Fixes for crashing tests (6ed0710b) · Commits · 钟慕尧 / deepchem

deepchem/models/tests/test_overfit.py

+0 −7

Original line number	Diff line number	Diff line
		@@ -716,11 +716,6 @@ class TestOverfitAPI(test_util.TensorFlowTestCase):
		evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
		scores = evaluator.compute_model_performance([classification_metric])

		############################################################ DEBUG
		print("scores")
		print(scores)
		############################################################ DEBUG

		assert scores[classification_metric.name] > .9

		def test_attn_lstm_multitask_classification_overfit(self):
		@@ -797,8 +792,6 @@ class TestOverfitAPI(test_util.TensorFlowTestCase):
		classification_metric, n_trials=5,
		n_pos=n_pos, n_neg=n_neg,
		exclude_support=False, replace=False)
		print("scores")
		print(scores)

		# Measure performance on 0-th task.
		assert scores[0] > .9

deepchem/models/tf_keras_models/graph_models.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -42,8 +42,8 @@ class SequentialGraphModel(object):
		# For graphical layers, add connectivity placeholders
		if type(layer).__name__ in ['GraphConv', 'GraphGather', 'GraphPool']:
		if (len(self.layers) > 0 and hasattr(self.layers[-1], "__name__")):
		assert (self.layers[-1].__name__ != "GraphGather",
		'Cannot use GraphConv or GraphGather layers after a GraphGather')
		assert self.layers[-1].__name__ != "GraphGather", \
		'Cannot use GraphConv or GraphGather layers after a GraphGather'

		self.output = layer(
		[self.output] + self.graph_topology.get_topology_placeholders())
		@@ -71,7 +71,7 @@ class SequentialGraphModel(object):

		class SequentialSupportGraphModel(object):
		"""An analog of Keras Sequential model for test/support models."""
		def __init__(self, n_feat, max_atoms_per_mol=60):
		def __init__(self, n_feat):
		"""
		Parameters
		----------
		@@ -99,7 +99,7 @@ class SequentialSupportGraphModel(object):

		# Update new value of x
		if type(layer).__name__ in ['GraphConv', 'GraphGather', 'GraphPool']:
		assert (self.bool_pre_gather, "Cannot apply graphical layers after gather.")
		assert self.bool_pre_gather, "Cannot apply graphical layers after gather."

		self.test = layer([self.test] + self.test_graph_topology.topology)
		self.support = layer([self.support] + self.support_graph_topology.topology)

deepchem/models/tf_keras_models/tests/test_graph_models.py

+4 −5

Original line number	Diff line number	Diff line
		@@ -32,7 +32,7 @@ class TestGraphModels(test_util.TensorFlowTestCase):
		n_atoms = 5
		n_feat = 10
		batch_size = 3
		graph_model = SequentialGraphModel(n_atoms, n_feat, batch_size)
		graph_model = SequentialGraphModel(n_feat)
		assert len(graph_model.layers) == 0

		def test_sample_sequential_architecture(self):
		@@ -40,7 +40,7 @@ class TestGraphModels(test_util.TensorFlowTestCase):
		n_atoms = 5
		n_feat = 10
		batch_size = 3
		graph_model = SequentialGraphModel(n_atoms, n_feat, batch_size)
		graph_model = SequentialGraphModel(n_feat)

		graph_model.add(GraphConv(64, activation='relu'))
		graph_model.add(BatchNormalization(epsilon=1e-5, mode=1))
		@@ -60,10 +60,9 @@ class TestGraphModels(test_util.TensorFlowTestCase):
		n_test = 5
		n_support = 11
		n_feat = 10
		nb_filter = 7
		batch_size = 3

		support_model = SequentialSupportGraphModel(n_test, n_support, n_feat)
		support_model = SequentialSupportGraphModel(n_feat)

		# Add layers
		support_model.add(GraphConv(64, activation='relu'))
		@@ -74,7 +73,7 @@ class TestGraphModels(test_util.TensorFlowTestCase):
		support_model.add(GraphPool())

		# Apply an attention lstm layer
		support_model.join(AttnLSTMEmbedding(max_depth))
		support_model.join(AttnLSTMEmbedding(n_test, n_support, max_depth))

		# Gather Projection
		support_model.add(Dense(128, activation='relu'))

deepchem/models/tf_keras_models/tests/test_graph_topology.py

+4 −5

Original line number	Diff line number	Diff line
		@@ -21,13 +21,12 @@ class TestGraphTopology(unittest.TestCase):
		def test_shapes(self):
		"""Simple test that Graph topology placeholders have correct shapes."""
		n_atoms = 5
		n_atom_feat = 10
		n_feat = 10
		batch_size = 3
		max_deg = 6
		min_deg = 0
		topology = GraphTopology(n_atoms, n_atom_feat, batch_size)
		topology = GraphTopology(n_feat)

		assert topology.get_batch_size() == 3
		# Degrees from 1 to max_deg inclusive
		# TODO(rbharath): Should this be 0 to max_deg inclusive?
		deg_adj_lists_placeholders = topology.get_deg_adjacency_lists_placeholders()
		@@ -37,9 +36,9 @@ class TestGraphTopology(unittest.TestCase):
		# Should have shape (?, deg)
		assert deg_adj_list.get_shape()[1] == deg

		# Shape of atom_features should be (?, n_atom_feat)
		# Shape of atom_features should be (?, n_feat)
		atom_features = topology.get_atom_features_placeholder()
		assert atom_features.get_shape()[1] == n_atom_feat
		assert atom_features.get_shape()[1] == n_feat

		# Shape of deg_slice placeholder should be (max_deg+1-min_deg, 2)
		deg_slice = topology.get_deg_slice_placeholder()

deepchem/models/tf_keras_models/tests/test_keras_layers.py

+7 −7

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ class TestKerasLayers(test_util.TensorFlowTestCase):
		n_feat = 10
		nb_filter = 7
		with self.test_session() as sess:
		graph_topology = GraphTopology(n_atoms, n_feat)
		graph_topology = GraphTopology(n_feat)
		graph_conv_layer = GraphConv(nb_filter)

		X = graph_topology.get_input_placeholders()
		@@ -50,7 +50,7 @@ class TestKerasLayers(test_util.TensorFlowTestCase):
		batch_size = 3
		nb_filter = 7
		with self.test_session() as sess:
		graph_topology = GraphTopology(n_atoms, n_feat)
		graph_topology = GraphTopology(n_feat)
		graph_gather_layer = GraphGather(batch_size)

		X = graph_topology.get_input_placeholders()
		@@ -65,7 +65,7 @@ class TestKerasLayers(test_util.TensorFlowTestCase):
		batch_size = 3
		nb_filter = 7
		with self.test_session() as sess:
		graph_topology = GraphTopology(n_atoms, n_feat, batch_size)
		graph_topology = GraphTopology(n_feat)
		graph_pool_layer = GraphPool()

		X = graph_topology.get_input_placeholders()
		@@ -85,16 +85,16 @@ class TestKerasLayers(test_util.TensorFlowTestCase):
		n_feat = 10
		nb_filter = 7
		with self.test_session() as sess:
		graph_topology_test = GraphTopology(n_test, n_feat)
		graph_topology_support = GraphTopology(n_support, n_feat)
		graph_topology_test = GraphTopology(n_feat)
		graph_topology_support = GraphTopology(n_feat)

		test = graph_topology_test.get_input_placeholders()[0]
		support = graph_topology_support.get_input_placeholders()[0]

		attn_embedding_layer = AttnLSTMEmbedding(max_depth)
		attn_embedding_layer = AttnLSTMEmbedding(n_test, n_support, max_depth)
		# Try concatenating the two lists of placeholders
		feed_dict = {test: np.zeros((n_test, n_feat)),
		support: np.zeros((n_support, n_feat))}
		test_out, support_out = attn_embedding_layer([test, support])
		assert test_out.get_shape() == (n_test, n_feat)
		assert support_out.get_shape() == (n_support, n_feat)
		assert support_out.get_shape()[1] == (n_feat)

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