 @@ def _sample(
     """
     skip_first = kwargs.get("skip_first", 0)
 
-    sampling = _iter_sample(
-        draws, step, start, trace, chain, tune, model, random_seed, callback
-    )
+    sampling = _iter_sample(draws, step, start, trace, chain, tune, model, random_seed, callback)
     _pbar_data = {"chain": chain, "divergences": 0}
     _desc = "Sampling chain {chain:d}, {divergences:,d} divergences"
     if progressbar:
@@ -909,9 +891,7 @@ def iter_sample(
         for trace in iter_sample(500, step):
             ...
     """
-    sampling = _iter_sample(
-        draws, step, start, trace, chain, tune, model, random_seed, callback
-    )
+    sampling = _iter_sample(draws, step, start, trace, chain, tune, model, random_seed, callback)
     for i, (strace, _) in enumerate(sampling):
         yield MultiTrace([strace[: i + 1]])
 
@@ -1012,8 +992,7 @@ def _iter_sample(
             if callback is not None:
                 warns = getattr(step, "warnings", None)
                 callback(
-                    trace=strace,
-                    draw=Draw(chain, i == draws, i, i < tune, stats, point, warns),
+                    trace=strace, draw=Draw(chain, i == draws, i, i < tune, stats, point, warns),
                 )
 
             yield strace, diverging
@@ -1067,9 +1046,7 @@ def __init__(self, steppers, parallelize, progressbar=True):
                 import multiprocessing
 
                 for c, stepper in (
-                    enumerate(progress_bar(steppers))
-                    if progressbar
-                    else enumerate(steppers)
+                    enumerate(progress_bar(steppers)) if progressbar else enumerate(steppers)
                 ):
                     secondary_end, primary_end = multiprocessing.Pipe()
                     stepper_dumps = pickle.dumps(stepper, protocol=4)
@@ -1136,9 +1113,7 @@ def _run_secondary(c, stepper_dumps, secondary_end):
             # but rather a CompoundStep. PopulationArrayStepShared.population
             # has to be updated, therefore we identify the substeppers first.
             population_steppers = []
-            for sm in (
-                stepper.methods if isinstance(stepper, CompoundStep) else [stepper]
-            ):
+            for sm in stepper.methods if isinstance(stepper, CompoundStep) else [stepper]:
                 if isinstance(sm, arraystep.PopulationArrayStepShared):
                     population_steppers.append(sm)
             while True:
@@ -1682,13 +1657,9 @@ def sample_posterior_predictive(
             nchain = 1
 
     if keep_size and samples is not None:
-        raise IncorrectArgumentsError(
-            "Should not specify both keep_size and samples arguments"
-        )
+        raise IncorrectArgumentsError("Should not specify both keep_size and samples arguments")
     if keep_size and size is not None:
-        raise IncorrectArgumentsError(
-            "Should not specify both keep_size and size arguments"
-        )
+        raise IncorrectArgumentsError("Should not specify both keep_size and size arguments")
 
     if samples is None:
         if isinstance(_trace, MultiTrace):
@@ -1714,15 +1685,11 @@ def sample_posterior_predictive(
 
     if var_names is not None:
         if vars is not None:
-            raise IncorrectArgumentsError(
-                "Should not specify both vars and var_names arguments."
-            )
+            raise IncorrectArgumentsError("Should not specify both vars and var_names arguments.")
         else:
             vars = [model[x] for x in var_names]
     elif vars is not None:  # var_names is None, and vars is not.
-        warnings.warn(
-            "vars argument is deprecated in favor of var_names.", DeprecationWarning
-        )
+        warnings.warn("vars argument is deprecated in favor of var_names.", DeprecationWarning)
     if vars is None:
         vars = model.observed_RVs
 
@@ -1741,11 +1708,7 @@ def sample_posterior_predictive(
                 # the trace object will either be a MultiTrace (and have _straces)...
                 if hasattr(_trace, "_straces"):
                     chain_idx, point_idx = np.divmod(idx, len_trace)
-                    param = (
-                        cast(MultiTrace, _trace)
-                        ._straces[chain_idx % nchain]
-                        .point(point_idx)
-                    )
+                    param = cast(MultiTrace, _trace)._straces[chain_idx % nchain].point(point_idx)
                 # ... or a PointList
                 else:
                     param = cast(PointList, _trace)[idx % len_trace]
@@ -1783,9 +1746,9 @@ def sample_posterior_predictive_w(
     Parameters
     ----------
     traces : list or list of lists
-        List of traces generated from MCMC sampling, or a list of list
-        containing dicts from find_MAP() or points. The number of traces should
-        be equal to the number of weights.
+        List of traces generated from MCMC sampling (xarray.Dataset, arviz.InferenceData, or 
+        MultiTrace), or a list of list containing dicts from find_MAP() or points. The number of
+        traces should be equal to the number of weights.
     samples : int, optional
         Number of posterior predictive samples to generate. Defaults to the
         length of the shorter trace in traces.
@@ -1811,6 +1774,17 @@ def sample_posterior_predictive_w(
     """
     np.random.seed(random_seed)
 
+    if isinstance(traces[0], InferenceData):
+        n_samples = [
+            trace.posterior.sizes["chain"] * trace.posterior.sizes["draw"] for trace in traces
+        ]
+        traces = [dataset_to_point_dict(trace.posterior) for trace in traces]
+    elif isinstance(traces[0], xarray.Dataset):
+        n_samples = [trace.sizes["chain"] * trace.sizes["draw"] for trace in traces]
+        traces = [dataset_to_point_dict(trace) for trace in traces]
+    else:
+        n_samples = [len(i) * i.nchains for i in traces]
+
     if models is None:
         models = [modelcontext(models)] * len(traces)
 
@@ -1830,7 +1804,7 @@ def sample_posterior_predictive_w(
     weights = np.asarray(weights)
     p = weights / np.sum(weights)
 
-    min_tr = min([len(i) * i.nchains for i in traces])
+    min_tr = min(n_samples)
 
     n = (min_tr * p).astype("int")
     # ensure n sum up to min_tr
@@ -1933,18 +1907,15 @@ def sample_prior_predictive(
     if vars is None and var_names is None:
         prior_pred_vars = model.observed_RVs
         prior_vars = (
-            get_default_varnames(model.unobserved_RVs, include_transformed=True)
-            + model.potentials
+            get_default_varnames(model.unobserved_RVs, include_transformed=True) + model.potentials
         )
         vars_ = [var.name for var in prior_vars + prior_pred_vars]
         vars = set(vars_)
     elif vars is None:
         vars = var_names
         vars_ = vars
     elif vars is not None:
-        warnings.warn(
-            "vars argument is deprecated in favor of var_names.", DeprecationWarning
-        )
+        warnings.warn("vars argument is deprecated in favor of var_names.", DeprecationWarning)
         vars_ = vars
     else:
         raise ValueError("Cannot supply both vars and var_names arguments.")
@@ -1974,13 +1945,7 @@ def sample_prior_predictive(
 
 
 def init_nuts(
-    init="auto",
-    chains=1,
-    n_init=500000,
-    model=None,
-    random_seed=None,
-    progressbar=True,
-    **kwargs,
+    init="auto", chains=1, n_init=500000, model=None, random_seed=None, progressbar=True, **kwargs,
 ):
     """Set up the mass matrix initialization for NUTS.
 
@@ -2036,9 +2001,7 @@ def init_nuts(
     if set(vars) != set(model.vars):
         raise ValueError("Must use init_nuts on all variables of a model.")
     if not all_continuous(vars):
-        raise ValueError(
-            "init_nuts can only be used for models with only " "continuous variables."
-        )
+        raise ValueError("init_nuts can only be used for models with only " "continuous variables.")
 
     if not isinstance(init, str):
         raise TypeError("init must be a string.")
@@ -2092,9 +2055,7 @@ def init_nuts(
         mean = approx.bij.rmap(approx.mean.get_value())
         mean = model.dict_to_array(mean)
         weight = 50
-        potential = quadpotential.QuadPotentialDiagAdaptGrad(
-            model.ndim, mean, cov, weight
-        )
+        potential = quadpotential.QuadPotentialDiagAdaptGrad(model.ndim, mean, cov, weight)
     elif init == "advi+adapt_diag":
         approx = pm.fit(
             random_seed=random_seed,

pymc3/tests/test_sampling.py

@@ -718,22 +718,24 @@ def test_sample_posterior_predictive_w(self):
             mu = pm.Normal("mu", mu=0, sigma=1)
             y = pm.Normal("y", mu=mu, sigma=1, observed=data0)
             trace_0 = pm.sample()
+            idata_0 = az.from_pymc3(trace_0)
 
         with pm.Model() as model_1:
             mu = pm.Normal("mu", mu=0, sigma=1, shape=len(data0))
             y = pm.Normal("y", mu=mu, sigma=1, observed=data0)
             trace_1 = pm.sample()
-
-        traces = [trace_0, trace_0]
-        models = [model_0, model_0]
-        ppc = pm.sample_posterior_predictive_w(traces, 100, models)
-        assert ppc["y"].shape == (100, 500)
+            idata_1 = az.from_pymc3(trace_1)
 
         traces = [trace_0, trace_1]
+        idatas = [idata_0, idata_1]
         models = [model_0, model_1]
+
         ppc = pm.sample_posterior_predictive_w(traces, 100, models)
         assert ppc["y"].shape == (100, 500)
 
+        ppc = pm.sample_posterior_predictive_w(idatas, 100, models)
+        assert ppc["y"].shape == (100, 500)
+
 
 @pytest.mark.parametrize(
     "method",