Release patch for python 3.7 incompatibility (#490)

* Release patch for python 3.7 incompatibility

* limit size of cache

examples/baseball.py

@@ -182,7 +182,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description="Baseball batting average using HMC")
     parser.add_argument("-n", "--num-samples", nargs="?", default=3000, type=int)
     parser.add_argument("--num-warmup", nargs='?', default=1500, type=int)

examples/bnn.py

@@ -133,7 +133,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/covtype.py

@@ -57,7 +57,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-samples', default=100, type=int, help='number of samples')
     parser.add_argument('--num-steps', default=10, type=int, help='number of steps (for "HMC")')

examples/funnel.py

@@ -84,7 +84,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description="Non-centered reparameterization example")
     parser.add_argument("-n", "--num-samples", nargs="?", default=1000, type=int)
     parser.add_argument("--num-warmup", nargs='?', default=1000, type=int)

examples/gp.py

@@ -126,7 +126,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/hmm.py

@@ -180,7 +180,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/minipyro.py

@@ -55,7 +55,7 @@ def body_fn(i, val):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/neutra.py

@@ -151,7 +151,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description="NeuTra HMC")
     parser.add_argument('-n', '--num-samples', nargs='?', default=10000, type=int)
     parser.add_argument('--num-warmup', nargs='?', default=1000, type=int)

examples/sparse_regression.py

@@ -319,7 +319,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/stochastic_volatility.py

@@ -108,7 +108,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     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)

examples/ucbadmit.py

@@ -126,7 +126,7 @@ def main(args):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description='UCBadmit gender discrimination using HMC')
     parser.add_argument('-n', '--num-samples', nargs='?', default=2000, type=int)
     parser.add_argument('--num-warmup', nargs='?', default=500, type=int)

examples/vae.py

@@ -128,7 +128,7 @@ def reconstruct_img(epoch, rng_key):
 
 
 if __name__ == '__main__':
-    assert numpyro.__version__.startswith('0.2.2')
+    assert numpyro.__version__.startswith('0.2.3')
     parser = argparse.ArgumentParser(description="parse args")
     parser.add_argument('-n', '--num-epochs', default=20, type=int, help='number of training epochs')
     parser.add_argument('-lr', '--learning-rate', default=1.0e-3, type=float, help='learning rate')

notebooks/source/bayesian_regression.ipynb

@@ -66,7 +66,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats('svg')\n",
     "\n",
-    "assert numpyro.__version__.startswith('0.2.2')"
+    "assert numpyro.__version__.startswith('0.2.3')"
    ]
   },
   {

notebooks/source/logistic_regression.ipynb

@@ -31,7 +31,7 @@
     "import numpyro.distributions as dist\n",
     "from numpyro.examples.datasets import COVTYPE, load_dataset\n",
     "from numpyro.infer import HMC, MCMC, NUTS\n",
-    "assert numpyro.__version__.startswith('0.2.2')\n",
+    "assert numpyro.__version__.startswith('0.2.3')\n",
     "\n",
     "# NB: replace gpu by cpu to run this notebook in cpu\n",
     "numpyro.set_platform(\"gpu\")"

notebooks/source/time_series_forecasting.ipynb

@@ -39,7 +39,7 @@
     "if \"NUMPYRO_SPHINXBUILD\" in os.environ:\n",
     "    set_matplotlib_formats('svg')\n",
     "\n",
-    "assert numpyro.__version__.startswith('0.2.2')"
+    "assert numpyro.__version__.startswith('0.2.3')"
    ]
   },
   {

numpyro/infer/mcmc.py

@@ -774,7 +774,7 @@ def _single_chain_mcmc(self, rng_key, init_state, init_params, args, kwargs, col
                                     return_last_val=True,
                                     collection_size=self._collection_params["collection_size"],
                                     progbar_desc=functools.partial(get_progbar_desc_str,
-                                                                   num_warmup=lower_idx),
+                                                                   lower_idx),
                                     diagnostics_fn=diagnostics)
         states, last_val = collect_vals
         # Get first argument of type `HMCState`

numpyro/util.py

@@ -1,4 +1,4 @@
-from collections import namedtuple
+from collections import namedtuple, OrderedDict
 from contextlib import contextmanager
 import os
 import random
@@ -143,13 +143,21 @@ def identity(x):
 
 
 def cached_by(outer_fn, *keys):
-    outer_fn._cache = getattr(outer_fn, '_cache', {})
+    # Restrict cache size to prevent ref cycles.
+    max_size = 8
+    outer_fn._cache = getattr(outer_fn, '_cache', OrderedDict())
 
     def _wrapped(fn):
         fn_cache = outer_fn._cache
         if keys in fn_cache:
-            return fn_cache[keys]
-        fn_cache[keys] = fn
+            fn = fn_cache[keys]
+            # update position
+            del fn_cache[keys]
+            fn_cache[keys] = fn
+        else:
+            fn_cache[keys] = fn
+        if len(fn_cache) > max_size:
+            fn_cache.popitem(last=False)
         return fn
 
     return _wrapped

numpyro/version.py

@@ -1 +1 @@
-__version__ = '0.2.2'
+__version__ = '0.2.3'