Attempt at fixing travis failures (9e6155ff) · Commits · 钟慕尧 / deepchem

deepchem/molnet/load_function/delaney_datasets.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ class _DelaneyLoader(_MolnetLoader):
		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)


		@@ -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)

deepchem/molnet/load_function/molnet_loader.py

+10 −8

Original line number	Diff line number	Diff line
		@@ -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
		@@ -102,6 +103,8 @@ class _MolnetLoader(object):
		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
		@@ -124,12 +127,13 @@ class _MolnetLoader(object):
		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.

		@@ -137,8 +141,6 @@ class _MolnetLoader(object):
		----------
		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.
		@@ -160,12 +162,12 @@ class _MolnetLoader(object):
		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

		@@ -190,7 +192,7 @@ class _MolnetLoader(object):
		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)
		@@ -200,7 +202,7 @@ class _MolnetLoader(object):
		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."""

Admin message