diff --git a/.gitignore b/.gitignore index 8e16a1a02..97019aa24 100644 --- 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 index ceb6a81fd..bcf393925 100644 --- 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 index 83da74a89..a04bad396 100644 --- 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 index b0a08ea25..16149df15 100644 --- 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 index 4376d88c6..806693052 100644 --- 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 index a5a972323..184a8c80a 100644 --- 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 index 988ff2386..0aa5d5ebb 100644 --- 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 index f0af3c095..b399e08cd 100644 --- 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 index 4c77b4cf7..8c9955a08 100644 --- 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 index 8d1290475..f6deb3122 100644 --- 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 index c1f88d3a1..8545473a7 100644 --- 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 index 081983eee..b92ef1998 100644 --- 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 index c99cfb26b..1c969c86a 100644 --- 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 index f1c8bf500..37fdff356 100644 --- 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 index 8ac495767..72f5ea602 100644 --- 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 index 6db17df49..3e6cdadc5 100644 --- 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 index 78d272061..2195d3fed 100644 --- 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 index 477c5695b..8dfd02877 100644 --- 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 index 48ea44d33..8fd00a0e3 100644 --- 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 index c1fafd232..288489484 100644 --- 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 index 906d71376..65e35f2d8 100644 --- 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 index 87a4df6ce..e3b0a12d1 100644 --- 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 index c4afe784f..8846678af 100644 --- 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 index 446e5a19f..b73d26ec7 100644 --- 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 index ddffcda44..8f3adf799 100644 --- 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 index cbf44ff15..0acf4ae76 100644 --- 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 index e11e0a3dc..4589ca8d6 100644 --- 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 index f4746341a..e0a6044cd 100644 --- 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 index aaf82160d..2c2f8878c 100644 --- 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 index 2deed7378..5da43483b 100644 --- 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 index 129bffede..28c4b347a 100644 --- 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 index 881bd0743..d40804145 100644 --- 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 index 6ea78044c..66f1508dd 100644 --- 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 index 377dfdaa7..cfba99f3e 100644 --- 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 index ad7f8340a..7ed20baf9 100644 --- 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 index 992a88f9f..03316ccfb 100644 --- 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 index 3744ebe0b..c09d8b269 100644 --- 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 index fecdff2f7..adcd7f2ad 100644 --- 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 index 5ff26e807..601b211d8 100644 --- 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"