add logger instead of print statements (ca40f1cb) · Commits · 钟慕尧 / deepchem

deepchem/init.py

+1 −2

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		"""
		Imports all submodules
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

+0 −1

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		"""
		Process an input dataset into a format suitable for machine learning.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import os

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		"""
		Contains wrapper class for datasets.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import json

+7 −6

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		"""
		Sample supports from datasets.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		import logging
		import time
		import numpy as np
		from deepchem.data import NumpyDataset

		logger = logging.getLogger(__name__)

		def remove_dead_examples(dataset):
		"""Removes compounds with no weight.
		@@ -133,7 +134,7 @@ def get_task_test(dataset, n_episodes, n_test, task, log_every_n=50):
		tests = []
		for episode in range(n_episodes):
		if episode % log_every_n == 0:
		print("Sampling test %d" % episode)
		logger.info("Sampling test %d" % episode)
		inds = ids[episode]
		X_batch = X_task[inds]
		y_batch = np.squeeze(y_task[inds, task])
		@@ -221,7 +222,7 @@ def get_task_support(dataset, n_episodes, n_pos, n_neg, task, log_every_n=50):
		supports = []
		for episode in range(n_episodes):
		if episode % log_every_n == 0:
		print("Sampling support %d" % episode)
		logger.info("Sampling support %d" % episode)
		# No replacement allowed for supports
		pos_ids = np.random.choice(len(pos_mols), (n_pos,), replace=False)
		neg_ids = np.random.choice(len(neg_mols), (n_neg,), replace=False)
		@@ -285,7 +286,7 @@ class EpisodeGenerator(object):
		self.task_num = 0
		self.trial_num = 0
		time_end = time.time()
		print("Constructing EpisodeGenerator took %s seconds" %
		logger.info("Constructing EpisodeGenerator took %s seconds" %
		str(time_end - time_start))

		def __iter__(self):

+2 −2

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		@@ -2,7 +2,7 @@ import os
		from unittest import TestCase
		from io import StringIO
		import tempfile

		import logging
		import shutil

		import deepchem as dc
		@@ -14,7 +14,7 @@ class TestCSVLoader(TestCase):
		fin = tempfile.NamedTemporaryFile(mode='w', delete=False)
		fin.write("smiles,endpoint\nc1ccccc1,1")
		fin.close()
		print(fin.name)
		logger.info(fin.name)
		featurizer = dc.feat.CircularFingerprint(size=1024)
		tasks = ["endpoint"]
		loader = dc.data.CSVLoader(