Bump to version 0.5.0 (#2075)

.travis.yml

@@ -24,6 +24,8 @@ cache:
 
 install:
     - pip install -U pip
+    # Keep track of pyro-api master branch
+    - pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
     - pip install torch==1.3.0+cpu torchvision==0.4.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
     - pip install .[test]
     - pip freeze

docs/requirements.txt

@@ -5,4 +5,5 @@ graphviz>=0.8
 numpy>=1.7
 observations>=0.1.4
 opt_einsum>=2.3.2
+pyro-api>=0.1.0
 tqdm>=4.31

docs/source/pyro.nn.txt

@@ -1,7 +1,15 @@
 AutoRegressiveNN
 ----------------
 
-.. automodule:: pyro.nn.auto_reg_nn
+.. autoclass:: pyro.nn.auto_reg_nn.AutoRegressiveNN
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+ConditionalAutoRegressiveNN
+---------------------------
+
+.. autoclass:: pyro.nn.auto_reg_nn.ConditionalAutoRegressiveNN
     :members:
     :undoc-members:
     :show-inheritance:

examples/air/main.py

@@ -245,7 +245,7 @@ def per_param_optim_args(module_name, param_name):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Pyro AIR example", argument_default=argparse.SUPPRESS)
     parser.add_argument('-n', '--num-steps', type=int, default=int(1e8),
                         help='number of optimization steps to take')

examples/baseball.py

@@ -359,7 +359,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Baseball batting average using HMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=200, type=int)
     parser.add_argument("--num-chains", nargs='?', default=4, type=int)

examples/bayesian_regression.py

@@ -137,7 +137,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=1000, type=int)
     parser.add_argument('-b', '--batch-size', default=N, type=int)

examples/contrib/autoname/mixture.py

@@ -72,7 +72,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=200, type=int)
     parser.add_argument('--jit', action='store_true')

examples/contrib/autoname/scoping_mixture.py

@@ -64,7 +64,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=200, type=int)
     args = parser.parse_args()

examples/contrib/autoname/tree_data.py

@@ -102,7 +102,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=100, type=int)
     args = parser.parse_args()

examples/contrib/gp/sv-dkl.py

@@ -162,7 +162,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='Pyro GP MNIST Example')
     parser.add_argument('--data-dir', type=str, default=None, metavar='PATH',
                         help='default directory to cache MNIST data')

examples/contrib/oed/ab_test.py

@@ -112,7 +112,7 @@ def main(num_vi_steps, num_bo_steps, seed):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="A/B test experiment design using VI")
     parser.add_argument("-n", "--num-vi-steps", nargs="?", default=5000, type=int)
     parser.add_argument('--num-bo-steps', nargs="?", default=5, type=int)

examples/dmm/dmm.py

@@ -433,7 +433,7 @@ def do_evaluation():
 
 # parse command-line arguments and execute the main method
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
 
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', type=int, default=5000)

examples/eight_schools/mcmc.py

@@ -40,7 +40,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='Eight Schools MCMC')
     parser.add_argument('--num-samples', type=int, default=1000,
                         help='number of MCMC samples (default: 1000)')

examples/eight_schools/svi.py

@@ -72,7 +72,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='Eight Schools SVI')
     parser.add_argument('--lr', type=float, default=0.01,
                         help='learning rate (default: 0.01)')

examples/hmm.py

@@ -626,7 +626,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="MAP Baum-Welch learning Bach Chorales")
     parser.add_argument("-m", "--model", default="1", type=str,
                         help="one of: {}".format(", ".join(sorted(models.keys()))))

examples/inclined_plane.py

@@ -121,7 +121,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=500, type=int)
     args = parser.parse_args()

examples/lda.py

@@ -135,7 +135,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Amortized Latent Dirichlet Allocation")
     parser.add_argument("-t", "--num-topics", default=8, type=int)
     parser.add_argument("-w", "--num-words", default=1024, type=int)

examples/lkj.py

@@ -46,7 +46,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Demonstrate the use of an LKJ Prior")
     parser.add_argument("--num-samples", nargs="?", default=200, type=int)
     parser.add_argument("--n", nargs="?", default=500, type=int)

examples/minipyro.py

@@ -62,7 +62,7 @@ def guide(data):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="Mini Pyro demo")
     parser.add_argument("-b", "--backend", default="minipyro")
     parser.add_argument("-n", "--num-steps", default=1001, type=int)

examples/rsa/generics.py

@@ -154,7 +154,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=10, type=int)
     args = parser.parse_args()

examples/rsa/hyperbole.py

@@ -151,7 +151,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=10, type=int)
     parser.add_argument('--price', default=10000, type=int)

examples/rsa/schelling.py

@@ -73,7 +73,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=10, type=int)
     parser.add_argument('--depth', default=2, type=int)

examples/rsa/schelling_false.py

@@ -86,7 +86,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=10, type=int)
     parser.add_argument('--depth', default=3, type=int)

examples/rsa/semantic_parsing.py

@@ -337,7 +337,7 @@ def is_all_qud(world):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=10, type=int)
     args = parser.parse_args()

examples/sparse_gamma_def.py

@@ -231,7 +231,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=1500, type=int, help='number of training epochs')

examples/sparse_regression.py

@@ -306,7 +306,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='Krylov KIT')
     parser.add_argument('--num-data', type=int, default=750)
     parser.add_argument('--num-steps', type=int, default=1000)

examples/vae/ss_vae_M2.py

@@ -380,7 +380,7 @@ def main(args):
               "-sup 3000 -zd 50 -hl 500 -lr 0.00042 -b1 0.95 -bs 200 -log ./tmp.log"
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
 
     parser = argparse.ArgumentParser(description="SS-VAE\n{}".format(EXAMPLE_RUN))
 

examples/vae/vae.py

@@ -198,7 +198,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=101, type=int, help='number of training epochs')

examples/vae/vae_comparison.py

@@ -243,7 +243,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('0.4.1')
+    assert pyro.__version__.startswith('0.5.0')
     parser = argparse.ArgumentParser(description='VAE using MNIST dataset')
     parser.add_argument('-n', '--num-epochs', nargs='?', default=10, type=int)
     parser.add_argument('--batch_size', nargs='?', default=128, type=int)

pyro/__init__.py

@@ -5,7 +5,7 @@
                              param, plate, plate_stack, random_module, sample, validation_enabled)
 from pyro.util import set_rng_seed
 
-version_prefix = '0.4.1'
+version_prefix = '0.5.0'
 
 # Get the __version__ string from the auto-generated _version.py file, if exists.
 try:

pyro/infer/abstract_infer.py

@@ -289,9 +289,8 @@ def __init__(self, model, posterior, num_samples, keep_sites=None):
         self.num_samples = num_samples
         self.keep_sites = keep_sites
         super(TracePredictive, self).__init__()
-        warnings.warn('This class will be deprecated in the next release. For MCMC, '
-                      'please use the `pyro.infer.mcmc.util.predictive` function '
-                      'instead.', PendingDeprecationWarning)
+        warnings.warn('This class will be removed in the next release. Use the '
+                      '`pyro.infer.Predictive` class instead.', DeprecationWarning)
 
     def _traces(self, *args, **kwargs):
         if not self.posterior.exec_traces:

pyro/infer/elbo.py

@@ -39,7 +39,7 @@ class ELBO(object, metaclass=ABCMeta):
         tracer. When this is True, all :class:`torch.jit.TracerWarning` will
         be ignored. Defaults to False.
     :param bool jit_options: Optional dict of options to pass to
-        :func:`torch.jit.trace` , e.g. ``{"optimize": False}``.
+        :func:`torch.jit.trace` , e.g. ``{"check_trace": True}``.
     :param bool retain_graph: Whether to retain autograd graph during an SVI
         step. Defaults to None (False).
     :param float tail_adaptive_beta: Exponent beta with ``-1.0 <= beta < 0.0`` for

pyro/infer/svi.py

@@ -1,3 +1,5 @@
+import warnings
+
 import torch
 
 import pyro
@@ -62,6 +64,9 @@ def _loss_and_grads(*args, **kwargs):
             self.loss_and_grads = loss_and_grads
 
     def run(self, *args, **kwargs):
+        warnings.warn('SVI will not derive from TracePosterior, and this method might be '
+                      'unavailable in future releases. For predictions, use the '
+                      '`pyro.infer.Predictive` class directly.', DeprecationWarning)
         if self.num_steps > 0:
             with poutine.block():
                 for i in range(self.num_steps):

setup.py

@@ -84,7 +84,7 @@
         # numpy is necessary for some functionality of PyTorch
         'numpy>=1.7',
         'opt_einsum>=2.3.2',
-        'pyro-api@https://api.github.com/repos/pyro-ppl/pyro-api/tarball/master',
+        'pyro-api>=0.1.0',
         'torch>=1.2.0',
         'tqdm>=4.31',
     ],
@@ -114,7 +114,6 @@
             'yapf',
         ],
     },
-    tests_require=['flake8', 'pytest>=4.1'],
     keywords='machine learning statistics probabilistic programming bayesian modeling pytorch',
     license='MIT License',
     classifiers=[

tutorial/source/air.ipynb

@@ -41,7 +41,7 @@
     "import numpy as np\n",
     "\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('0.4.1')\n",
+    "assert pyro.__version__.startswith('0.5.0')\n",
     "pyro.enable_validation(True)"
    ]
   },

tutorial/source/bayesian_regression.ipynb

@@ -55,7 +55,7 @@
     "\n",
     "# for CI testing\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('0.4.1')\n",
+    "assert pyro.__version__.startswith('0.5.0')\n",
     "pyro.enable_validation(True)\n",
     "pyro.set_rng_seed(1)\n",
     "pyro.enable_validation(True)\n",

tutorial/source/bayesian_regression_ii.ipynb

@@ -39,7 +39,7 @@
     "import pyro.optim as optim\n",
     "\n",
     "pyro.set_rng_seed(1)\n",
-    "assert pyro.__version__.startswith('0.4.1')"
+    "assert pyro.__version__.startswith('0.5.0')"
    ]
   },
   {

tutorial/source/bo.ipynb

@@ -54,7 +54,7 @@
     "import pyro\n",
     "import pyro.contrib.gp as gp\n",
     "\n",
-    "assert pyro.__version__.startswith('0.4.1')\n",
+    "assert pyro.__version__.startswith('0.5.0')\n",
     "pyro.enable_validation(True)  # can help with debugging\n",
     "pyro.set_rng_seed(1)"
    ]

tutorial/source/easyguide.ipynb

@@ -45,7 +45,7 @@
     "\n",
     "pyro.enable_validation(True)\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('0.4.1')"
+    "assert pyro.__version__.startswith('0.5.0')"
    ]
   },
   {

tutorial/source/ekf.ipynb

@@ -98,7 +98,7 @@
     "from pyro.contrib.tracking.measurements import PositionMeasurement\n",
     "\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('0.4.1')\n",
+    "assert pyro.__version__.startswith('0.5.0')\n",
     "pyro.enable_validation(True)"
    ]
   },

tutorial/source/enumeration.ipynb

@@ -50,7 +50,7 @@
     "from pyro.ops.indexing import Vindex\n",
     "\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('0.4.1')\n",
+    "assert pyro.__version__.startswith('0.5.0')\n",
     "pyro.enable_validation()\n",
     "pyro.set_rng_seed(0)"
    ]