Merge pull request #561 from lilleswing/stable-travis (09c97cd2) · Commits · 钟慕尧 / deepchem

.travis.yml

+1 −1

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		@@ -20,7 +20,7 @@ install:
		- pip install coveralls
		- python setup.py install
		script:
		- nosetests --with-coverage --cover-package=deepchem -v deepchem --nologcapture
		- nosetests -a '!slow' --with-timer --with-coverage --cover-package=deepchem -v deepchem --nologcapture
		- find ./deepchem \| grep .py$ \|xargs python -m doctest -v
		- bash devtools/travis-ci/test_format_code.sh
		after_success:

+4 −4

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		"""
		Tests for Docking
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import print_function
		from __future__ import unicode_literals

		__author__ = "Bharath Ramsundar"
		@@ -10,10 +10,8 @@ __copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import unittest
		import tempfile
		import os
		import shutil
		import numpy as np
		from nose.plugins.attrib import attr
		import sys
		import deepchem as dc

		@@ -35,6 +33,7 @@ class TestDocking(unittest.TestCase):
		return
		docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=True)

		@attr("slow")
		def test_vina_grid_dnn_docker_init(self):
		"""Test that VinaGridDNNDocker can be initialized."""
		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=False)
		@@ -117,6 +116,7 @@ class TestDocking(unittest.TestCase):
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)

		@attr('slow')
		def test_pocket_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		if sys.version_info >= (3, 0):

+3 −4

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		"""
		Tests for Pose Generation
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import print_function
		from __future__ import unicode_literals

		__author__ = "Bharath Ramsundar"
		@@ -12,10 +12,8 @@ __license__ = "MIT"
		import os
		import sys
		import unittest
		import tempfile
		import shutil
		import numpy as np
		import deepchem as dc
		from nose.plugins.attrib import attr


		class TestPoseGeneration(unittest.TestCase):
		@@ -50,6 +48,7 @@ class TestPoseGeneration(unittest.TestCase):
		assert os.path.exists(protein_pose_file)
		assert os.path.exists(ligand_pose_file)

		@attr('slow')
		def test_pocket_vina_poses(self):
		"""Test that VinaPoseGenerator creates pose files."""
		if sys.version_info >= (3, 0):

+2 −0

Original line number	Diff line number	Diff line
		from unittest import TestCase

		from nose.tools import assert_equals
		from nose.plugins.attrib import attr
		from rdkit import Chem

		import deepchem as dc
		@@ -11,6 +12,7 @@ from deepchem.models.autoencoder_models.autoencoder import TensorflowMoleculeEnc

		class TestTensorflowEncoders(TestCase):

		@attr('slow')
		def test_fit(self):
		tf_enc = TensorflowMoleculeEncoder.zinc_encoder()

+1 −1

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		@@ -151,7 +151,7 @@ class TestTensorGraph(unittest.TestCase):
		label = Label(shape=(None, 2))
		smce = SoftMaxCrossEntropy(in_layers=[label, dense])
		loss = ReduceMean(in_layers=[smce])
		tg = dc.models.TensorGraph(learning_rate=1.0, use_queue=False)
		tg = dc.models.TensorGraph(learning_rate=0.1, use_queue=False)
		tg.add_output(output)
		tg.set_loss(loss)
		tg.fit(dataset, nb_epoch=1000)