Bump to version 1.1.0 (#2215)

docs/source/inference_algos.rst

@@ -51,6 +51,12 @@ ELBO
     :show-inheritance:
     :member-order: bysource
 
+.. automodule:: pyro.infer.tracetmc_elbo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
 Importance
 ----------
 

examples/air/main.py

@@ -245,7 +245,7 @@ def per_param_optim_args(module_name, param_name):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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

@@ -327,7 +327,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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/contrib/autoname/mixture.py

@@ -72,7 +72,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=100, type=int)
     args = parser.parse_args()

examples/contrib/cevae/synthetic.py

@@ -78,7 +78,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     parser = argparse.ArgumentParser(description="Causal Effect Variational Autoencoder")
     parser.add_argument("--num-data", default=1000, type=int)
     parser.add_argument("--feature-dim", default=5, type=int)

examples/contrib/gp/sv-dkl.py

@@ -162,7 +162,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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/contrib/timeseries/gp_models.py

@@ -146,7 +146,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     parser = argparse.ArgumentParser(description="contrib.timeseries example usage")
     parser.add_argument("-n", "--num-steps", default=300, type=int)
     parser.add_argument("-s", "--seed", default=0, type=int)

examples/dmm/dmm.py

@@ -447,7 +447,7 @@ def do_evaluation():
 
 # parse command-line arguments and execute the main method
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
 
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', type=int, default=5000)

examples/eight_schools/mcmc.py

@@ -39,7 +39,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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

@@ -635,7 +635,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     # 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

@@ -309,7 +309,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert pyro.__version__.startswith('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
 
     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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     # 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('1.0.0')
+    assert pyro.__version__.startswith('1.1.0')
     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

@@ -6,7 +6,7 @@
                              param, plate, plate_stack, random_module, sample, validation_enabled)
 from pyro.util import set_rng_seed
 
-version_prefix = '1.0.0'
+version_prefix = '1.1.0'
 
 # Get the __version__ string from the auto-generated _version.py file, if exists.
 try:

pyro/util.py

@@ -6,7 +6,6 @@
 from collections import defaultdict
 from itertools import zip_longest
 
-import graphviz
 import torch
 from contextlib import contextmanager
 
@@ -92,22 +91,28 @@ def warn_if_inf(value, msg="", allow_posinf=False, allow_neginf=False):
 
 def save_visualization(trace, graph_output):
     """
-    :param pyro.poutine.Trace trace: a trace to be visualized
-    :param graph_output: the graph will be saved to graph_output.pdf
-    :type graph_output: str
-
-    Take a trace generated by poutine.trace with `graph_type='dense'` and render
-    the graph with the output saved to file.
+    (DEPRECATED) Take a trace generated by poutine.trace with `graph_type='dense'`
+    and render the graph with the output saved to file.
 
     - non-reparameterized stochastic nodes are salmon
     - reparameterized stochastic nodes are half salmon, half grey
     - observation nodes are green
 
+    :param pyro.poutine.Trace trace: a trace to be visualized
+    :param graph_output: the graph will be saved to graph_output.pdf
+    :type graph_output: str
+
+
     Example:
 
     trace = pyro.poutine.trace(model, graph_type="dense").get_trace()
     save_visualization(trace, 'output')
     """
+    warnings.warn("`save_visualization` function is deprecated and will be removed in "
+                  "a future version.")
+
+    import graphviz
+
     g = graphviz.Digraph()
 
     for label, node in trace.nodes.items():

setup.py

@@ -55,6 +55,7 @@
 # examples/tutorials
 EXTRAS_REQUIRE = [
     'jupyter>=1.0.0',
+    'graphviz>=0.8',
     'matplotlib>=1.3',
     'pillow',
     'torchvision>=0.4.0',
@@ -78,7 +79,6 @@
     install_requires=[
         # if you add any additional libraries, please also
         # add them to `docs/requirements.txt`
-        'graphviz>=0.8',
         # numpy is necessary for some functionality of PyTorch
         'numpy>=1.7',
         'opt_einsum>=2.3.2',

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('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\n",
     "pyro.enable_validation(True)"
    ]
   },

tutorial/source/bayesian_regression.ipynb

@@ -69,7 +69,7 @@
     "\n",
     "# for CI testing\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\n",
     "pyro.enable_validation(True)\n",
     "pyro.set_rng_seed(1)\n",
     "pyro.enable_validation(True)\n",

tutorial/source/bayesian_regression_ii.ipynb

@@ -44,7 +44,7 @@
     "import pyro.optim as optim\n",
     "\n",
     "pyro.set_rng_seed(1)\n",
-    "assert pyro.__version__.startswith('1.0.0')"
+    "assert pyro.__version__.startswith('1.1.0')"
    ]
   },
   {

tutorial/source/bo.ipynb

@@ -54,7 +54,7 @@
     "import pyro\n",
     "import pyro.contrib.gp as gp\n",
     "\n",
-    "assert pyro.__version__.startswith('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\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('1.0.0')"
+    "assert pyro.__version__.startswith('1.1.0')"
    ]
   },
   {

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('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\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('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\n",
     "pyro.enable_validation()\n",
     "pyro.set_rng_seed(0)"
    ]

tutorial/source/gmm.ipynb

@@ -41,7 +41,7 @@
     "from pyro.infer import SVI, TraceEnum_ELBO, config_enumerate, infer_discrete\n",
     "\n",
     "smoke_test = ('CI' in os.environ)\n",
-    "assert pyro.__version__.startswith('1.0.0')\n",
+    "assert pyro.__version__.startswith('1.1.0')\n",
     "pyro.enable_validation(True)"
    ]
   },