Merge pull request #1191 from jburnim/r0.12

Prepare branch for the TFP 0.12.0rc4 release

.github/workflows/continuous-integration.yml

@@ -0,0 +1,70 @@
+# Copyright 2020 The TensorFlow Probability Authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ============================================================================
+name: Tests
+on: [push, pull_request]
+env:
+  TEST_VENV_PATH: ~/test_virtualenv
+jobs:
+  lints:
+    name: Lints
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+        with:
+          fetch-depth: 20
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup virtualenv
+        run: |
+          sudo apt install virtualenv
+          virtualenv -p python${{ matrix.python-version }} ${TEST_VENV_PATH}
+      - name: Lints
+        run: |
+          source ${TEST_VENV_PATH}/bin/activate
+          ./testing/run_github_lints.sh
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7]
+        shard: [0, 1, 2, 3, 4]
+    env:
+      TEST_VENV_PATH: ~/test_virtualenv
+      SHARD: ${{ matrix.shard }}
+      NUM_SHARDS: 5
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+        with:
+          fetch-depth: 1
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup virtualenv
+        run: |
+          sudo apt install virtualenv
+          virtualenv -p python${{ matrix.python-version }} ${TEST_VENV_PATH}
+      - name: Tests
+        run: |
+          source ${TEST_VENV_PATH}/bin/activate
+          ./testing/run_github_tests.sh

CONTRIBUTING.md

@@ -32,20 +32,19 @@ repository (with credit to the original author) and closes the pull request.
 
 ## Continuous Integration
 
-We use [Travis CI](https://travis-ci.org/tensorflow/probability) to do automated
-style checking and run unit-tests (discussed in more detail below). A build
-will be triggered when you open a pull request, or update the pull request by
-adding a commit, rebasing etc.
+We use [GitHub Actions](https://github.com/tensorflow/probability/actions) to do
+automated style checking and run unit-tests (discussed in more detail below). A
+build will be triggered when you open a pull request, or update the pull request
+by adding a commit, rebasing etc.
 
-We test against TensorFlow nightly on Python 2.7 and 3.6. We shard our tests
+We test against TensorFlow nightly on Python 3.7. We shard our tests
 across several build jobs (identified by the `SHARD` environment variable).
-Linting, in particular, is only done on the first shard, so look at that shard's
-logs for lint errors if any.
+Lints are also done in a separate job.
 
 All pull-requests will need to pass the automated lint and unit-tests before
-being merged. As Travis-CI tests can take a bit of time, see the following
-sections on how to run the lint checks and unit-tests locally while you're
-developing your change.
+being merged. As the tests can take a bit of time, see the following sections
+on how to run the lint checks and unit-tests locally while you're developing
+your change.
 
 ## Style
 

discussion/fun_mcmc/prefab.py

@@ -347,7 +347,7 @@ def kernel(adaptive_hmc_state):
       hmc_state.state,
       axis=tuple(range(chain_ndims)) if chain_ndims else None,
       window_size=int(np.prod(hmc_state.target_log_prob.shape)) *
-      variance_window_steps)
+      variance_window_steps)  # pytype: disable=wrong-arg-types
 
   if num_adaptation_steps is not None:
     # Take care of adaptation for variance and step size.

spinoffs/inference_gym/inference_gym/BUILD

@@ -16,7 +16,7 @@
 #   A package for target densities and benchmarking of inference algorithms
 #   against the same.
 
-# [internal] load pytype.bzl (pytype_library, pytype_strict_library)
+# [internal] load pytype.bzl (pytype_strict_library)
 # [internal] load dummy dependency
 
 package(
@@ -42,7 +42,6 @@ py_library(
     ],
 )
 
-# pytype
 py_library(
     name = "using_numpy",
     srcs = ["using_numpy.py"],
@@ -56,7 +55,6 @@ py_library(
     ],
 )
 
-# pytype
 py_library(
     name = "using_jax",
     srcs = ["using_jax.py"],
@@ -71,7 +69,6 @@ py_library(
     ],
 )
 
-# pytype
 py_library(
     name = "using_tensorflow",
     srcs = ["using_tensorflow.py"],

spinoffs/oryx/oryx/core/interpreters/harvest.py

@@ -333,22 +333,27 @@ def process_higher_order_primitive(self, primitive, f, tracers, params,
     if is_map:
       # TODO(sharadmv): figure out if invars are mapped or unmapped
       params = params.copy()
+      out_axes_thunk = params['out_axes_thunk']
+      @jax_util.as_hashable_function(closure=('harvest', out_axes_thunk))
+      def new_out_axes_thunk():
+        out_axes = out_axes_thunk()
+        assert all(out_axis == 0 for out_axis in out_axes)
+        return (0,) * out_tree().num_leaves
       new_params = dict(
           params,
-          in_axes=(0,) * len(tree_util.tree_leaves(plants)) +
-          params['in_axes'])
+          in_axes=(0,) * len(tree_util.tree_leaves(plants)) + params['in_axes'],
+          out_axes_thunk=new_out_axes_thunk)
     else:
       new_params = dict(params)
     all_args, all_tree = tree_util.tree_flatten((plants, vals))
     num_plants = len(all_args) - len(vals)
     if 'donated_invars' in params:
       new_params['donated_invars'] = ((False,) * num_plants
                                       + params['donated_invars'])
-    f, aux = harvest_eval(f, self, context.settings, all_tree)
+    f, out_tree = harvest_eval(f, self, context.settings, all_tree)
     out_flat = primitive.bind(
         f, *all_args, **new_params, name=jax_util.wrap_name(name, 'harvest'))
-    out_tree = aux()
-    out, reaps = tree_util.tree_unflatten(out_tree, out_flat)
+    out, reaps = tree_util.tree_unflatten(out_tree(), out_flat)
     out_tracers = safe_map(self.pure, out)
     reap_tracers = tree_util.tree_map(self.pure, reaps)
     if primitive is nest_p and reap_tracers:

spinoffs/oryx/oryx/core/interpreters/inverse/core.py

@@ -178,7 +178,7 @@ def wrapped(*args, **kwargs):
     flat_incells = [InverseAndILDJ.unknown(aval) for aval in flat_forward_avals]
     flat_outcells = safe_map(InverseAndILDJ.new, flat_args)
     env = propagate.propagate(InverseAndILDJ, ildj_registry, jaxpr.jaxpr,
-                              flat_constcells, flat_incells, flat_outcells)
+                              flat_constcells, flat_incells, flat_outcells)  # pytype: disable=wrong-arg-types
     flat_incells = [env.read(invar) for invar in jaxpr.jaxpr.invars]
     if any(not flat_incell.top() for flat_incell in flat_incells):
       raise ValueError('Cannot invert function.')
@@ -332,7 +332,7 @@ def hop_inverse_rule(prim):
 def initial_ildj(incells, outcells, *, jaxpr, num_consts, **_):
   const_cells, incells = jax_util.split_list(incells, [num_consts])
   env = propagate.propagate(InverseAndILDJ, ildj_registry, jaxpr, const_cells,
-                            incells, outcells)
+                            incells, outcells)  # pytype: disable=wrong-arg-types
   new_incells = [env.read(invar) for invar in jaxpr.invars]
   new_outcells = [env.read(outvar) for outvar in jaxpr.outvars]
   return const_cells + new_incells, new_outcells, None
@@ -377,6 +377,12 @@ def remove_slice(cell):
   new_params = dict(params, in_axes=new_in_axes)
   if 'donated_invars' in params:
     new_params['donated_invars'] = (False,) * len(flat_vals)
+  if 'out_axes' in params:
+    assert all(out_axis == 0 for out_axis in params['out_axes'])
+    new_params['out_axes_thunk'] = jax_util.HashableFunction(
+        lambda: (0,) * aux().num_leaves,
+        closure=('ildj', params['out_axes']))
+    del new_params['out_axes']
   subenv_vals = prim.bind(f, *flat_vals, **new_params)
   subenv_tree = aux()
   subenv = tree_util.tree_unflatten(subenv_tree, subenv_vals)

spinoffs/oryx/oryx/core/interpreters/inverse/inverse_test.py

@@ -249,6 +249,14 @@ def f(x, y):
     onp.testing.assert_allclose(y, np.ones(2))
     onp.testing.assert_allclose(ildj_, 0., atol=1e-6, rtol=1e-6)
 
+  def test_inverse_of_reshape(self):
+    def f(x):
+      return np.reshape(x, (4,))
+    f_inv = core.inverse_and_ildj(f, np.ones((2, 2)))
+    x, ildj_ = f_inv(np.ones(4))
+    onp.testing.assert_allclose(x, np.ones((2, 2)))
+    onp.testing.assert_allclose(ildj_, 0.)
+
   def test_sigmoid_ildj(self):
     def naive_sigmoid(x):
       # This is the default JAX implementation of sigmoid.

spinoffs/oryx/oryx/core/interpreters/inverse/rules.py

@@ -166,9 +166,8 @@ def reshape_ildj(incells, outcells, **params):
     ))], None
   elif outcell.top() and not incell.top():
     val = outcell.val
-    ndslice = NDSlice.new(np.reshape(val, incell.aval.shape))
     new_incells = [
-        InverseAndILDJ(incell.aval, [ndslice])
+        InverseAndILDJ.new(np.reshape(val, incell.aval.shape))
     ]
     return new_incells, outcells, None
   return incells, outcells, None

spinoffs/oryx/oryx/core/interpreters/unzip.py

@@ -288,19 +288,29 @@ def handle_call_primitive(self, call_primitive, f, tracers, params, is_map):
       in_pvals = [pval if pval.is_known() or in_axis is None else
                   unknown(mapped_aval(params['axis_size'], in_axis, pval[0]))
                   for pval, in_axis in zip(in_pvals, params['in_axes'])]
+      out_axes_thunk = params['out_axes_thunk']
+      @jax_util.as_hashable_function(closure=('unzip', out_axes_thunk))
+      def new_out_axes_thunk():
+        out_axes = out_axes_thunk()
+        assert all(out_axis == 0 for out_axis in out_axes)
+        _, num_outputs, _ = aux()
+        return (0,) * num_outputs
+      new_params = dict(params, out_axes_thunk=new_out_axes_thunk)
+    else:
+      new_params = params
     pvs, in_consts = jax_util.unzip2(t.pval for t in tracers)
     keys = tuple(t.is_key() for t in tracers)
     new_settings = UnzipSettings(settings.tag, call_primitive in block_registry)
     fun, aux = unzip_eval(f, self, keys, tuple(pvs), new_settings)
-    out_flat = call_primitive.bind(fun, *in_consts, **params)
-    success, results = aux()
+    out_flat = call_primitive.bind(fun, *in_consts, **new_params)
+    success, _, results = aux()
     if not success:
       out_pvs, out_keys, jaxpr, env = results
       out_pv_consts, consts = jax_util.split_list(out_flat, [len(out_pvs)])
-      out_tracers = self._bound_output_tracers(call_primitive, params, jaxpr,
-                                               consts, env, tracers, out_pvs,
-                                               out_pv_consts, out_keys, name,
-                                               is_map)
+      out_tracers = self._bound_output_tracers(call_primitive, new_params,
+                                               jaxpr, consts, env, tracers,
+                                               out_pvs, out_pv_consts,
+                                               out_keys, name, is_map)
       return out_tracers
     init_name = jax_util.wrap_name(name, 'init')
     apply_name = jax_util.wrap_name(name, 'apply')
@@ -319,15 +329,16 @@ def handle_call_primitive(self, call_primitive, f, tracers, params, is_map):
                                                         [len(apply_pvs)])
 
     variable_tracers = self._bound_output_tracers(
-        call_primitive, params, init_jaxpr, init_consts, init_env, key_tracers,
-        init_pvs, init_pv_consts, [True] * len(init_pvs), init_name, is_map)
+        call_primitive, new_params, init_jaxpr, init_consts, init_env,
+        key_tracers, init_pvs, init_pv_consts, [True] * len(init_pvs),
+        init_name, is_map)
 
     unflat_variables = tree_util.tree_unflatten(variable_tree, variable_tracers)
     if call_primitive is harvest.nest_p:
       variable_dict = harvest.sow(
           dict(safe_zip(variable_names, unflat_variables)),
           tag=settings.tag,
-          name=params['scope'],
+          name=new_params['scope'],
           mode='strict')
       unflat_variables = tuple(variable_dict[name] for name in variable_names)
     else:
@@ -342,7 +353,7 @@ def handle_call_primitive(self, call_primitive, f, tracers, params, is_map):
     variable_tracers = tree_util.tree_leaves(unflat_variables)
 
     out_tracers = self._bound_output_tracers(
-        call_primitive, params, apply_jaxpr, apply_consts, apply_env,
+        call_primitive, new_params, apply_jaxpr, apply_consts, apply_env,
         variable_tracers + abstract_tracers, apply_pvs, apply_pv_consts,
         apply_keys, apply_name, is_map)
     return out_tracers
@@ -365,6 +376,11 @@ def _bound_output_tracers(self, primitive, params, jaxpr, consts, env,
           tuple(v for v, t in zip(params['donated_invars'], in_tracers)
                 if not t.pval.is_known()))
       new_params['donated_invars'] = new_donated_invars
+    if is_map:
+      out_axes = params['out_axes_thunk']()
+      assert all(out_axis == 0 for out_axis in out_axes)
+      new_params['out_axes'] = (0,) * len(out_tracers)
+      del new_params['out_axes_thunk']
     eqn = pe.new_eqn_recipe(
         tuple(const_tracers + env_tracers + in_tracers), out_tracers, primitive,
         new_params, source_info_util.current())  # pytype: disable=wrong-arg-types
@@ -442,14 +458,16 @@ def unzip_eval_wrapper(pvs, *consts):
     out = (
         tuple(init_pv_consts) + tuple(init_consts) + tuple(apply_pv_consts) +
         tuple(apply_consts))
-    yield out, (success, ((init_pvs, len(init_consts), apply_pvs),
-                          (init_jaxpr, apply_jaxpr), (init_env,
-                                                      apply_env), metadata))
+    yield out, (success, len(out),
+                ((init_pvs, len(init_consts), apply_pvs),
+                 (init_jaxpr, apply_jaxpr),
+                 (init_env, apply_env),
+                 metadata))
   else:
     jaxpr, (out_pvals, out_keys, consts, env) = result
     out_pvs, out_consts = jax_util.unzip2(out_pvals)
     out = tuple(out_consts) + tuple(consts)
-    yield out, (success, (out_pvs, out_keys, jaxpr, env))
+    yield out, (success, len(out), (out_pvs, out_keys, jaxpr, env))
 
 
 @lu.transformation

spinoffs/oryx/oryx/core/state/module.py

@@ -168,4 +168,4 @@ def variables(self) -> Dict[str, Any]:
 
 @ppl.log_prob.register(Module)
 def module_log_prob(module, *args, **kwargs):
-  return log_prob.log_prob(module, *args, **kwargs)
+  return log_prob.log_prob(module, *args, **kwargs)  # pytype: disable=wrong-arg-count