Bump to version 0.5.0 (#888)

fehiepsi · fritzo · web-flow · commit 6a1f5226f180 · 2021-01-24T14:31:24.000-06:00
* Support .to_event() in TransformReparam

* Strengthen test

* add forward shape for transforms

* add forward shapes and tests

* simplify nested independent Constraint

* shape check for affine transform

* add missing commit

* Bump to version 0.5.0

* fix tests, addresses comments

* port some fixes from hmcgibbs PR

* pin to specific version

* run isort

Co-authored-by: Fritz Obermeyer &lt;fritz.obermeyer@gmail.com&gt;
diff --git a/examples/annotation.py b/examples/annotation.py
@@ -266,7 +266,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.4.1")
+    assert numpyro.__version__.startswith("0.5.0")
     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/baseball.py b/examples/baseball.py
@@ -196,7 +196,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -138,7 +138,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -58,7 +58,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=100, type=int, help='number of samples')
     parser.add_argument('--num-steps', default=10, type=int, help='number of steps (for "HMC")')
diff --git a/examples/funnel.py b/examples/funnel.py
@@ -87,7 +87,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Non-centered reparameterization 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/gp.py b/examples/gp.py
@@ -142,7 +142,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -191,7 +191,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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/minipyro.py b/examples/minipyro.py
@@ -58,7 +58,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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/neutra.py b/examples/neutra.py
@@ -146,7 +146,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -103,7 +103,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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/proportion_test.py b/examples/proportion_test.py
@@ -128,7 +128,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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
@@ -112,7 +112,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     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/ucbadmit.py b/examples/ucbadmit.py
@@ -131,7 +131,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='UCBadmit gender discrimination using HMC')
     parser.add_argument('-n', '--num-samples', nargs='?', default=2000, type=int)
     parser.add_argument('--num-warmup', nargs='?', default=500, type=int)
diff --git a/examples/vae.py b/examples/vae.py
@@ -131,7 +131,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.4.1')
+    assert numpyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=15, type=int, help='number of training epochs')
     parser.add_argument('-lr', '--learning-rate', default=1.0e-3, type=float, help='learning rate')
diff --git a/notebooks/source/bayesian_imputation.ipynb b/notebooks/source/bayesian_imputation.ipynb
@@ -46,7 +46,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.4.1\")"
+    "assert numpyro.__version__.startswith(\"0.5.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_regression.ipynb b/notebooks/source/bayesian_regression.ipynb
@@ -66,7 +66,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats('svg')\n",
     "\n",
-    "assert numpyro.__version__.startswith('0.4.1')"
+    "assert numpyro.__version__.startswith('0.5.0')"
    ]
   },
   {
diff --git a/notebooks/source/logistic_regression.ipynb b/notebooks/source/logistic_regression.ipynb
@@ -31,7 +31,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.examples.datasets import COVTYPE, load_dataset\n",
     "from numpyro.infer import HMC, MCMC, NUTS\n",
-    "assert numpyro.__version__.startswith('0.4.1')\n",
+    "assert numpyro.__version__.startswith('0.5.0')\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"
diff --git a/notebooks/source/ordinal_regression.ipynb b/notebooks/source/ordinal_regression.ipynb
@@ -30,7 +30,7 @@
     "from numpyro.infer import MCMC, NUTS\n",
     "import pandas as pd\n",
     "import seaborn as sns\n",
-    "assert numpyro.__version__.startswith('0.4.1')"
+    "assert numpyro.__version__.startswith('0.5.0')"
    ]
   },
   {
diff --git a/notebooks/source/time_series_forecasting.ipynb b/notebooks/source/time_series_forecasting.ipynb
@@ -39,7 +39,7 @@
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
     "numpyro.set_host_device_count(4)\n",
-    "assert numpyro.__version__.startswith(\"0.4.1\")"
+    "assert numpyro.__version__.startswith(\"0.5.0\")"
    ]
   },
   {
diff --git a/numpyro/contrib/einstein/kernels.py b/numpyro/contrib/einstein/kernels.py
@@ -11,8 +11,8 @@
 import jax.scipy.linalg
 import jax.scipy.stats
 
-import numpyro.distributions as dist
 from numpyro.contrib.einstein.utils import posdef, safe_norm, sqrth
+import numpyro.distributions as dist
 
 
 class PrecondMatrix(ABC):
diff --git a/numpyro/infer/hmc_gibbs.py b/numpyro/infer/hmc_gibbs.py
@@ -5,7 +5,7 @@
 import copy
 from functools import partial
 
-from jax import device_put, jacfwd, grad, ops, random, value_and_grad
+from jax import device_put, grad, jacfwd, ops, random, value_and_grad
 import jax.numpy as jnp
 from jax.scipy.special import expit
 
diff --git a/numpyro/infer/hmc_util.py b/numpyro/infer/hmc_util.py
@@ -3,7 +3,7 @@
 
 from collections import namedtuple
 
-from jax import jacfwd, grad, random, value_and_grad, vmap
+from jax import grad, jacfwd, random, value_and_grad, vmap
 from jax.flatten_util import ravel_pytree
 import jax.numpy as jnp
 from jax.ops import index_update
diff --git a/numpyro/infer/reparam.py b/numpyro/infer/reparam.py
@@ -3,8 +3,8 @@
 
 from abc import ABC, abstractmethod
 
-import jax.numpy as jnp
 from jax import lax
+import jax.numpy as jnp
 
 import numpyro
 import numpyro.distributions as dist
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__ = '0.4.1'
+__version__ = '0.5.0'
diff --git a/setup.py b/setup.py
@@ -33,9 +33,9 @@
     author='Uber AI Labs',
     install_requires=[
         # TODO: pin to a specific version for the release (until JAX's API becomes stable)
-        'jax>=0.2.7',
+        'jax==0.2.8',
         # check min version here: https://github.com/google/jax/blob/master/jax/lib/__init__.py#L26
-        'jaxlib>=0.1.56',
+        'jaxlib==0.1.59',
         'tqdm',
     ],
     extras_require={
