Merge pull request #1884 from lilleswing/pytest (6563234c) · Commits · 钟慕尧 / deepchem

.travis.yml

+1 −2

Original line number	Diff line number	Diff line
		@@ -39,8 +39,7 @@ install:
		- pip install coveralls
		- python setup.py install
		script:
		- nosetests -q --with-flaky -a '!slow' --with-coverage --cover-package=deepchem
		-v deepchem --nologcapture
		- pytest -m "not slow" --cov=deepchem deepchem
		- if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then
		find ./deepchem \| grep .py$ \|xargs python -m doctest -v;
		fi

contrib/autoencoder_models/test_tensorflowEncoders.py

+3 −4

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

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

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

		class TestTensorflowEncoders(TestCase):

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

		@@ -36,4 +35,4 @@ class TestTensorflowEncoders(TestCase):
		tf_de = TensorflowMoleculeDecoder.zinc_decoder()
		one_hot_decoded = tf_de.predict_on_batch(prediction)
		decoded_smiles = featurizer.untransform(one_hot_decoded)
		assert_equals(len(decoded_smiles), len(smiles))
		assert len(decoded_smiles) == len(smiles)

deepchem/dock/tests/test_binding_pocket.py

+3 −2

Original line number	Diff line number	Diff line
		@@ -10,8 +10,9 @@ import logging
		import unittest
		import os
		import numpy as np
		import pytest

		import deepchem as dc
		from nose.tools import nottest
		from deepchem.utils import rdkit_util

		logger = logging.getLogger(__name__)
		@@ -147,7 +148,7 @@ class TestBindingPocket(unittest.TestCase):

		assert len(pockets) < len(all_pockets)

		@nottest
		@pytest.mark.skip(reason="Unknown")
		def test_rf_convex_find_pockets(self):
		"""Test that filter with pre-trained RF models works."""
		if sys.version_info >= (3, 0):

deepchem/dock/tests/test_docking.py

+10 −44

Original line number	Diff line number	Diff line
		@@ -5,11 +5,12 @@ __author__ = "Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import unittest
		import os
		from nose.plugins.attrib import attr
		from nose.tools import nottest
		import sys
		import unittest

		import pytest

		import deepchem as dc


		@@ -18,14 +19,14 @@ class TestDocking(unittest.TestCase):
		Does sanity checks on pose generation.
		"""

		@nottest
		@pytest.mark.skip(reason="Unknown")
		def test_vina_grid_rf_docker_init(self):
		"""Test that VinaGridRFDocker can be initialized."""
		if sys.version_info >= (3, 0):
		return
		docker = dc.dock.VinaGridRFDocker(exhaustiveness=1, detect_pockets=False)

		@nottest
		@pytest.mark.skip(reason="Unknown")
		def test_pocket_vina_grid_rf_docker_init(self):
		"""Test that VinaGridRFDocker w/pockets can be initialized."""
		if sys.version_info >= (3, 0):
		@@ -45,7 +46,7 @@ class TestDocking(unittest.TestCase):
		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=True)
		'''

		@attr("slow")
		@pytest.mark.slow
		def test_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		if sys.version_info >= (3, 0):
		@@ -64,7 +65,7 @@ class TestDocking(unittest.TestCase):
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)

		@nottest
		@pytest.mark.skip(reason="Unknown")
		def test_vina_grid_rf_docker_specified_pocket(self):
		"""Test that VinaGridRFDocker can dock into spec. pocket."""
		if sys.version_info >= (3, 0):
		@@ -85,7 +86,7 @@ class TestDocking(unittest.TestCase):
		# Check returned files exist
		assert score.shape == (1,)

		@nottest
		@pytest.mark.skip(reason="Unknown")
		def test_pocket_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		if sys.version_info >= (3, 0):
		@@ -104,38 +105,3 @@ class TestDocking(unittest.TestCase):
		return

		assert score.shape == (1,)

		'''
		@attr("slow")
		def test_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir, "1jld_protein.pdb")
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=False)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file)

		# Check returned files exist
		assert score.shape == (1,)
		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):
		return

		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir, "1jld_protein.pdb")
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		docker = dc.dock.VinaGridDNNDocker(exhaustiveness=1, detect_pockets=True)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file, dry_run=True)

		# Check returned files exist
		assert score.shape == (1,)
		'''

deepchem/dock/tests/test_pose_generation.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -9,7 +9,7 @@ import os
		import sys
		import unittest
		import deepchem as dc
		from nose.plugins.attrib import attr
		import pytest


		class TestPoseGeneration(unittest.TestCase):
		@@ -17,13 +17,13 @@ class TestPoseGeneration(unittest.TestCase):
		Does sanity checks on pose generation.
		"""

		@attr("slow")
		@pytest.mark.slow
		def test_vina_initialization(self):
		"""Test that VinaPoseGenerator can be initialized."""
		# Note this may download autodock Vina...
		vpg = dc.dock.VinaPoseGenerator(detect_pockets=False, exhaustiveness=1)

		@attr("slow")
		@pytest.mark.slow("slow")
		def test_pocket_vina_initialization(self):
		"""Test that VinaPoseGenerator can be initialized."""
		# Note this may download autodock Vina...
		@@ -31,7 +31,7 @@ class TestPoseGeneration(unittest.TestCase):
		return
		vpg = dc.dock.VinaPoseGenerator(detect_pockets=True, exhaustiveness=1)

		@attr("slow")
		@pytest.mark.slow("slow")
		def test_vina_poses(self):
		"""Test that VinaPoseGenerator creates pose files."""
		current_dir = os.path.dirname(os.path.realpath(__file__))
		@@ -47,7 +47,7 @@ class TestPoseGeneration(unittest.TestCase):
		assert os.path.exists(protein_pose_file)
		assert os.path.exists(ligand_pose_file)

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

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