Upgrade to TF 1.14, Fixes to tests, attr(slow) for test_gan (ee600b31) · Commits · 钟慕尧 / deepchem

deepchem/models/layers.py

+8 −10

Original line number	Diff line number	Diff line
		@@ -1789,7 +1789,7 @@ class WeaveLayer(tf.keras.layers.Layer):
		"""
		super(WeaveLayer, self).__init__(**kwargs)
		self.init = init # Set weight initialization
		self.activation = activation # Get activations
		self.activation = activations.get(activation) # Get activations
		self.update_pair = update_pair # last weave layer does not need to update
		self.n_hidden_AA = n_hidden_AA
		self.n_hidden_PA = n_hidden_PA
		@@ -1845,8 +1845,6 @@ class WeaveLayer(tf.keras.layers.Layer):

		inputs: [atom_features, pair_features], pair_split, atom_to_pair
		"""
		activation = activations.get(self.activation) # Get activations

		atom_features = inputs[0]
		pair_features = inputs[1]

		@@ -1854,30 +1852,30 @@ class WeaveLayer(tf.keras.layers.Layer):
		atom_to_pair = inputs[3]

		AA = tf.matmul(atom_features, self.W_AA) + self.b_AA
		AA = activation(AA)
		AA = self.activation(AA)
		PA = tf.matmul(pair_features, self.W_PA) + self.b_PA
		PA = activation(PA)
		PA = self.activation(PA)
		PA = tf.segment_sum(PA, pair_split)

		A = tf.matmul(tf.concat([AA, PA], 1), self.W_A) + self.b_A
		A = activation(A)
		A = self.activation(A)

		if self.update_pair:
		AP_ij = tf.matmul(
		tf.reshape(
		tf.gather(atom_features, atom_to_pair),
		[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
		AP_ij = activation(AP_ij)
		AP_ij = self.activation(AP_ij)
		AP_ji = tf.matmul(
		tf.reshape(
		tf.gather(atom_features, tf.reverse(atom_to_pair, [1])),
		[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
		AP_ji = activation(AP_ji)
		AP_ji = self.activation(AP_ji)

		PP = tf.matmul(pair_features, self.W_PP) + self.b_PP
		PP = activation(PP)
		PP = self.activation(PP)
		P = tf.matmul(tf.concat([AP_ij + AP_ji, PP], 1), self.W_P) + self.b_P
		P = activation(P)
		P = self.activation(P)
		else:
		P = pair_features

deepchem/models/tensorgraph/layers.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -2636,10 +2636,10 @@ class AttnLSTMEmbedding(KerasLayer):
		result = layer(inputs)
		if set_tensors:
		self.out_tensor = result[1]
		self.trainable_variables = layer.trainable_variables + layer.states_init
		self.trainable_variables = layer.trainable_variables
		if tf.executing_eagerly() and not self._built:
		self._built = True
		self.trainable_variables = layer.trainable_variables + layer.states_init
		self.trainable_variables = layer.trainable_variables
		return result


		@@ -2691,10 +2691,10 @@ class IterRefLSTMEmbedding(KerasLayer):
		result = layer(inputs)
		if set_tensors:
		self.out_tensor = result[1]
		self.trainable_variables = layer.trainable_variables + layer.support_states_init + layer.test_states_init
		self.trainable_variables = layer.trainable_variables
		if tf.executing_eagerly() and not self._built:
		self._built = True
		self.trainable_variables = layer.trainable_variables + layer.support_states_init + layer.test_states_init
		self.trainable_variables = layer.trainable_variables
		return result

deepchem/models/tensorgraph/tests/test_gan.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -4,6 +4,7 @@ import tensorflow as tf
		import unittest
		from tensorflow.keras.layers import Input, Concatenate, Dense
		from flaky import flaky
		from nose.plugins.attrib import attr


		def generate_batch(batch_size):
		@@ -70,7 +71,7 @@ class TestGAN(unittest.TestCase):
		assert np.std(deltas) > 1.0
		assert gan.get_global_step() == 500

		@flaky
		@attr("slow")
		def test_mix_gan(self):
		"""Test a GAN with multiple generators and discriminators."""

scripts/install_deepchem_conda.sh

+1 −1

Original line number	Diff line number	Diff line
		@@ -63,4 +63,4 @@ conda install -y -q -c deepchem -c rdkit -c conda-forge -c omnia \
		setuptools=39.0.1 \
		biopython=1.71 \
		numpy=1.14
		yes \| pip install $tensorflow==1.13.1
		yes \| pip install $tensorflow==1.14

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