Now have failing test case. (0e8c56f5) · Commits · 钟慕尧 / deepchem

deepchem/datasets/tests/test_load.py

+45 −0

Original line number	Diff line number	Diff line
		@@ -26,6 +26,51 @@ class TestLoad(TestAPI):
		Test singletask/multitask data loading.
		"""

		def test_move_load(self):
		"""Test that datasets can be moved and loaded."""
		verbosity = "high"
		current_dir = os.path.dirname(os.path.realpath(__file__))
		feature_dir = os.path.join(self.base_dir, "features")
		moved_feature_dir = os.path.join(self.base_dir, "moved_features")
		samples_dir = os.path.join(self.base_dir, "samples")
		moved_samples_dir = os.path.join(self.base_dir, "moved_samples")
		data_dir = os.path.join(self.base_dir, "data")
		moved_data_dir = os.path.join(self.base_dir, "moved_data")
		dataset_file = os.path.join(
		current_dir, "../../models/tests/example.csv")

		featurizers = [CircularFingerprint(size=1024)]
		tasks = ["log-solubility"]
		featurizer = DataFeaturizer(tasks=tasks,
		smiles_field="smiles",
		compound_featurizers=featurizers,
		verbosity=verbosity)
		featurized_samples = featurizer.featurize(
		dataset_file, feature_dir,
		samples_dir, reload=reload)
		dataset = Dataset(data_dir=data_dir, samples=featurized_samples,
		featurizers=featurizers, tasks=tasks,
		verbosity=verbosity, reload=reload)

		X, y, w, ids = dataset.to_numpy()
		shutil.move(feature_dir, moved_feature_dir)
		shutil.move(samples_dir, moved_samples_dir)
		shutil.move(data_dir, moved_data_dir)

		moved_dataset = Dataset(
		data_dir=moved_data_dir, samples=featurized_samples,
		featurizers=featurizers, tasks=tasks,
		verbosity=verbosity, reload=reload)

		X_moved, y_moved, w_moved, ids_moved = moved_dataset.to_numpy()

		np.testing.assert_allclose(X, X_moved)
		np.testing.assert_allclose(y, y_moved)
		np.testing.assert_allclose(w, w_moved)
		np.testing.assert_allclose(ids, ids_moved)



		def test_multiload(self):
		"""Check can re-use featurization for multiple task selections."""
		# Only for debug!

deepchem/featurizers/tests/test_featurized_samples.py

+36 −10

Original line number	Diff line number	Diff line
		@@ -13,25 +13,18 @@ import os
		import unittest
		import tempfile
		import shutil
		from deepchem.models.tests import TestAPI
		from deepchem.splits import RandomSplitter
		from deepchem.splits import ScaffoldSplitter
		from deepchem.splits import SpecifiedSplitter
		from deepchem.featurizers.featurize import DataFeaturizer
		from deepchem.featurizers.fingerprints import CircularFingerprint
		from deepchem.featurizers.featurize import FeaturizedSamples

		class TestFeaturizedSamples(unittest.TestCase):
		class TestFeaturizedSamples(TestAPI):
		"""
		Test Featurized Samples class.
		"""
		def setUp(self):
		self.current_dir = os.path.dirname(os.path.abspath(__file__))
		self.smiles_field = "smiles"
		self.feature_dir = tempfile.mkdtemp()
		self.samples_dir = tempfile.mkdtemp()
		self.train_dir = tempfile.mkdtemp()
		self.valid_dir = tempfile.mkdtemp()
		self.test_dir = tempfile.mkdtemp()

		def _featurize_train_valid_test_split(self, splittype, input_file, tasks,
		frac_train, frac_valid, frac_test):
		# Featurize input
		@@ -141,3 +134,36 @@ class TestFeaturizedSamples(unittest.TestCase):
		frac_valid=0, frac_test=.2))
		assert len(train_samples) == 8
		assert len(test_samples) == 2

		def test_samples_move(self):
		"""Test that featurized samples can be moved and reloaded."""
		verbosity = "high"
		current_dir = os.path.dirname(os.path.realpath(__file__))
		feature_dir = os.path.join(self.base_dir, "features")
		moved_feature_dir = os.path.join(self.base_dir, "moved_features")
		samples_dir = os.path.join(self.base_dir, "samples")
		moved_samples_dir = os.path.join(self.base_dir, "moved_samples")
		dataset_file = os.path.join(
		current_dir, "../../models/tests/example.csv")

		featurizers = [CircularFingerprint(size=1024)]
		tasks = ["log-solubility"]
		featurizer = DataFeaturizer(tasks=tasks,
		smiles_field="smiles",
		compound_featurizers=featurizers,
		verbosity=verbosity)
		featurized_samples = featurizer.featurize(
		dataset_file, feature_dir,
		samples_dir, reload=reload)
		n_samples = len(featurized_samples)

		# Now perform move
		shutil.move(feature_dir, moved_feature_dir)
		shutil.move(samples_dir, moved_samples_dir)

		moved_featurized_samples = FeaturizedSamples(
		samples_dir=moved_samples_dir, featurizers=featurizers,
		reload=True)

		assert len(moved_featurized_samples) == n_samples

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