Bump to 0.16.0 (#1917)

* Bump to 0.16.0

examples/annotation.py

@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Bayesian Models of Annotation")
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/ar2.py

@@ -138,7 +138,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="AR2 example")
     parser.add_argument("--num-data", nargs="?", default=142, type=int)
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)

examples/baseball.py

@@ -210,7 +210,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Baseball batting average using MCMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=3000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1500, type=int)

examples/bnn.py

@@ -160,7 +160,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Bayesian neural network example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=2000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/covtype.py

@@ -206,7 +206,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-samples", default=1000, type=int, help="number of samples"

examples/funnel.py

@@ -139,7 +139,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(
         description="Non-centered reparameterization example"
     )

examples/gaussian_shells.py

@@ -120,7 +120,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
 
     parser = argparse.ArgumentParser(description="Nested sampler for Gaussian shells")
     parser.add_argument("-n", "--num-samples", nargs="?", default=10000, type=int)

examples/gp.py

@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Gaussian Process example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/hmm.py

@@ -263,7 +263,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Semi-supervised Hidden Markov Model")
     parser.add_argument("--num-categories", default=3, type=int)
     parser.add_argument("--num-words", default=10, type=int)

examples/holt_winters.py

@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Holt-Winters")
     parser.add_argument("--T", nargs="?", default=6, type=int)
     parser.add_argument("--future", nargs="?", default=1, type=int)

examples/horseshoe_regression.py

@@ -162,7 +162,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Horseshoe regression example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=2000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/minipyro.py

@@ -58,7 +58,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Mini Pyro demo")
     parser.add_argument("-f", "--full-pyro", action="store_true", default=False)
     parser.add_argument("-n", "--num-steps", default=1001, type=int)

examples/mortality.py

@@ -220,7 +220,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
 
     parser = argparse.ArgumentParser(description="Mortality regression model")
     parser.add_argument("-n", "--num-samples", nargs="?", default=500, type=int)

examples/neutra.py

@@ -197,7 +197,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="NeuTra HMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=4000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/ode.py

@@ -117,7 +117,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Predator-Prey Model")
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)

examples/prodlda.py

@@ -315,7 +315,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(
         description="Probabilistic topic modelling with Flax and Haiku"
     )

examples/proportion_test.py

@@ -158,7 +158,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Testing whether  ")
     parser.add_argument("-n", "--num-samples", nargs="?", default=500, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1500, type=int)

examples/sparse_regression.py

@@ -384,7 +384,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Gaussian Process example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=500, type=int)

examples/stochastic_volatility.py

@@ -122,7 +122,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Stochastic Volatility Model")
     parser.add_argument("-n", "--num-samples", nargs="?", default=600, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=600, type=int)

examples/thompson_sampling.py

@@ -292,7 +292,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Thompson sampling example")
     parser.add_argument(
         "--num-random", nargs="?", default=2, type=int, help="number of random draws"

examples/toy_mixture_model_discrete_enumeration.py

@@ -126,7 +126,7 @@ def get_true_pred_CPDs(CPD, posterior_param):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="Toy mixture model")
     parser.add_argument("-n", "--num-steps", default=4000, type=int)
     parser.add_argument("-o", "--num-obs", default=10000, type=int)

examples/ucbadmit.py

@@ -151,7 +151,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(
         description="UCBadmit gender discrimination using HMC"
     )

examples/vae.py

@@ -160,7 +160,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.3")
+    assert numpyro.__version__.startswith("0.16.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-epochs", default=15, type=int, help="number of training epochs"

notebooks/source/bad_posterior_geometry.ipynb

@@ -49,7 +49,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.infer import MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
+    "assert numpyro.__version__.startswith(\"0.16.0\")\n",
     "\n",
     "# NB: replace cpu by gpu to run this notebook on gpu\n",
     "numpyro.set_platform(\"cpu\")"

notebooks/source/bayesian_hierarchical_linear_regression.ipynb

@@ -246,7 +246,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.infer import MCMC, NUTS, Predictive\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/bayesian_hierarchical_stacking.ipynb

@@ -97,7 +97,7 @@
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
     "numpyro.set_host_device_count(4)\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/bayesian_imputation.ipynb

@@ -52,7 +52,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/bayesian_regression.ipynb

@@ -91,7 +91,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/censoring.ipynb

@@ -60,7 +60,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=0)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
+    "assert numpyro.__version__.startswith(\"0.16.0\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

notebooks/source/gmm.ipynb

@@ -54,7 +54,7 @@
     "%matplotlib inline\n",
     "\n",
     "smoke_test = \"CI\" in os.environ\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/hsgp_example.ipynb

@@ -62,7 +62,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=42)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
+    "assert numpyro.__version__.startswith(\"0.16.0\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

notebooks/source/logistic_regression.ipynb

@@ -41,7 +41,7 @@
     "from numpyro.examples.datasets import COVTYPE, load_dataset\n",
     "from numpyro.infer import HMC, MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
+    "assert numpyro.__version__.startswith(\"0.16.0\")\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"

notebooks/source/model_rendering.ipynb

@@ -38,7 +38,7 @@
     "import numpyro.distributions as dist\n",
     "import numpyro.distributions.constraints as constraints\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/ordinal_regression.ipynb

@@ -54,7 +54,7 @@
     "from numpyro.infer import MCMC, NUTS\n",
     "from numpyro.infer.reparam import TransformReparam\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

notebooks/source/other_samplers.ipynb

@@ -67,7 +67,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=42)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
+    "assert numpyro.__version__.startswith(\"0.16.0\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

notebooks/source/time_series_forecasting.ipynb

@@ -48,7 +48,7 @@
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
     "numpyro.set_host_device_count(4)\n",
-    "assert numpyro.__version__.startswith(\"0.15.3\")"
+    "assert numpyro.__version__.startswith(\"0.16.0\")"
    ]
   },
   {

numpyro/contrib/control_flow/scan.py

@@ -198,9 +198,10 @@ def body_fn(wrapped_carry, x, prefix=None):
             )
         return (i + 1, rng_key, new_carry), (PytreeTrace(trace), y)
 
-    with handlers.block(
-        hide_fn=lambda site: not site["name"].startswith("_PREV_")
-    ), enum(first_available_dim=first_available_dim):
+    with (
+        handlers.block(hide_fn=lambda site: not site["name"].startswith("_PREV_")),
+        enum(first_available_dim=first_available_dim),
+    ):
         wrapped_carry = (0, rng_key, init)
         y0s = []
         # We run unroll_steps + 1 where the last step is used for rolling with `lax.scan`

numpyro/infer/autoguide.py

@@ -1463,8 +1463,10 @@ def _sample_latent(self, *args, **kwargs):
         if self.global_guide is not None:
             global_latents = self.global_guide(*args, **kwargs)
             rng_key = numpyro.prng_key()
-            with handlers.block(), handlers.seed(rng_seed=rng_key), handlers.substitute(
-                data=global_latents
+            with (
+                handlers.block(),
+                handlers.seed(rng_seed=rng_key),
+                handlers.substitute(data=global_latents),
             ):
                 global_outputs = self.global_guide.model(*args, **kwargs)
             local_args = (global_outputs,)
@@ -1575,9 +1577,12 @@ def fn(x):
             if self.local_guide is not None:
                 key = numpyro.prng_key()
                 subsample_guide = partial(_subsample_model, self.local_guide)
-                with handlers.block(), handlers.trace() as tr, handlers.seed(
-                    rng_seed=key
-                ), handlers.substitute(data=local_guide_params):
+                with (
+                    handlers.block(),
+                    handlers.trace() as tr,
+                    handlers.seed(rng_seed=key),
+                    handlers.substitute(data=local_guide_params),
+                ):
                     with warnings.catch_warnings():
                         warnings.simplefilter("ignore")
                         subsample_guide(*local_args, **local_kwargs)

numpyro/infer/elbo.py

@@ -893,8 +893,11 @@ def get_importance_trace_enum(
         trace as _trace,
     )
 
-    with plate_to_enum_plate(), enum(
-        first_available_dim=(-max_plate_nesting - 1) if max_plate_nesting else None
+    with (
+        plate_to_enum_plate(),
+        enum(
+            first_available_dim=(-max_plate_nesting - 1) if max_plate_nesting else None
+        ),
     ):
         guide = substitute(guide, data=params)
         with _without_rsample_stop_gradient():