Merge tag '1.8.4'

.github/workflows/ci.yml

@@ -62,6 +62,40 @@ jobs:
         run: |
           make docs
           make doctest
+  tutorials-html:
+    runs-on: ubuntu-20.04
+    needs: lint
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+          sudo apt-get update
+          sudo apt-get install gcc-8 g++-8 ninja-build graphviz pandoc
+          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          # Keep track of pyro-api master branch
+          pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
+          pip install torch==1.11.0+cpu torchvision==0.12.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+          pip install .[test]
+          pip install -r docs/requirements.txt
+          # requirements for tutorials (from .[dev])
+          sudo apt-get install pandoc
+          pip install nbformat
+          pip install nbsphinx>=0.3.2
+          pip install nbstripout
+          pip install pypandoc
+          pip install ninja
+          pip freeze
+      - name: Build HTML from tutorials
+        run: |
+          SPHINXOPTS="-E" make tutorial
   unit:
     runs-on: ubuntu-20.04
     needs: docs
@@ -96,7 +130,7 @@ jobs:
           COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
   examples:
     runs-on: ubuntu-20.04
-    needs: docs
+    needs: [docs, tutorials-html]
     strategy:
       matrix:
         python-version: [3.7]

docs/source/distributions.rst

@@ -190,6 +190,13 @@ GaussianScaleMixture
     :undoc-members:
     :show-inheritance:
 
+GroupedNormalNormal
+-------------------
+.. autoclass:: pyro.distributions.GroupedNormalNormal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 ImproperUniform
 ---------------
 .. autoclass:: pyro.distributions.improper_uniform.ImproperUniform

examples/air/main.py

@@ -272,7 +272,7 @@ def per_param_optim_args(param_name):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Pyro AIR example", argument_default=argparse.SUPPRESS
     )

examples/baseball.py

@@ -392,7 +392,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -74,7 +74,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -71,7 +71,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -104,7 +104,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -86,7 +86,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Causal Effect Variational Autoencoder"
     )

examples/contrib/epidemiology/regional.py

@@ -166,7 +166,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Regional compartmental epidemiology modeling using HMC"
     )

examples/contrib/epidemiology/sir.py

@@ -334,7 +334,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Compartmental epidemiology modeling using HMC"
     )

examples/contrib/forecast/bart.py

@@ -166,7 +166,7 @@ def transform(pred, truth):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="Bart Ridership Forecasting Example")
     parser.add_argument("--train-window", default=2160, type=int)
     parser.add_argument("--test-window", default=336, type=int)

examples/contrib/funsor/hmm.py

@@ -820,7 +820,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="MAP Baum-Welch learning Bach Chorales"
     )

examples/contrib/gp/sv-dkl.py

@@ -193,7 +193,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="Pyro GP MNIST Example")
     parser.add_argument(
         "--data-dir",

examples/contrib/oed/ab_test.py

@@ -125,7 +125,7 @@ def main(num_vi_steps, num_bo_steps, seed):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -186,7 +186,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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/cvae/main.py

@@ -87,7 +87,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(

examples/dmm.py

@@ -571,7 +571,7 @@ def do_evaluation():
 
 # parse command-line arguments and execute the main method
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
 
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument("-n", "--num-epochs", type=int, default=5000)

examples/eight_schools/mcmc.py

@@ -43,7 +43,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="Eight Schools MCMC")
     parser.add_argument(
         "--num-samples",

examples/eight_schools/svi.py

@@ -81,7 +81,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -734,7 +734,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="MAP Baum-Welch learning Bach Chorales"
     )

examples/inclined_plane.py

@@ -145,7 +145,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument("-n", "--num-samples", default=500, type=int)
     args = parser.parse_args()

examples/lda.py

@@ -149,7 +149,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Amortized Latent Dirichlet Allocation"
     )

examples/lkj.py

@@ -56,7 +56,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -65,7 +65,7 @@ def guide(data):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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/neutra.py

@@ -232,7 +232,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(
         description="Example illustrating NeuTra Reparametrizer"
     )

examples/rsa/generics.py

@@ -177,7 +177,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument("-n", "--num-samples", default=10, type=int)
     args = parser.parse_args()

examples/rsa/hyperbole.py

@@ -217,7 +217,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -79,7 +79,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -96,7 +96,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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

@@ -351,7 +351,7 @@ def is_all_qud(world):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument("-n", "--num-samples", default=10, type=int)
     args = parser.parse_args()

examples/scanvi/scanvi.py

@@ -407,7 +407,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     # Parse command line arguments
     parser = argparse.ArgumentParser(
         description="single-cell ANnotation using Variational Inference"

examples/sir_hmc.py

@@ -633,7 +633,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="SIR epidemiology modeling using HMC")
     parser.add_argument("-p", "--population", default=10, type=int)
     parser.add_argument("-m", "--min-observations", default=3, type=int)

examples/sparse_gamma_def.py

@@ -269,7 +269,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(

examples/sparse_regression.py

@@ -364,7 +364,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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/svi_horovod.py

@@ -154,7 +154,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     parser = argparse.ArgumentParser(description="Distributed training via Horovod")
     parser.add_argument("-o", "--outfile")
     parser.add_argument("-s", "--size", default=1000000, type=int)

examples/toy_mixture_model_discrete_enumeration.py

@@ -133,7 +133,7 @@ def get_true_pred_CPDs(CPD, posterior_param):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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)

examples/vae/ss_vae_M2.py

@@ -433,7 +433,7 @@ def main(args):
 )
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
 
     parser = argparse.ArgumentParser(description="SS-VAE\n{}".format(EXAMPLE_RUN))
 

examples/vae/vae.py

@@ -216,7 +216,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(

examples/vae/vae_comparison.py

@@ -262,7 +262,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.8.3")
+    assert pyro.__version__.startswith("1.8.4")
     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)