bypass tensorflow imports (6f065998) · Commits · 钟慕尧 / deepchem

deepchem/metalearning/init.py

+4 −2

Original line number	Diff line number	Diff line
		# flake8: noqa

		try:
		from deepchem.metalearning.maml import MAML, MetaLearner
		except ModuleNotFoundError:
		pass

deepchem/models/init.py

+31 −26

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		Gathers all models in one place for convenient imports
		"""
		# flake8: noqa
		try:
		from deepchem.models.models import Model
		from deepchem.models.keras_model import KerasModel
		from deepchem.models.multitask import SingletaskToMultitask
		@@ -24,6 +25,8 @@ from deepchem.models.cnn import CNN
		from deepchem.models.text_cnn import TextCNNModel
		from deepchem.models.atomic_conv import AtomicConvModel
		from deepchem.models.chemnet_models import Smiles2Vec, ChemCeption
		except ModuleNotFoundError:
		pass

		# scikit-learn model
		from deepchem.models.sklearn_models import SklearnModel
		@@ -50,7 +53,9 @@ from deepchem.models.gbdt_models.gbdt_model import XGBoostModel
		########################################################################################
		# Compatibility imports for renamed TensorGraph models. Remove below with DeepChem 3.0.
		########################################################################################

		try:
		from deepchem.models.text_cnn import TextCNNTensorGraph
		from deepchem.models.graph_models import WeaveTensorGraph, DTNNTensorGraph, DAGTensorGraph, GraphConvTensorGraph, MPNNTensorGraph
		from deepchem.models.IRV import TensorflowMultitaskIRVClassifier
		except ModuleNotFoundError:
		pass

deepchem/rl/init.py

+5 −3

Original line number	Diff line number	Diff line
		"""Interface for reinforcement learning."""

		try:
		from deepchem.rl.a2c import A2C # noqa: F401
		from deepchem.rl.ppo import PPO # noqa: F401
		except ModuleNotFoundError:
		pass


		class Environment(object):

deepchem/trans/transformers.py

+7 −2

Original line number	Diff line number	Diff line
		@@ -10,7 +10,6 @@ from typing import Any, List, Optional, Tuple, Union
		import numpy as np
		import scipy
		import scipy.ndimage
		import tensorflow as tf

		import deepchem as dc
		from deepchem.data import Dataset, NumpyDataset, DiskDataset
		@@ -1611,6 +1610,7 @@ class IRVTransformer(Transformer):
		n_samples * np.array of size (2*K,)
		each array includes K similarity values and corresponding labels
		"""
		import tensorflow as tf
		features = []
		similarity_xs = similarity * np.sign(w)
		[target_len, reference_len] = similarity_xs.shape
		@@ -1994,6 +1994,7 @@ class ANITransformer(Transformer):
		"""
		Only X can be transformed
		"""
		import tensorflow as tf
		self.max_atoms = max_atoms
		self.radial_cutoff = radial_cutoff
		self.angular_cutoff = angular_cutoff
		@@ -2038,6 +2039,7 @@ class ANITransformer(Transformer):

		def build(self):
		""" tensorflow computation graph for transform """
		import tensorflow as tf
		graph = tf.Graph()
		with graph.as_default():
		self.inputs = tf.keras.Input(
		@@ -2065,6 +2067,7 @@ class ANITransformer(Transformer):

		def distance_matrix(self, coordinates, flags):
		""" Generate distance matrix """
		import tensorflow as tf
		max_atoms = self.max_atoms
		tensor1 = tf.stack([coordinates] * max_atoms, axis=1)
		tensor2 = tf.stack([coordinates] * max_atoms, axis=2)
		@@ -2077,6 +2080,7 @@ class ANITransformer(Transformer):

		def distance_cutoff(self, d, cutoff, flags):
		""" Generate distance matrix with trainable cutoff """
		import tensorflow as tf
		# Cutoff with threshold Rc
		d_flag = flags * tf.sign(cutoff - d)
		d_flag = tf.nn.relu(d_flag)
		@@ -2087,6 +2091,7 @@ class ANITransformer(Transformer):

		def radial_symmetry(self, d_cutoff, d, atom_numbers):
		""" Radial Symmetry Function """
		import tensorflow as tf
		embedding = tf.eye(np.max(self.atom_cases) + 1)
		atom_numbers_embedded = tf.nn.embedding_lookup(embedding, atom_numbers)

		@@ -2113,7 +2118,7 @@ class ANITransformer(Transformer):

		def angular_symmetry(self, d_cutoff, d, atom_numbers, coordinates):
		""" Angular Symmetry Function """

		import tensorflow as tf
		max_atoms = self.max_atoms
		embedding = tf.eye(np.max(self.atom_cases) + 1)
		atom_numbers_embedded = tf.nn.embedding_lookup(embedding, atom_numbers)

setup.py

+1 −3

Original line number	Diff line number	Diff line
		@@ -10,9 +10,7 @@ else:
		IS_RELEASE = False

		# Environment-specific dependencies.
		extras = {
		'jax': ['git+https://github.com/deepmind/dm-haiku', 'git+git://github.com/deepmind/optax.git']
		}
		extras = {'jax': ['dm-haiku==0.0.3', 'optax==0.0.8']}


		# get the version from deepchem/__init__.py

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