Merge pull request #753 from rbharath/deprecation (d5875180) · Commits · 钟慕尧 / deepchem

deepchem/models/autoencoder_models/autoencoder.py

+5 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		TODO(LESWING) Remove h5py dependency
		TODO(LESWING) Remove keras dependency and replace with functional keras API
		"""

		import warnings
		from deepchem.models import Model
		from deepchem.models.autoencoder_models.model import MoleculeVAE
		from deepchem.feat.one_hot import zinc_charset
		@@ -38,6 +38,8 @@ class TensorflowMoleculeEncoder(Model):
		latent_rep_size: int
		How large a 1D Vector for latent representation
		"""
		warnings.warn("TensorflowMoleculeEncoder Deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)
		super(TensorflowMoleculeEncoder, self).__init__(
		model_dir=model_dir, verbose=verbose)
		weights_file = os.path.join(model_dir, weights_file)
		@@ -105,6 +107,8 @@ class TensorflowMoleculeDecoder(Model):
		latent_rep_size: int
		How large a 1D Vector for latent representation
		"""
		warnings.warn("TensorflowMoleculeDecoder Deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)
		super(TensorflowMoleculeDecoder, self).__init__(
		model_dir=model_dir, verbose=verbose)
		weights_file = os.path.join(model_dir, weights_file)

+5 −0

Original line number	Diff line number	Diff line
		import warnings
		from keras import backend as K
		from keras import objectives
		from keras.layers import Input, Lambda
		@@ -12,6 +13,10 @@ class MoleculeVAE():

		autoencoder = None

		def __init__(self):
		warnings.warn("Deprecated. Will be removed in DeepChem 1.4.",
		DeprecationWarning)

		def create(self,
		charset_length,
		max_length=120,

+8 −5

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@ from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		import warnings
		import time
		import numpy as np
		import tensorflow as tf
		@@ -58,7 +59,9 @@ class TensorflowMultiTaskIRVClassifier(TensorflowLogisticRegression):
		If not none, is used as random seed for tensorflow.

		"""

		warnings.warn("The TensorflowMultiTaskIRVClassifier is "
		"deprecated. Will be removed in DeepChem 1.4.",
		DeprecationWarning)
		self.n_tasks = n_tasks
		self.K = K
		self.n_features = 2 * self.K * self.n_tasks
		@@ -89,8 +92,8 @@ class TensorflowMultiTaskIRVClassifier(TensorflowLogisticRegression):

		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750043/
		"""
		placeholder_scope = TensorflowGraph.get_placeholder_scope(graph,
		name_scopes)
		placeholder_scope = TensorflowGraph.get_placeholder_scope(
		graph, name_scopes)
		K = self.K
		with graph.as_default():
		output = []
		@@ -104,8 +107,8 @@ class TensorflowMultiTaskIRVClassifier(TensorflowLogisticRegression):
		b2 = tf.Variable(tf.constant([0.01]), name="b2", dtype=tf.float32)

		label_placeholders = self.add_label_placeholders(graph, name_scopes)
		weight_placeholders = self.add_example_weight_placeholders(graph,
		name_scopes)
		weight_placeholders = self.add_example_weight_placeholders(
		graph, name_scopes)
		if training:
		graph.queue = tf.FIFOQueue(
		capacity=5,

+6 −0

Original line number	Diff line number	Diff line
		@@ -4,6 +4,7 @@ from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		import warnings
		import collections
		import pickle
		import os
		@@ -50,6 +51,8 @@ class TensorflowGraph(object):

		def __init__(self, graph, session, name_scopes, output, labels, weights,
		loss):
		warnings.warn("TensorflowGraph is deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)
		self.graph = graph
		self.session = session
		self.name_scopes = name_scopes
		@@ -175,6 +178,9 @@ class TensorflowGraphModel(Model):
		seed: int
		If not none, is used as random seed for tensorflow.
		"""
		warnings.warn("TensorflowGraphModel is deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)

		# Save hyperparameters
		self.n_tasks = n_tasks
		self.n_features = n_features

+8 −0

Original line number	Diff line number	Diff line
		@@ -4,6 +4,7 @@ from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		import warnings
		import time
		import numpy as np
		import tensorflow as tf
		@@ -388,6 +389,8 @@ class TensorflowMultiTaskClassifier(TensorflowClassifier):
		mol_features: Molecule descriptor (e.g. fingerprint) tensor with shape
		batch_size x n_features.
		"""
		warnings.warn("TensorflowMultiTaskClassifier is deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)
		placeholder_scope = TensorflowGraph.get_placeholder_scope(
		graph, name_scopes)
		n_features = self.n_features
		@@ -485,6 +488,8 @@ class TensorflowMultiTaskRegressor(TensorflowRegressor):
		mol_features: Molecule descriptor (e.g. fingerprint) tensor with shape
		batch_size x n_features.
		"""
		warnings.warn("TensorflowMultiTaskRegressor is deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)
		n_features = self.n_features
		placeholder_scope = TensorflowGraph.get_placeholder_scope(
		graph, name_scopes)
		@@ -662,6 +667,9 @@ class TensorflowMultiTaskFitTransformRegressor(TensorflowMultiTaskRegressor):
		If not none, is used as random seed for tensorflow.

		"""
		warnings.warn("TensorflowMultiTaskFitTransformRegressor "
		"is deprecated. "
		"Will be removed in DeepChem 1.4.", DeprecationWarning)

		self.fit_transformers = fit_transformers
		self.n_evals = n_evals