Skip to content

Commit

Permalink
Attempt at fixing travis failures
Browse files Browse the repository at this point in the history
  • Loading branch information
peastman committed Oct 19, 2020
1 parent 1894509 commit 9e6155f
Show file tree
Hide file tree
Showing 2 changed files with 14 additions and 12 deletions.
8 changes: 4 additions & 4 deletions deepchem/molnet/load_function/delaney_datasets.py
Expand Up @@ -22,7 +22,7 @@ def create_dataset(self) -> Dataset:
if not os.path.exists(dataset_file):
dc.utils.data_utils.download_url(url=DELANEY_URL, dest_dir=self.data_dir)
loader = dc.data.CSVLoader(
tasks=DELANEY_TASKS, feature_field="smiles", featurizer=self.featurizer)
tasks=self.tasks, feature_field="smiles", featurizer=self.featurizer)
return loader.create_dataset(dataset_file, shard_size=8192)


Expand Down Expand Up @@ -79,6 +79,6 @@ def load_delaney(
molecular structure." Journal of chemical information and computer
sciences 44.3 (2004): 1000-1005.
"""
loader = _DelaneyLoader(featurizer, splitter, transformers, data_dir,
save_dir, **kwargs)
return loader.load_dataset('delaney', DELANEY_TASKS, reload)
loader = _DelaneyLoader(featurizer, splitter, transformers, DELANEY_TASKS,
data_dir, save_dir, **kwargs)
return loader.load_dataset('delaney', reload)
18 changes: 10 additions & 8 deletions deepchem/molnet/load_function/molnet_loader.py
Expand Up @@ -85,7 +85,8 @@ class _MolnetLoader(object):
def __init__(self, featurizer: Union[dc.feat.Featurizer, str],
splitter: Union[dc.splits.Splitter, str, None],
transformer_generators: List[Union[TransformerGenerator, str]],
data_dir: Optional[str], save_dir: Optional[str], **kwargs):
tasks: List[str], data_dir: Optional[str],
save_dir: Optional[str], **kwargs):
"""Construct an object for loading a dataset.
Parameters
Expand All @@ -102,6 +103,8 @@ def __init__(self, featurizer: Union[dc.feat.Featurizer, str],
the Transformers to apply to the data. Each one is specified by a
TransformerGenerator or, as a shortcut, one of the names from
dc.molnet.transformers.
tasks: List[str]
the names of the tasks in the dataset
data_dir: str
a directory to save the raw data in
save_dir: str
Expand All @@ -124,21 +127,20 @@ def __init__(self, featurizer: Union[dc.feat.Featurizer, str],
transformers[t.lower()] if isinstance(t, str) else t
for t in transformer_generators
]
self.tasks = list(tasks)
self.data_dir = data_dir
self.save_dir = save_dir
self.args = kwargs

def load_dataset(
self, name: str, tasks: List[str], reload: bool
self, name: str, reload: bool
) -> Tuple[List[str], Tuple[Dataset, ...], List[dc.trans.Transformer]]:
"""Load the dataset.
Parameters
----------
name: str
the name of the dataset, used to identify the directory on disk
tasks: List[str]
the names of the tasks in this dataset
reload: bool
if True, the first call for a particular featurizer and splitter will cache
the datasets to disk, and subsequent calls will reload the cached datasets.
Expand All @@ -160,12 +162,12 @@ def load_dataset(
if self.splitter is None:
if os.path.exists(save_folder):
transformers = dc.utils.data_utils.load_transformers(save_folder)
return tasks, (DiskDataset(save_folder),), transformers
return self.tasks, (DiskDataset(save_folder),), transformers
else:
loaded, all_dataset, transformers = dc.utils.data_utils.load_dataset_from_disk(
save_folder)
if all_dataset is not None:
return tasks, all_dataset, transformers
return self.tasks, all_dataset, transformers

# Create the dataset

Expand All @@ -190,7 +192,7 @@ def load_dataset(
if reload and isinstance(dataset, DiskDataset):
dataset.move(save_folder)
dc.utils.data_utils.save_transformers(save_folder, transformers)
return tasks, (dataset,), transformers
return self.tasks, (dataset,), transformers

for transformer in transformers:
train = transformer.transform(train)
Expand All @@ -200,7 +202,7 @@ def load_dataset(
valid, DiskDataset) and isinstance(test, DiskDataset):
dc.utils.data_utils.save_dataset_to_disk(save_folder, train, valid, test,
transformers)
return tasks, (train, valid, test), transformers
return self.tasks, (train, valid, test), transformers

def create_dataset(self) -> Dataset:
"""Subclasses must implement this to load the dataset."""
Expand Down

0 comments on commit 9e6155f

Please sign in to comment.