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Merge pull request #2040 from deepchem/log_fix2
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Fixing Featurizer Logging Issues
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Bharath Ramsundar committed Jul 31, 2020
2 parents 5984e9e + 5811e3b commit b13f82d
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405 changes: 240 additions & 165 deletions deepchem/data/data_loader.py
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10 changes: 5 additions & 5 deletions deepchem/data/datasets.py
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Expand Up @@ -19,7 +19,7 @@
from deepchem.utils.save import save_to_disk, save_metadata
from deepchem.utils.save import load_from_disk

from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Sequence, Tuple
from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Sequence, Tuple, Union
from deepchem.utils.typing import OneOrMany, Shape

Batch = Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]
Expand Down Expand Up @@ -2034,8 +2034,8 @@ class ImageDataset(Dataset):
"""A Dataset that loads data from image files on disk."""

def __init__(self,
X: Sequence,
y: Optional[Sequence],
X: Union[np.ndarray, List[str]],
y: Optional[Union[np.ndarray, List[str]]],
w: Optional[Sequence] = None,
ids: Optional[Sequence] = None) -> None:
"""Create a dataset whose X and/or y array is defined by image files on disk.
Expand All @@ -2050,10 +2050,10 @@ def __init__(self,
The dataset's labels. This may be either a single NumPy array
directly containing the data, or a list containing the paths to
the image files
w: ndarray
w: ndarray, optional, (default, None)
a 1D or 2D array containing the weights for each sample or
sample/task pair
ids: ndarray
ids: ndarray, optional (default None)
the sample IDs
"""
n_samples = len(X)
Expand Down
218 changes: 218 additions & 0 deletions deepchem/data/tests/membrane_permeability.sdf
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@@ -0,0 +1,218 @@
10_filipski_40
RDKit 3D

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3 11 1 0
4 5 1 0
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6 32 1 0
7 8 1 0
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8 10 1 0
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M END
> <LogP(RRCK)> (1)
-5.08

$$$$
10_filipski_42
RDKit 3D

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13.8284 -3.5714 -1.0035 H 0 0 0 0 0 0 0 0 0 0 0 0
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M END
> <LogP(RRCK)> (2)
-4.82

$$$$
107 changes: 107 additions & 0 deletions deepchem/data/tests/singleton.sdf
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@@ -0,0 +1,107 @@
10_filipski_40
RDKit 3D

48 50 0 0 1 0 0 0 0 0999 V2000
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M END
> <LogP(RRCK)> (1)
-5.08

$$$$
27 changes: 11 additions & 16 deletions deepchem/data/tests/test_csv_loader.py
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@@ -1,24 +1,19 @@
import os
from unittest import TestCase
from io import StringIO
import tempfile
import shutil

import deepchem as dc


class TestCSVLoader(TestCase):

def test_load_singleton_csv(self):
fin = tempfile.NamedTemporaryFile(mode='w', delete=False)
fin.write("smiles,endpoint\nc1ccccc1,1")
fin.close()
print(fin.name)
featurizer = dc.feat.CircularFingerprint(size=1024)
tasks = ["endpoint"]
loader = dc.data.CSVLoader(
tasks=tasks, smiles_field="smiles", featurizer=featurizer)
def test_load_singleton_csv():
fin = tempfile.NamedTemporaryFile(mode='w', delete=False)
fin.write("smiles,endpoint\nc1ccccc1,1")
fin.close()
featurizer = dc.feat.CircularFingerprint(size=1024)
tasks = ["endpoint"]
loader = dc.data.CSVLoader(
tasks=tasks, feature_field="smiles", featurizer=featurizer)

X = loader.create_dataset(fin.name)
self.assertEqual(1, len(X))
os.remove(fin.name)
X = loader.create_dataset(fin.name)
assert len(X) == 1
os.remove(fin.name)

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