Bump to version 0.12.0 (#1593)

fehiepsi · web-flow · commit f981b29f0fbe · 2023-05-30T22:24:59.000-04:00
* Bump to version 0.12.0

* Fix docs of MCMC class which does not display sharding example

* add get_transforms and unconstrain_fn to docs
diff --git a/docs/source/utilities.rst b/docs/source/utilities.rst
@@ -40,6 +40,10 @@ log_density
 -----------
 .. autofunction:: numpyro.infer.util.log_density
 
+get_transforms
+--------------
+.. autofunction:: numpyro.infer.util.get_transforms
+
 transform_fn
 ------------
 .. autofunction:: numpyro.infer.util.transform_fn
@@ -48,6 +52,10 @@ constrain_fn
 ------------
 .. autofunction:: numpyro.infer.util.constrain_fn
 
+unconstrain_fn
+--------------
+.. autofunction:: numpyro.infer.util.unconstrain_fn
+
 potential_energy
 ----------------
 .. autofunction:: numpyro.infer.util.potential_energy
diff --git a/examples/annotation.py b/examples/annotation.py
@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/ar2.py b/examples/ar2.py
@@ -114,7 +114,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/baseball.py b/examples/baseball.py
@@ -210,7 +210,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/bnn.py b/examples/bnn.py
@@ -160,7 +160,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/covtype.py b/examples/covtype.py
@@ -206,7 +206,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-samples", default=1000, type=int, help="number of samples"
diff --git a/examples/funnel.py b/examples/funnel.py
@@ -139,7 +139,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(
         description="Non-centered reparameterization example"
     )
diff --git a/examples/gaussian_shells.py b/examples/gaussian_shells.py
@@ -120,7 +120,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(description="Nested sampler for Gaussian shells")
     parser.add_argument("-n", "--num-samples", nargs="?", default=10000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)
diff --git a/examples/gp.py b/examples/gp.py
@@ -170,7 +170,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/hmm.py b/examples/hmm.py
@@ -263,7 +263,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/holt_winters.py b/examples/holt_winters.py
@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(description="Holt-Winters")
     parser.add_argument("--T", nargs="?", default=6, type=int)
     parser.add_argument("--future", nargs="?", default=1, type=int)
diff --git a/examples/horseshoe_regression.py b/examples/horseshoe_regression.py
@@ -162,7 +162,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/minipyro.py b/examples/minipyro.py
@@ -58,7 +58,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/mortality.py b/examples/mortality.py
@@ -220,7 +220,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
 
     parser = argparse.ArgumentParser(description="Mortality regression model")
     parser.add_argument("-n", "--num-samples", nargs="?", default=500, type=int)
diff --git a/examples/neutra.py b/examples/neutra.py
@@ -197,7 +197,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/ode.py b/examples/ode.py
@@ -117,7 +117,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/prodlda.py b/examples/prodlda.py
@@ -314,7 +314,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(
         description="Probabilistic topic modelling with Flax and Haiku"
     )
diff --git a/examples/proportion_test.py b/examples/proportion_test.py
@@ -160,7 +160,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/sparse_regression.py b/examples/sparse_regression.py
@@ -384,7 +384,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/stochastic_volatility.py b/examples/stochastic_volatility.py
@@ -122,7 +122,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/thompson_sampling.py b/examples/thompson_sampling.py
@@ -292,7 +292,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(description="Thompson sampling example")
     parser.add_argument(
         "--num-random", nargs="?", default=2, type=int, help="number of random draws"
diff --git a/examples/toy_mixture_model_discrete_enumeration.py b/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("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     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)
diff --git a/examples/ucbadmit.py b/examples/ucbadmit.py
@@ -151,7 +151,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(
         description="UCBadmit gender discrimination using HMC"
     )
diff --git a/examples/vae.py b/examples/vae.py
@@ -160,7 +160,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.11.0")
+    assert numpyro.__version__.startswith("0.12.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-epochs", default=15, type=int, help="number of training epochs"
diff --git a/notebooks/source/bad_posterior_geometry.ipynb b/notebooks/source/bad_posterior_geometry.ipynb
@@ -50,7 +50,7 @@
     "\n",
     "from numpyro.infer import MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")\n",
+    "assert numpyro.__version__.startswith(\"0.12.0\")\n",
     "\n",
     "# NB: replace cpu by gpu to run this notebook on gpu\n",
     "numpyro.set_platform(\"cpu\")"
diff --git a/notebooks/source/bayesian_hierarchical_linear_regression.ipynb b/notebooks/source/bayesian_hierarchical_linear_regression.ipynb
@@ -245,7 +245,7 @@
     "import numpyro.distributions as dist\n",
     "from jax import random\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_hierarchical_stacking.ipynb b/notebooks/source/bayesian_hierarchical_stacking.ipynb
@@ -96,7 +96,7 @@
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
     "numpyro.set_host_device_count(4)\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_imputation.ipynb b/notebooks/source/bayesian_imputation.ipynb
@@ -55,7 +55,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_regression.ipynb b/notebooks/source/bayesian_regression.ipynb
@@ -95,7 +95,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ],
    "execution_count": 2,
    "outputs": []
diff --git a/notebooks/source/gmm.ipynb b/notebooks/source/gmm.ipynb
@@ -54,7 +54,7 @@
     "%matplotlib inline\n",
     "\n",
     "smoke_test = \"CI\" in os.environ\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/logistic_regression.ipynb b/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(\"0.11.0\")\n",
+    "assert numpyro.__version__.startswith(\"0.12.0\")\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"
diff --git a/notebooks/source/model_rendering.ipynb b/notebooks/source/model_rendering.ipynb
@@ -37,7 +37,7 @@
     "import numpyro.distributions as dist\n",
     "import numpyro.distributions.constraints as constraints\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/ordinal_regression.ipynb b/notebooks/source/ordinal_regression.ipynb
@@ -53,7 +53,7 @@
     "import pandas as pd\n",
     "import seaborn as sns\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/notebooks/source/time_series_forecasting.ipynb b/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(\"0.11.0\")"
+    "assert numpyro.__version__.startswith(\"0.12.0\")"
    ]
   },
   {
diff --git a/numpyro/infer/mcmc.py b/numpyro/infer/mcmc.py
@@ -206,11 +206,11 @@ class MCMC(object):
         correctly. If you are using Jupyter Notebook or Jupyter Lab, please also install the
         corresponding extension package like `widgetsnbextension` or `jupyterlab_widgets`.
 
-    ..note:: If your dataset is large and you have access to multiple acceleration devices,
+    .. note:: If your dataset is large and you have access to multiple acceleration devices,
         you can distribute the computation across multiple devices. Make sure that your jax version
         is v0.4.4 or newer. For example,
 
-        .. code-block::python
+        .. code-block:: python
 
             import jax
             from jax.experimental import mesh_utils
diff --git a/numpyro/version.py b/numpyro/version.py
@@ -1,4 +1,4 @@
 # Copyright Contributors to the Pyro project.
 # SPDX-License-Identifier: Apache-2.0
 
-__version__ = "0.11.0"
+__version__ = "0.12.0"

Original file line number	Diff line number	Diff line change
`@@ -139,7 +139,7 @@ def main(args):`
`139`	`139`
`140`	`140`
`141`	`141`	`if __name__ == "__main__":`
`142`		`- assert numpyro.__version__.startswith("0.11.0")`
	`142`	`+ assert numpyro.__version__.startswith("0.12.0")`
`143`	`143`	`parser = argparse.ArgumentParser(`
`144`	`144`	`description="Non-centered reparameterization example"`
`145`	`145`	`)`