Bump to 0.15.3 (#1858)

* Bump to 0.15.3 * update gitignore * remove jax's clip warning
pyro-ppl · Sep 17, 2024 · 3cde93d · 3cde93d
1 parent 7d50393
commit 3cde93d
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Showing 39 changed files with 39 additions and 38 deletions.
diff --git a/.gitignore b/.gitignore
@@ -38,3 +38,4 @@ docs/.DS_Store
 docs/source/examples
 docs/source/tutorials
 docs/source/getting_started.rst
+docs/source/sg_execution_times.rst
diff --git a/examples/annotation.py b/examples/annotation.py
@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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
@@ -138,7 +138,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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
@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
 
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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
@@ -315,7 +315,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     parser = argparse.ArgumentParser(
         description="Probabilistic topic modelling with Flax and Haiku"
     )

diff --git a/examples/proportion_test.py b/examples/proportion_test.py
@@ -158,7 +158,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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("0.15.2")
+    assert numpyro.__version__.startswith("0.15.3")
     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
@@ -49,7 +49,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.infer import MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")\n",
+    "assert numpyro.__version__.startswith(\"0.15.3\")\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
@@ -246,7 +246,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.infer import MCMC, NUTS, Predictive\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/bayesian_hierarchical_stacking.ipynb b/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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/bayesian_imputation.ipynb b/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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/bayesian_regression.ipynb b/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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/censoring.ipynb b/notebooks/source/censoring.ipynb
@@ -60,7 +60,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=0)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")\n",
+    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/hsgp_example.ipynb b/notebooks/source/hsgp_example.ipynb
@@ -62,7 +62,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=42)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")\n",
+    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

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(\"0.15.2\")\n",
+    "assert numpyro.__version__.startswith(\"0.15.3\")\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
@@ -38,7 +38,7 @@
     "import numpyro.distributions as dist\n",
     "import numpyro.distributions.constraints as constraints\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/ordinal_regression.ipynb b/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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/notebooks/source/other_samplers.ipynb b/notebooks/source/other_samplers.ipynb
@@ -67,7 +67,7 @@
     "\n",
     "rng_key = random.PRNGKey(seed=42)\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.15.2\")\n",
+    "assert numpyro.__version__.startswith(\"0.15.3\")\n",
     "\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",

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(\"0.15.2\")"
+    "assert numpyro.__version__.startswith(\"0.15.3\")"
    ]
   },
   {

diff --git a/numpyro/distributions/truncated.py b/numpyro/distributions/truncated.py
@@ -562,7 +562,7 @@ def cdf_when_alpha_eq_neg1():
                 cdf_when_alpha_neq_neg1(),
                 cdf_when_alpha_eq_neg1(),
             )
-            return jnp.clip(cdf_val, a_min=0.0, a_max=1.0)
+            return jnp.clip(cdf_val, 0.0, 1.0)
 
         @f.defjvp
         def f_jvp(primals, tangents):

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__ = "0.15.2"
+__version__ = "0.15.3"