Passing tests (588801cf) · Commits · 钟慕尧 / deepchem

deepchem/data/datasets.py

+7 −0

Original line number	Diff line number	Diff line
		@@ -395,6 +395,13 @@ class NumpyDataset(Dataset):
		ids = self.ids[indices]
		return NumpyDataset(X, y, w, ids)

		@staticmethod
		def from_DiskDataset(ds):
		"""
		:param ds: DiskDataset
		:return: NumpyDataset with the same data
		"""
		return NumpyDataset(ds.X, ds.y, ds.w, ds.ids)

		class DiskDataset(Dataset):
		"""

deepchem/splits/splitters.py

+11 −4

Original line number	Diff line number	Diff line
		@@ -60,7 +60,10 @@ class Splitter(object):
		directories = [tempfile.mkdtemp() for _ in range(k)]
		else:
		assert len(directories) == k
		fold_datasets = []
		all_ids = dataset.ids
		cv_datasets = []
		train_ds_base = None
		train_datasets = []
		# rem_dataset is remaining portion of dataset
		rem_dataset = dataset
		for fold in range(k):
		@@ -73,11 +76,15 @@ class Splitter(object):
		frac_train=frac_fold,
		frac_valid=1 - frac_fold,
		frac_test=0)
		fold_dataset = rem_dataset.select(fold_inds, fold_dir)
		cv_dataset = rem_dataset.select(fold_inds, fold_dir)
		rem_dir = tempfile.mkdtemp()
		rem_dataset = rem_dataset.select(rem_inds, rem_dir)
		fold_datasets.append(fold_dataset)
		return fold_datasets

		train_dataset = DiskDataset.merge(filter(lambda x: x is not None, [train_ds_base, cv_dataset]))
		train_datasets.append(train_dataset)
		train_ds_base = DiskDataset.merge(filter(lambda x: x is not None, [train_ds_base, cv_dataset]))
		cv_datasets.append(cv_dataset)
		return list(zip(train_datasets, cv_datasets))

		def train_valid_test_split(self,
		dataset,

deepchem/splits/tests/test_splitter.py

+11 −9

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ from __future__ import unicode_literals

		from rdkit.Chem.Fingerprints import FingerprintMols


		__author__ = "Bharath Ramsundar, Aneesh Pappu"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"
		@@ -15,6 +16,7 @@ import tempfile
		import unittest
		import numpy as np
		import deepchem as dc
		from deepchem.data import NumpyDataset
		from rdkit import Chem, DataStructs


		@@ -133,7 +135,7 @@ class TestSplitters(unittest.TestCase):
		K = 5
		fold_datasets = random_splitter.k_fold_split(solubility_dataset, K)
		for fold in range(K):
		fold_dataset = fold_datasets[fold]
		fold_dataset = fold_datasets[fold][1]
		# Verify lengths is 10/k == 2
		assert len(fold_dataset) == 2
		# Verify that compounds in this fold are subset of original compounds
		@@ -143,11 +145,11 @@ class TestSplitters(unittest.TestCase):
		for other_fold in range(K):
		if fold == other_fold:
		continue
		other_fold_dataset = fold_datasets[other_fold]
		other_fold_dataset = fold_datasets[other_fold][1]
		other_fold_ids_set = set(other_fold_dataset.ids)
		assert fold_ids_set.isdisjoint(other_fold_ids_set)

		merged_dataset = dc.data.DiskDataset.merge(fold_datasets)
		merged_dataset = dc.data.DiskDataset.merge([x[1] for x in fold_datasets])
		assert len(merged_dataset) == len(solubility_dataset)
		assert sorted(merged_dataset.ids) == (sorted(solubility_dataset.ids))

		@@ -163,7 +165,7 @@ class TestSplitters(unittest.TestCase):
		fold_datasets = index_splitter.k_fold_split(solubility_dataset, K)

		for fold in range(K):
		fold_dataset = fold_datasets[fold]
		fold_dataset = fold_datasets[fold][1]
		# Verify lengths is 10/k == 2
		assert len(fold_dataset) == 2
		# Verify that compounds in this fold are subset of original compounds
		@@ -173,11 +175,11 @@ class TestSplitters(unittest.TestCase):
		for other_fold in range(K):
		if fold == other_fold:
		continue
		other_fold_dataset = fold_datasets[other_fold]
		other_fold_dataset = fold_datasets[other_fold][1]
		other_fold_ids_set = set(other_fold_dataset.ids)
		assert fold_ids_set.isdisjoint(other_fold_ids_set)

		merged_dataset = dc.data.DiskDataset.merge(fold_datasets)
		merged_dataset = dc.data.DiskDataset.merge([x[1] for x in fold_datasets])
		assert len(merged_dataset) == len(solubility_dataset)
		assert sorted(merged_dataset.ids) == (sorted(solubility_dataset.ids))

		@@ -193,7 +195,7 @@ class TestSplitters(unittest.TestCase):
		fold_datasets = scaffold_splitter.k_fold_split(solubility_dataset, K)

		for fold in range(K):
		fold_dataset = fold_datasets[fold]
		fold_dataset = fold_datasets[fold][1]
		# Verify lengths is 10/k == 2
		assert len(fold_dataset) == 2
		# Verify that compounds in this fold are subset of original compounds
		@@ -203,11 +205,11 @@ class TestSplitters(unittest.TestCase):
		for other_fold in range(K):
		if fold == other_fold:
		continue
		other_fold_dataset = fold_datasets[other_fold]
		other_fold_dataset = fold_datasets[other_fold][1]
		other_fold_ids_set = set(other_fold_dataset.ids)
		assert fold_ids_set.isdisjoint(other_fold_ids_set)

		merged_dataset = dc.data.DiskDataset.merge(fold_datasets)
		merged_dataset = dc.data.DiskDataset.merge([x[1] for x in fold_datasets])
		assert len(merged_dataset) == len(solubility_dataset)
		assert sorted(merged_dataset.ids) == (sorted(solubility_dataset.ids))

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