Merge pull request #4 from pymc-devs/master

Sync Fork from Upstream Repo

Author: sthagen

.travis.yml

@@ -31,7 +31,6 @@ env:
   - FLOATX='float64' TESTCMD="--durations=10 --cov-append pymc3/tests/test_distributions_random.py pymc3/tests/test_shared.py pymc3/tests/test_smc.py pymc3/tests/test_sampling.py pymc3/tests/test_parallel_sampling.py pymc3/tests/test_dist_math.py pymc3/tests/test_distribution_defaults.py pymc3/tests/test_distributions_timeseries.py pymc3/tests/test_random.py"
   - FLOATX='float64' TESTCMD="--durations=10 --cov-append pymc3/tests/test_examples.py pymc3/tests/test_posteriors.py pymc3/tests/test_gp.py"
   - FLOATX='float64' TESTCMD="--durations=10 --cov-append pymc3/tests/test_variational_inference.py pymc3/tests/test_updates.py pymc3/tests/test_shape_handling.py"
-  - PYTHON_VERSION=3.5 FLOATX='float64' ENVNAME="py35_testenv" TESTCMD="--cov-append pymc3/tests/test_sampling.py pymc3/tests/test_model_graph.py"
 
 script:
   - . ./scripts/test.sh $TESTCMD

pymc3/step_methods/hmc/quadpotential.py

@@ -126,8 +126,16 @@ def isquadpotential(value):
 class QuadPotentialDiagAdapt(QuadPotential):
     """Adapt a diagonal mass matrix from the sample variances."""
 
-    def __init__(self, n, initial_mean, initial_diag=None, initial_weight=0,
-                 adaptation_window=101, dtype=None):
+    def __init__(
+        self,
+        n,
+        initial_mean,
+        initial_diag=None,
+        initial_weight=0,
+        adaptation_window=101,
+        adaptation_window_multiplier=1,
+        dtype=None,
+    ):
         """Set up a diagonal mass matrix."""
         if initial_diag is not None and initial_diag.ndim != 1:
             raise ValueError('Initial diagonal must be one-dimensional.')
@@ -158,6 +166,7 @@ def __init__(self, n, initial_mean, initial_diag=None, initial_weight=0,
         self._background_var = _WeightedVariance(self._n, dtype=self.dtype)
         self._n_samples = 0
         self.adaptation_window = adaptation_window
+        self.adaptation_window_multiplier = float(adaptation_window_multiplier)
 
     def velocity(self, x, out=None):
         """Compute the current velocity at a position in parameter space."""
@@ -190,15 +199,14 @@ def update(self, sample, grad, tune):
         if not tune:
             return
 
-        window = self.adaptation_window
-
         self._foreground_var.add_sample(sample, weight=1)
         self._background_var.add_sample(sample, weight=1)
         self._update_from_weightvar(self._foreground_var)
 
-        if self._n_samples > 0 and self._n_samples % window == 0:
+        if self._n_samples > 0 and self._n_samples % self.adaptation_window == 0:
             self._foreground_var = self._background_var
             self._background_var = _WeightedVariance(self._n, dtype=self.dtype)
+            self.adaptation_window = int(self.adaptation_window * self.adaptation_window_multiplier)
 
         self._n_samples += 1
 
@@ -458,22 +466,16 @@ def velocity_energy(self, x, v_out):
 
 
 class QuadPotentialFullAdapt(QuadPotentialFull):
-    """Adapt a dense mass matrix using the sample covariances
-
-    If the parameter ``doubling`` is true, the adaptation window is doubled
-    every time it is passed. This can lead to better convergence of the mass
-    matrix estimation.
-
-    """
+    """Adapt a dense mass matrix using the sample covariances."""
     def __init__(
         self,
         n,
         initial_mean,
         initial_cov=None,
         initial_weight=0,
         adaptation_window=101,
+        adaptation_window_multiplier=2,
         update_window=1,
-        doubling=True,
         dtype=None,
     ):
         warnings.warn("QuadPotentialFullAdapt is an experimental feature")
@@ -511,8 +513,8 @@ def __init__(
         self._background_cov = _WeightedCovariance(self._n, dtype=self.dtype)
         self._n_samples = 0
 
-        self._doubling = doubling
         self._adaptation_window = int(adaptation_window)
+        self._adaptation_window_multiplier = float(adaptation_window_multiplier)
         self._update_window = int(update_window)
         self._previous_update = 0
 
@@ -538,16 +540,16 @@ def update(self, sample, grad, tune):
         if (delta + 1) % self._update_window == 0:
             self._update_from_weightvar(self._foreground_cov)
 
-        # Reset the background covariance if we are at the end of the adaptation window.
+        # Reset the background covariance if we are at the end of the adaptation
+        # window.
         if delta >= self._adaptation_window:
             self._foreground_cov = self._background_cov
             self._background_cov = _WeightedCovariance(
                 self._n, dtype=self.dtype
             )
 
             self._previous_update = self._n_samples
-            if self._doubling:
-                self._adaptation_window *= 2
+            self._adaptation_window = int(self._adaptation_window * self._adaptation_window_multiplier)
 
         self._n_samples += 1
 

pymc3/tests/test_quadpotential.py

@@ -225,15 +225,15 @@ def test_full_adapt_adaptation_window(seed=8978):
     for i in range(window + 1):
         pot.update(np.random.randn(2), None, True)
     assert pot._previous_update == window
-    assert pot._adaptation_window == window * 2
+    assert pot._adaptation_window == window * pot._adaptation_window_multiplier
 
     pot = quadpotential.QuadPotentialFullAdapt(
-        2, np.zeros(2), np.eye(2), 1, adaptation_window=window, doubling=False
+        2, np.zeros(2), np.eye(2), 1, adaptation_window=window
     )
     for i in range(window + 1):
         pot.update(np.random.randn(2), None, True)
     assert pot._previous_update == window
-    assert pot._adaptation_window == window
+    assert pot._adaptation_window == window * pot._adaptation_window_multiplier
 
 
 def test_full_adapt_not_invertible():

setup.py

@@ -14,7 +14,6 @@
 classifiers = ['Development Status :: 5 - Production/Stable',
                'Programming Language :: Python',
                'Programming Language :: Python :: 3',
-               'Programming Language :: Python :: 3.5',
                'Programming Language :: Python :: 3.6',
                'Programming Language :: Python :: 3.7',
                'License :: OSI Approved :: Apache Software License',
@@ -59,7 +58,7 @@ def get_version():
           package_data={'docs': ['*']},
           include_package_data=True,
           classifiers=classifiers,
-          python_requires=">=3.5.4",
+          python_requires=">=3.6",
           install_requires=install_reqs,
           tests_require=test_reqs,
           test_suite='nose.collector')