Bump to version 0.11.0 (#1520)

fehiepsi · web-flow · commit c6358416e0d4 · 2023-01-22T23:11:00.000-05:00
* Bump to version 0.11.0

* Drop Python 3.7 support

* reorder distribution entries

* add path to TFP kernel

* Update some docstring to render better

* clarify HMCState in MCMC.run

* Add docs for TraceEnum_ELBO
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -51,7 +51,7 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        python-version: [3.7,3.8]
+        python-version: [3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -81,7 +81,7 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        python-version: [3.7,3.8]
+        python-version: [3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -119,7 +119,7 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        python-version: [3.7,3.8]
+        python-version: [3.8]
 
     steps:
     - uses: actions/checkout@v2
diff --git a/docs/source/distributions.rst b/docs/source/distributions.rst
@@ -176,6 +176,22 @@ Gumbel
     :show-inheritance:
     :member-order: bysource
 
+GaussianCopula
+^^^^^^^^^^^^^^
+.. autoclass:: numpyro.distributions.copula.GaussianCopula
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+GaussianCopulaBeta
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: numpyro.distributions.copula.GaussianCopulaBeta
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
 GaussianRandomWalk
 ^^^^^^^^^^^^^^^^^^
 .. autoclass:: numpyro.distributions.continuous.GaussianRandomWalk
@@ -264,6 +280,14 @@ Logistic
     :show-inheritance:
     :member-order: bysource
 
+LowRankMultivariateNormal
+^^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: numpyro.distributions.continuous.LowRankMultivariateNormal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
 MatrixNormal
 ^^^^^^^^^^^^
 .. autoclass:: numpyro.distributions.continuous.MatrixNormal
@@ -288,30 +312,6 @@ MultivariateStudentT
     :show-inheritance:
     :member-order: bysource
 
-GaussianCopula
-^^^^^^^^^^^^^^^^^^^^
-.. autoclass:: numpyro.distributions.copula.GaussianCopula
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
-GaussianCopulaBeta
-^^^^^^^^^^^^^^^^^^^^
-.. autoclass:: numpyro.distributions.copula.GaussianCopulaBeta
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
-LowRankMultivariateNormal
-^^^^^^^^^^^^^^^^^^^^^^^^^
-.. autoclass:: numpyro.distributions.continuous.LowRankMultivariateNormal
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
 Normal
 ^^^^^^
 .. autoclass:: numpyro.distributions.continuous.Normal
diff --git a/docs/source/svi.rst b/docs/source/svi.rst
@@ -32,6 +32,16 @@ Trace_ELBO
     :member-order: bysource
 
 
+TraceEnum_ELBO
+---------------
+
+.. autoclass:: numpyro.infer.elbo.TraceEnum_ELBO
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+
 TraceGraph_ELBO
 ---------------
 
diff --git a/examples/annotation.py b/examples/annotation.py
@@ -320,7 +320,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/ar2.py b/examples/ar2.py
@@ -114,7 +114,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="AR2 example")
     parser.add_argument("--num-data", nargs="?", default=142, type=int)
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
diff --git a/examples/baseball.py b/examples/baseball.py
@@ -210,7 +210,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="Baseball batting average using MCMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=3000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1500, type=int)
diff --git a/examples/bnn.py b/examples/bnn.py
@@ -160,7 +160,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/covtype.py b/examples/covtype.py
@@ -206,7 +206,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-samples", default=1000, type=int, help="number of samples"
diff --git a/examples/funnel.py b/examples/funnel.py
@@ -139,7 +139,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(
         description="Non-centered reparameterization example"
     )
diff --git a/examples/gaussian_shells.py b/examples/gaussian_shells.py
@@ -120,7 +120,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="Nested sampler for Gaussian shells")
     parser.add_argument("-n", "--num-samples", nargs="?", default=10000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)
diff --git a/examples/gp.py b/examples/gp.py
@@ -170,7 +170,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/hmm.py b/examples/hmm.py
@@ -263,7 +263,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/holt_winters.py b/examples/holt_winters.py
@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="Holt-Winters")
     parser.add_argument("--T", nargs="?", default=6, type=int)
     parser.add_argument("--future", nargs="?", default=1, type=int)
diff --git a/examples/horseshoe_regression.py b/examples/horseshoe_regression.py
@@ -162,7 +162,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="Horseshoe regression example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=2000, type=int)
     parser.add_argument("--num-warmup", nargs="?", default=1000, type=int)
diff --git a/examples/minipyro.py b/examples/minipyro.py
@@ -58,7 +58,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/mortality.py b/examples/mortality.py
@@ -220,7 +220,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
 
     parser = argparse.ArgumentParser(description="Mortality regression model")
     parser.add_argument("-n", "--num-samples", nargs="?", default=500, type=int)
diff --git a/examples/neutra.py b/examples/neutra.py
@@ -197,7 +197,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/ode.py b/examples/ode.py
@@ -117,7 +117,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/prodlda.py b/examples/prodlda.py
@@ -314,7 +314,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(
         description="Probabilistic topic modelling with Flax and Haiku"
     )
diff --git a/examples/proportion_test.py b/examples/proportion_test.py
@@ -160,7 +160,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/sparse_regression.py b/examples/sparse_regression.py
@@ -384,7 +384,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/stochastic_volatility.py b/examples/stochastic_volatility.py
@@ -122,7 +122,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     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)
diff --git a/examples/thompson_sampling.py b/examples/thompson_sampling.py
@@ -294,7 +294,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="Thompson sampling example")
     parser.add_argument(
         "--num-random", nargs="?", default=2, type=int, help="number of random draws"
diff --git a/examples/ucbadmit.py b/examples/ucbadmit.py
@@ -151,7 +151,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(
         description="UCBadmit gender discrimination using HMC"
     )
diff --git a/examples/vae.py b/examples/vae.py
@@ -160,7 +160,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith("0.10.1")
+    assert numpyro.__version__.startswith("0.11.0")
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument(
         "-n", "--num-epochs", default=15, type=int, help="number of training epochs"
diff --git a/notebooks/source/bad_posterior_geometry.ipynb b/notebooks/source/bad_posterior_geometry.ipynb
@@ -50,7 +50,7 @@
     "\n",
     "from numpyro.infer import MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")\n",
+    "assert numpyro.__version__.startswith(\"0.11.0\")\n",
     "\n",
     "# NB: replace cpu by gpu to run this notebook on gpu\n",
     "numpyro.set_platform(\"cpu\")"
diff --git a/notebooks/source/bayesian_hierarchical_linear_regression.ipynb b/notebooks/source/bayesian_hierarchical_linear_regression.ipynb
@@ -244,7 +244,7 @@
     "import numpyro.distributions as dist\n",
     "from jax import random\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_hierarchical_stacking.ipynb b/notebooks/source/bayesian_hierarchical_stacking.ipynb
@@ -96,7 +96,7 @@
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
     "numpyro.set_host_device_count(4)\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_imputation.ipynb b/notebooks/source/bayesian_imputation.ipynb
@@ -55,7 +55,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ]
   },
   {
diff --git a/notebooks/source/bayesian_regression.ipynb b/notebooks/source/bayesian_regression.ipynb
@@ -95,7 +95,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats(\"svg\")\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ],
    "execution_count": 2,
    "outputs": []
diff --git a/notebooks/source/logistic_regression.ipynb b/notebooks/source/logistic_regression.ipynb
@@ -41,7 +41,7 @@
     "from numpyro.examples.datasets import COVTYPE, load_dataset\n",
     "from numpyro.infer import HMC, MCMC, NUTS\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")\n",
+    "assert numpyro.__version__.startswith(\"0.11.0\")\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"
diff --git a/notebooks/source/model_rendering.ipynb b/notebooks/source/model_rendering.ipynb
@@ -37,7 +37,7 @@
     "import numpyro.distributions as dist\n",
     "import numpyro.distributions.constraints as constraints\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ]
   },
   {
diff --git a/notebooks/source/ordinal_regression.ipynb b/notebooks/source/ordinal_regression.ipynb
@@ -53,7 +53,7 @@
     "import pandas as pd\n",
     "import seaborn as sns\n",
     "\n",
-    "assert numpyro.__version__.startswith(\"0.10.1\")"
+    "assert numpyro.__version__.startswith(\"0.11.0\")"
    ]
   },
   {
diff --git a/notebooks/source/tbip.ipynb b/notebooks/source/tbip.ipynb
diff --git a/notebooks/source/time_series_forecasting.ipynb b/notebooks/source/time_series_forecasting.ipynb
diff --git a/numpyro/contrib/tfp/mcmc.py b/numpyro/contrib/tfp/mcmc.py
diff --git a/numpyro/distributions/copula.py b/numpyro/distributions/copula.py
diff --git a/numpyro/infer/mcmc.py b/numpyro/infer/mcmc.py
diff --git a/numpyro/version.py b/numpyro/version.py
diff --git a/setup.py b/setup.py

Original file line number	Diff line number	Diff line change
`@@ -139,7 +139,7 @@ def main(args):`
`139`	`139`
`140`	`140`
`141`	`141`	`if __name__ == "__main__":`
`142`		`- assert numpyro.__version__.startswith("0.10.1")`
	`142`	`+ assert numpyro.__version__.startswith("0.11.0")`
`143`	`143`	`parser = argparse.ArgumentParser(`
`144`	`144`	`description="Non-centered reparameterization example"`
`145`	`145`	`)`
Original file line number	Diff line number	Diff line change
`@@ -314,7 +314,7 @@ def main(args):`
`314`	`314`
`315`	`315`
`316`	`316`	`if __name__ == "__main__":`
`317`		`- assert numpyro.__version__.startswith("0.10.1")`
	`317`	`+ assert numpyro.__version__.startswith("0.11.0")`
`318`	`318`	`parser = argparse.ArgumentParser(`
`319`	`319`	`description="Probabilistic topic modelling with Flax and Haiku"`
`320`	`320`	`)`
Original file line number	Diff line number	Diff line change
`@@ -151,7 +151,7 @@ def main(args):`
`151`	`151`
`152`	`152`
`153`	`153`	`if __name__ == "__main__":`
`154`		`- assert numpyro.__version__.startswith("0.10.1")`
	`154`	`+ assert numpyro.__version__.startswith("0.11.0")`
`155`	`155`	`parser = argparse.ArgumentParser(`
`156`	`156`	`description="UCBadmit gender discrimination using HMC"`
`157`	`157`	`)`
Original file line number	Diff line number	Diff line change
`@@ -244,7 +244,7 @@`
`244`	`244`	`"import numpyro.distributions as dist\n",`
`245`	`245`	`"from jax import random\n",`
`246`	`246`	`"\n",`
`247`		`- "assert numpyro.__version__.startswith(\"0.10.1\")"`
	`247`	`+ "assert numpyro.__version__.startswith(\"0.11.0\")"`
`248`	`248`	`]`
`249`	`249`	`},`
`250`	`250`	`{`
Original file line number	Diff line number	Diff line change
`@@ -96,7 +96,7 @@`
`96`	`96`	`" set_matplotlib_formats(\"svg\")\n",`
`97`	`97`	`"\n",`
`98`	`98`	`"numpyro.set_host_device_count(4)\n",`
`99`		`- "assert numpyro.__version__.startswith(\"0.10.1\")"`
	`99`	`+ "assert numpyro.__version__.startswith(\"0.11.0\")"`
`100`	`100`	`]`
`101`	`101`	`},`
`102`	`102`	`{`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@`
`55`	`55`	`"if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",`
`56`	`56`	`" set_matplotlib_formats(\"svg\")\n",`
`57`	`57`	`"\n",`
`58`		`- "assert numpyro.__version__.startswith(\"0.10.1\")"`
	`58`	`+ "assert numpyro.__version__.startswith(\"0.11.0\")"`
`59`	`59`	`]`
`60`	`60`	`},`
`61`	`61`	`{`
Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@`
`37`	`37`	`"import numpyro.distributions as dist\n",`
`38`	`38`	`"import numpyro.distributions.constraints as constraints\n",`
`39`	`39`	`"\n",`
`40`		`- "assert numpyro.__version__.startswith(\"0.10.1\")"`
	`40`	`+ "assert numpyro.__version__.startswith(\"0.11.0\")"`
`41`	`41`	`]`
`42`	`42`	`},`
`43`	`43`	`{`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@`
`53`	`53`	`"import pandas as pd\n",`
`54`	`54`	`"import seaborn as sns\n",`
`55`	`55`	`"\n",`
`56`		`- "assert numpyro.__version__.startswith(\"0.10.1\")"`
	`56`	`+ "assert numpyro.__version__.startswith(\"0.11.0\")"`
`57`	`57`	`]`
`58`	`58`	`},`
`59`	`59`	`{`