Time the tests (c0b143b9) · Commits · 钟慕尧 / deepchem

.travis.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@ install:
		- pip install coveralls
		- python setup.py install
		script:
		- nosetests --with-coverage --cover-package=deepchem -v deepchem --nologcapture
		- nosetests --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:

deepchem/utils/test/test_generator_evaluator.py

+12 −18

Original line number	Diff line number	Diff line
		import numpy as np
		from nose.tools import assert_true, with_setup
		from nose.tools import assert_true, attr
		from unittest import TestCase

		import deepchem as dc
		from deepchem.data import NumpyDataset
		from deepchem.data.datasets import Databag
		from deepchem.models.tensorgraph.layers import Dense, ReduceMean, SoftMax, \
		SoftMaxCrossEntropy, L2Loss
		from deepchem.models.tensorgraph.layers import Dense, ReduceMean, SoftMax, SoftMaxCrossEntropy, L2Loss
		from deepchem.models.tensorgraph.layers import Feature, Label
		from deepchem.models.tensorgraph.layers import ReduceSquareDifference

		RANDOM_SEED = 42


		def set_random_seeds():
		np.random.seed(RANDOM_SEED)


		class TestGeneratorEvaluator(TestCase):

		@with_setup(set_random_seeds)
		@attr('slow')
		def test_compute_model_performance_multitask_classifier(self):
		n_data_points = 20
		n_features = 2
		@@ -55,7 +48,7 @@ class TestGeneratorEvaluator(TestCase):

		total_loss = ReduceMean(in_layers=entropies)

		tg = dc.models.TensorGraph(learning_rate=0.1, random_seed=RANDOM_SEED)
		tg = dc.models.TensorGraph(learning_rate=0.1)
		for output in outputs:
		tg.add_output(output)
		tg.set_loss(total_loss)
		@@ -72,7 +65,7 @@ class TestGeneratorEvaluator(TestCase):
		# Loosening atol to see if tests stop failing sporadically
		assert_true(np.all(np.isclose(scores, [1.0, 1.0], atol=0.50)))

		@with_setup(set_random_seeds)
		@attr('slow')
		def test_compute_model_performance_singletask_classifier(self):
		n_data_points = 20
		n_features = 10
		@@ -107,7 +100,7 @@ class TestGeneratorEvaluator(TestCase):

		total_loss = ReduceMean(in_layers=entropies)

		tg = dc.models.TensorGraph(learning_rate=0.1, random_seed=RANDOM_SEED)
		tg = dc.models.TensorGraph(learning_rate=0.1)
		for output in outputs:
		tg.add_output(output)
		tg.set_loss(total_loss)
		@@ -123,10 +116,12 @@ class TestGeneratorEvaluator(TestCase):
		scores = list(scores[1].values())
		assert_true(np.isclose(scores, [1.0], atol=0.05))

		@with_setup(set_random_seeds)
		@attr('slow')
		def test_compute_model_performance_multitask_regressor(self):
		random_seed = 42
		n_data_points = 20
		n_features = 2
		np.random.seed(seed=random_seed)

		X = np.random.rand(n_data_points, n_features)
		y1 = np.expand_dims(np.array([0.5 for x in range(n_data_points)]), axis=-1)
		@@ -157,7 +152,7 @@ class TestGeneratorEvaluator(TestCase):
		tg = dc.models.TensorGraph(
		mode="regression",
		batch_size=20,
		random_seed=RANDOM_SEED,
		random_seed=random_seed,
		learning_rate=0.1)
		for output in outputs:
		tg.add_output(output)
		@@ -175,7 +170,7 @@ class TestGeneratorEvaluator(TestCase):
		scores = list(scores[1].values())
		assert_true(np.all(np.isclose(scores, [0.0, 0.0], atol=1.0)))

		@with_setup(set_random_seeds)
		@attr('slow')
		def test_compute_model_performance_singletask_regressor(self):
		n_data_points = 20
		n_features = 2
		@@ -205,8 +200,7 @@ class TestGeneratorEvaluator(TestCase):

		total_loss = ReduceMean(in_layers=losses)

		tg = dc.models.TensorGraph(
		mode="regression", learning_rate=0.1, random_seed=RANDOM_SEED)
		tg = dc.models.TensorGraph(mode="regression", learning_rate=0.1)
		for output in outputs:
		tg.add_output(output)
		tg.set_loss(total_loss)

scripts/install_deepchem_conda.sh

+1 −0

Original line number	Diff line number	Diff line
		@@ -39,3 +39,4 @@ conda install -y -c pillow
		conda install -y -c anaconda pandas=0.19.2
		yes \| pip install $tensorflow==1.0.1
		yes \| pip install nose
		yes \| pip install nose-timer

Admin message