Cleanup (752c9ba7) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+0 −20

Original line number	Diff line number	Diff line
		@@ -57,10 +57,6 @@ def featurize_smiles_df(df, featurizer, field, log_every_N=1000, verbose=True):
		or macromolecules, compute & add features for that compound to the
		features dataframe
		"""
		######################################################## DEBUG
		print("field")
		print(field)
		######################################################## DEBUG
		sample_elems = df[field].tolist()

		features = []
		@@ -69,12 +65,10 @@ def featurize_smiles_df(df, featurizer, field, log_every_N=1000, verbose=True):
		if ind % log_every_N == 0:
		log("Featurizing sample %d" % ind, verbose)
		features.append(featurizer.featurize([mol]))
		########################################################## DEBUG
		valid_inds = np.array([1 if elt.size > 0 else 0 for elt in features],
		dtype=bool)
		features = [elt for (is_valid, elt) in zip(valid_inds, features) if is_valid]
		return np.squeeze(np.array(features)), valid_inds
		########################################################### DEBUG

		def get_user_specified_features(df, featurizer, verbose=True):
		"""Extract and merge user specified features.
		@@ -114,12 +108,10 @@ def featurize_mol_df(df, featurizer, field, verbose=True, log_every_N=1000):
		if ind % log_every_N == 0:
		log("Featurizing sample %d" % ind, verbose)
		features.append(featurizer.featurize([mol]))
		########################################################## DEBUG
		valid_inds = np.array([1 if elt.size > 0 else 0 for elt in features],
		dtype=bool)
		features = [elt for (is_valid, elt) in zip(valid_inds, features) if is_valid]
		return np.squeeze(np.array(features)), valid_inds
		########################################################### DEBUG

		class DataLoader(object):
		"""
		@@ -148,10 +140,6 @@ class DataLoader(object):
		self.user_specified_features = featurizer.feature_fields
		self.featurizer = featurizer
		self.log_every_n = log_every_n
		##################################################### DEBUG
		print("self.smiles_field")
		print(self.smiles_field)
		##################################################### DEBUG

		def featurize(self, input_files, data_dir=None, shard_size=8192):
		"""Featurize provided files and write to specified location."""
		@@ -163,10 +151,6 @@ class DataLoader(object):
		def shard_generator():
		for shard_num, shard in enumerate(self.get_shards(input_files, shard_size)):
		time1 = time.time()
		##################################################### DEBUG
		print("self.smiles_field")
		print(self.smiles_field)
		##################################################### DEBUG
		X, valid_inds = self.featurize_shard(shard)
		ids, y, w = convert_df_to_numpy(shard, self.tasks, self.id_field)
		# Filter out examples where featurization failed.
		@@ -196,10 +180,6 @@ class CSVLoader(DataLoader):

		def featurize_shard(self, shard):
		"""Featurizes a shard of an input dataframe."""
		######################################################### DEBUG
		print("self.smiles_field")
		print(self.smiles_field)
		######################################################### DEBUG
		return featurize_smiles_df(shard, self.featurizer,
		field=self.smiles_field)

deepchem/data/datasets.py

+0 −6

Original line number	Diff line number	Diff line
		@@ -366,12 +366,6 @@ class DiskDataset(Dataset):
		(self.tasks, self.metadata_df) = load_from_disk(
		self._get_metadata_filename())
		else:
		################################################ DEBUG
		print("self.data_dir")
		print(self.data_dir)
		print("os.listdir(self.data_dir)")
		print(os.listdir(self.data_dir))
		################################################ DEBUG
		raise ValueError("No metadata found.")
		return

deepchem/data/tests/init.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -25,10 +25,6 @@ def load_solubility_data():
		input_file = os.path.join(current_dir, "../../models/tests/example.csv")
		loader = dc.data.CSVLoader(
		tasks=tasks, smiles_field="smiles", featurizer=featurizer)
		##################################################### DEBUG
		print("loader.smiles_field")
		print(loader.smiles_field)
		##################################################### DEBUG

		return loader.featurize(input_file)

deepchem/data/tests/test_drop.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -34,8 +34,4 @@ class TestDrop(unittest.TestCase):
		dataset = loader.featurize(dataset_file)

		X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
		############################################################ DEBUG
		print("ids.shape, X.shape, y.shape, w.shape")
		print(ids.shape, X.shape, y.shape, w.shape)
		############################################################ DEBUG
		assert len(X) == len(y) == len(w) == len(ids)

deepchem/data/tests/test_load.py

+0 −4

Original line number	Diff line number	Diff line
		@@ -39,10 +39,6 @@ class TestLoad(unittest.TestCase):
		X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
		shutil.move(data_dir, moved_data_dir)

		################################################ DEBUG
		print("data_dir, moved_data_dir")
		print(data_dir, moved_data_dir)
		################################################ DEBUG
		moved_dataset = dc.data.DiskDataset(
		data_dir=moved_data_dir, reload=True)

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