Merge branch 'dev'

.github/workflows/ci.yml

@@ -7,8 +7,8 @@ on:
     branches: [dev, master]
 
 env:
-  CXX: g++-8
-  CC: gcc-8
+  CXX: g++-9
+  CC: gcc-9
   # See coveralls-python - Github Actions support:
   # https://github.com/TheKevJames/coveralls-python/blob/master/docs/usage/configuration.rst#github-actions-support
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -50,7 +50,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build graphviz
           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
@@ -78,7 +78,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 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
@@ -112,7 +112,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build
           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
@@ -146,7 +146,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build
           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
@@ -180,7 +180,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build
           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
@@ -212,7 +212,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build
           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
@@ -244,7 +244,7 @@ jobs:
         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
+          sudo apt-get install gcc-9 g++-9 ninja-build
           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

Makefile

@@ -3,7 +3,7 @@
 all: docs test
 
 install: FORCE
-	pip install -e .[dev,profile]
+	pip install -e .[dev,profile] --config-settings editable_mode=strict
 
 uninstall: FORCE
 	pip uninstall pyro-ppl
@@ -21,7 +21,7 @@ lint: FORCE
 	ruff check .
 	black --check *.py pyro examples tests scripts profiler
 	python scripts/update_headers.py --check
-	mypy --install-types --non-interactive pyro scripts
+	mypy --install-types --non-interactive pyro scripts tests
 
 license: FORCE
 	python scripts/update_headers.py

docker/Makefile

@@ -22,6 +22,8 @@ cmd?=bash
 # Determine name of docker image
 build run notebook: img_prefix=pyro-cpu
 build-gpu run-gpu notebook-gpu: img_prefix=pyro-gpu
+build run lab: img_prefix=pyro-cpu
+build-gpu run-gpu lab-gpu: img_prefix=pyro-gpu
 
 ifeq ($(img), )
 	IMG_NAME=${img_prefix}-${pyro_branch}-${python_version}
@@ -121,10 +123,32 @@ notebook: ##
 
 notebook-gpu: create-host-workspace
 notebook-gpu: ##
-	## Start a juptyer notebook on the Pyro GPU docker container.
+	## Start a jupyter notebook on the Pyro GPU docker container.
 	## Args:
 	##   img: use image name given by `img`.
 	##
 	docker run --runtime=nvidia --init -it -p 8888:8888 --user ${USER} \
 	-v ${HOST_WORK_DIR}:${DOCKER_WORK_DIR} \
 	${IMG_NAME}
+
+	notebook: create-host-workspace
+lab: ##
+	## Start jupyterlab on the Pyro CPU docker container.
+	## Args:
+	##   img: use image name given by `img`.
+	##
+	docker run --init -it -p 8888:8888 --user ${USER} \
+	-v ${HOST_WORK_DIR}:${DOCKER_WORK_DIR} \
+	${IMG_NAME} jupyter lab --port=8888 --no-browser --ip=0.0.0.0
+
+lab-gpu: create-host-workspace
+lab-gpu: ##
+	## Start jupyterlab on the Pyro GPU docker container.
+	## Args:
+	##   img: use image name given by `img`.
+	##
+	docker run --runtime=nvidia --init -it -p 8888:8888 --user ${USER} \
+	-v ${HOST_WORK_DIR}:${DOCKER_WORK_DIR} \
+	${IMG_NAME} jupyter lab --port=8888 --no-browser --ip=0.0.0.0
+
+

docker/install.sh

@@ -2,7 +2,7 @@
 set -xe
 
 pip install --upgrade pip
-pip install jupyter matplotlib
+pip install notebook ipywidgets matplotlib
 
 # 1. Install PyTorch
 # Use conda package if pytorch_branch = 'release'.

docs/source/distributions.rst

@@ -407,6 +407,13 @@ Stable
     :undoc-members:
     :show-inheritance:
 
+StableWithLogProb
+-----------------
+.. autoclass:: pyro.distributions.StableWithLogProb
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 TruncatedPolyaGamma
 -------------------
 .. autoclass:: pyro.distributions.TruncatedPolyaGamma

examples/air/main.py

@@ -270,7 +270,7 @@ def per_param_optim_args(param_name):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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

@@ -823,7 +823,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     parser = argparse.ArgumentParser(description="Pyro GP MNIST Example")
     parser.add_argument(
         "--data-dir",

examples/contrib/mue/FactorMuE.py

@@ -86,9 +86,7 @@ def main(args):
         indices = torch.randperm(sum(data_lengths), device=device).tolist()
         dataset_train, dataset_test = [
             torch.utils.data.Subset(dataset, indices[(offset - length) : offset])
-            for offset, length in zip(
-                torch._utils._accumulate(data_lengths), data_lengths
-            )
+            for offset, length in zip(np.cumsum(data_lengths), data_lengths)
         ]
     else:
         dataset_train = dataset

examples/contrib/mue/ProfileHMM.py

@@ -92,9 +92,7 @@ def main(args):
         indices = torch.randperm(sum(data_lengths), device=device).tolist()
         dataset_train, dataset_test = [
             torch.utils.data.Subset(dataset, indices[(offset - length) : offset])
-            for offset, length in zip(
-                torch._utils._accumulate(data_lengths), data_lengths
-            )
+            for offset, length in zip(np.cumsum(data_lengths), data_lengths)
         ]
     else:
         dataset_train = dataset

examples/contrib/oed/ab_test.py

@@ -124,7 +124,7 @@ def main(num_vi_steps, num_bo_steps, seed):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     # parse command line arguments
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(

examples/dmm.py

@@ -569,7 +569,7 @@ def do_evaluation():
 
 # parse command-line arguments and execute the main method
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
 
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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

@@ -737,7 +737,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert pyro.__version__.startswith("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     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("1.9.0")
+    assert pyro.__version__.startswith("1.9.1")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument("-n", "--num-samples", default=10, type=int)
     args = parser.parse_args()