Partial fixes for python3 failures (06a1d604) · Commits · 钟慕尧 / deepchem

deepchem/featurizers/graph_features.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -13,13 +13,13 @@ def one_of_k_encoding(x, allowable_set):
		if x not in allowable_set:
		raise Exception(
		"input {0} not in allowable set{1}:".format(x, allowable_set))
		return map(lambda s: x == s, allowable_set)
		return list(map(lambda s: x == s, allowable_set))

		def one_of_k_encoding_unk(x, allowable_set):
		"""Maps inputs not in the allowable set to the last element."""
		if x not in allowable_set:
		x = allowable_set[-1]
		return map(lambda s: x == s, allowable_set)
		return list(map(lambda s: x == s, allowable_set))

		def get_intervals(l):
		"""For list of lists, gets the cumulative products of the lengths"""

+1 −1

Original line number	Diff line number	Diff line
		@@ -92,7 +92,7 @@ class ConvMol(object):
		self.deg_block_indices = np.array(deg_block_indices)

		def get_atoms_with_deg(self, deg):
		# Retrieves atom_features with the specific degree
		"""Retrieves atom_features with the specific degree"""
		start_ind = self.deg_slice[deg-self.min_deg,0]
		size = self.deg_slice[deg-self.min_deg,1]
		return self.atom_features[start_ind:(start_ind+size),:]

+3 −3

Original line number	Diff line number	Diff line
		@@ -90,8 +90,8 @@ def graph_conv(atoms, deg_adj_lists, deg_slice, max_deg, min_deg, W_list,
		self_atoms = tf.slice(atoms, begin, size)

		# Apply hidden affine to relevant atoms and append
		rel_out = affine(rel_atoms, W.next(), b.next())
		self_out = affine(self_atoms, W.next(), b.next())
		rel_out = affine(rel_atoms, next(W), next(b))
		self_out = affine(self_atoms, next(W), next(b))
		out = rel_out + self_out

		new_rel_atoms_collection[deg-min_deg] = out
		@@ -105,7 +105,7 @@ def graph_conv(atoms, deg_adj_lists, deg_slice, max_deg, min_deg, W_list,
		self_atoms = tf.slice(atoms, begin, size)

		# Only use the self layer
		out = affine(self_atoms, W.next(), b.next())
		out = affine(self_atoms, next(W), next(b))

		new_rel_atoms_collection[deg-min_deg] = out

+28 −22

Original line number	Diff line number	Diff line
		@@ -10,6 +10,8 @@ __copyright__ = "Copyright 2016, Stanford University"
		__license__ = "GPL"

		import unittest
		import tensorflow as tf
		from keras import backend as K
		from tensorflow.python.framework import test_util
		from keras.layers import Dense, BatchNormalization
		from deepchem.models.tf_keras_models.graph_models import SequentialGraphModel
		@@ -55,7 +57,11 @@ class TestGraphModels(test_util.TensorFlowTestCase):
		assert len(graph_model.layers) == 6

		def test_sample_attn_lstm_architecture(self):
		"""Tests that a representative attention architecture can be created."""
		"""Tests that an attention architecture can be created without crash."""
		g = tf.Graph()
		sess = tf.Session(graph=g)
		K.set_session(sess)
		with g.as_default():
		max_depth = 5
		n_test = 5
		n_support = 11