Bump to version 0.3.0 (#697)

README.md

@@ -182,7 +182,7 @@ Pyro users will note that the API for model specification and inference is large
 
 ## Installation
 
-> **Limited Windows Support:** Note that NumPyro is untested on Windows, and will require building jaxlib from source. See this [JAX issue](https://github.com/google/jax/issues/438) for more details.
+> **Limited Windows Support:** Note that NumPyro is untested on Windows, and might require building jaxlib from source. See this [JAX issue](https://github.com/google/jax/issues/438) for more details. Alternatively, you can install [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/) and use NumPyro on it as on a Linux system. See also [CUDA on Windows Subsystem for Linux](https://developer.nvidia.com/cuda/wsl) if you want to use GPUs on Windows.
 
 To install NumPyro with a CPU version of JAX, you can use pip:
 
@@ -199,7 +199,7 @@ You can also install NumPyro from source:
 ```
 git clone https://github.com/pyro-ppl/numpyro.git
 # install jax/jaxlib first for CUDA support
-pip install -e .[dev]
+pip install -e .[dev]  # contains additional dependencies for NumPyro development
 ```
 
 ## Frequently Asked Questions

examples/annotation.py

@@ -264,7 +264,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.2.4")
+    assert numpyro.__version__.startswith("0.3.0")
     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/baseball.py

@@ -196,7 +196,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     parser = argparse.ArgumentParser(description="Baseball batting average using HMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=3000, type=int)
     parser.add_argument("--num-warmup", nargs='?', default=1500, type=int)

examples/bnn.py

@@ -136,7 +136,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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

@@ -58,7 +58,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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")')

examples/funnel.py

@@ -90,7 +90,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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)

examples/gp.py

@@ -129,7 +129,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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

@@ -189,7 +189,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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/minipyro.py

@@ -58,7 +58,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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/neutra.py

@@ -145,7 +145,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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

@@ -98,7 +98,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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/proportion_test.py

@@ -125,7 +125,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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

@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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

@@ -110,7 +110,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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/ucbadmit.py

@@ -128,7 +128,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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)

examples/vae.py

@@ -131,7 +131,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.4')
+    assert numpyro.__version__.startswith('0.3.0')
     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')

notebooks/source/bayesian_imputation.ipynb

@@ -44,7 +44,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.2.4\")"
+    "assert numpyro.__version__.startswith(\"0.3.0\")"
    ]
   },
   {

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('0.2.4')"
+    "assert numpyro.__version__.startswith('0.3.0')"
    ]
   },
   {

notebooks/source/conf.py

@@ -99,7 +99,8 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['.ipynb_checkpoints', 'logistic_regression.ipynb']
+exclude_patterns = ['.ipynb_checkpoints', 'logistic_regression.ipynb',
+                    'examples/*ipynb', 'examples/*py']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -178,8 +179,9 @@ def __call__(self, block, block_vars, gallery_conf):
 
 sphinx_gallery_conf = {
     'examples_dirs': ['../../examples'],
-    'gallery_dirs': 'examples',
-    'filename_pattern': '.py',
+    'gallery_dirs': ['examples'],
+    # slow examples can be added to here to avoid execution
+    'filename_pattern': r'(?!hmm_enum)\b\w+.py\b',
     'ignore_pattern': '(minipyro|covtype|__init__)',
     'within_subsection_order': GalleryFileNameSortKey,
     'image_scrapers': ('matplotlib', PNGScraper()),

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('0.2.4')\n",
+    "assert numpyro.__version__.startswith('0.3.0')\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"

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(\"0.2.4\")"
+    "assert numpyro.__version__.startswith(\"0.3.0\")"
    ]
   },
   {

numpyro/contrib/funsor/__init__.py

@@ -4,7 +4,10 @@
 try:
     import funsor
 except ImportError:
-    raise ImportError("`funsor` package is missing. You can install it with `pip install funsor`.")
+    raise ImportError("Looking like you want to do inference for models with "
+                      "discrete latent variables. This is an experimental feature. "
+                      "You need to install `funsor` to be able to use this feature. "
+                      "It can be installed with `pip install funsor`.")
 
 from numpyro.contrib.funsor.enum_messenger import enum, infer_config, markov, plate, to_data, to_funsor, trace
 from numpyro.contrib.funsor.infer_util import config_enumerate, log_density, plate_to_enum_plate

numpyro/version.py

@@ -1,4 +1,4 @@
 # Copyright Contributors to the Pyro project.
 # SPDX-License-Identifier: Apache-2.0
 
-__version__ = '0.2.4'
+__version__ = '0.3.0'

setup.py

@@ -34,9 +34,9 @@
     author_email='[email protected]',
     install_requires=[
         # TODO: pin to a specific version for the release (until JAX's API becomes stable)
-        'jax>=0.1.70',
+        'jax==0.1.73',
         # check min version here: https://github.com/google/jax/blob/master/jax/lib/__init__.py#L20
-        'jaxlib>=0.1.47',
+        'jaxlib==0.1.51',
         'tqdm',
     ],
     extras_require={
@@ -47,7 +47,7 @@
             'pyro-api>=0.1.1'
         ],
         'dev': [
-            'funsor @ git+https://github.com/pyro-ppl/funsor.git@b4db46acc5ab615abd2e1297f65ff5e70e961876#egg=funsor',
+            'funsor',
             'ipython',
             'isort',
         ],