Merge pull request #2197 from micimize/examples_to_docs (9ce7a2a4) · Commits · 钟慕尧 / deepchem

.gitignore

+2 −0

Original line number	Diff line number	Diff line
		@@ -99,3 +99,5 @@ datasets/pdbbind_v2019_PP.tar.gz
		datasets/pdbbind_v2019_other_PL.tar.gz
		datasets/pdbbind_v2019_refined.tar.gz
		datasets/qm8.csv

		.vscode/

.travis.yml

+11 −0

Original line number	Diff line number	Diff line
		@@ -14,6 +14,12 @@ jobs:
		language: c
		python: '3.7'
		os: windows
		- name: DocTest Examples
		language: python
		python: '3.7'
		sudo: required
		dist: xenial
		env: DOCTEST_EXAMPLES=true
		cache: pip
		install:
		- if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
		@@ -34,6 +40,11 @@ install:
		- conda activate deepchem
		- pip install -e .
		script:
		- if [[ "$DOCTEST_EXAMPLES" == "true" ]]; then
		cd docs && pip install -r requirements.txt;
		make doctest_examples;
		travis_terminate $?;
		fi
		- bash devtools/run_yapf.sh
		- bash devtools/run_flake8.sh
		- mypy -p deepchem

deepchem/splits/splitters.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ import random
		import tempfile
		import itertools
		import logging
		from typing import Any, Dict, List, Iterator, Optional, Sequence, Tuple, Union
		from typing import Any, Dict, List, Iterator, Optional, Sequence, Tuple

		import numpy as np
		import pandas as pd

deepchem/utils/data_utils.py

+26 −16

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ import tarfile
		import zipfile
		import logging
		from urllib.request import urlretrieve
		from typing import Any, Iterator, List, Optional, Tuple, Union
		from typing import Any, Iterator, List, Optional, Tuple, Union, cast, IO

		import pandas as pd
		import numpy as np
		@@ -323,8 +323,30 @@ def load_json_files(input_files: List[str],
		yield df


		def load_pickle_file(input_file: str) -> Any:
		"""Load from single, possibly gzipped, pickle file.

		Parameters
		----------
		input_file: str
		The filename of pickle file. This function can load from
		gzipped pickle file like `XXXX.pkl.gz`.

		Returns
		-------
		Any
		The object which is loaded from the pickle file.
		"""
		if ".gz" in input_file:
		with gzip.open(input_file, "rb") as unzipped_file:
		return pickle.load(cast(IO[bytes], unzipped_file))
		else:
		with open(input_file, "rb") as opened_file:
		return pickle.load(opened_file)


		def load_pickle_files(input_files: List[str]) -> Iterator[Any]:
		"""Load dataset from pickle file.
		"""Load dataset from pickle files.

		Parameters
		----------
		@@ -338,13 +360,7 @@ def load_pickle_files(input_files: List[str]) -> Iterator[Any]:
		Generator which yields the objects which is loaded from each pickle file.
		"""
		for input_file in input_files:
		if ".gz" in input_file:
		with gzip.open(input_file, "rb") as f:
		df = pickle.load(f)
		else:
		with open(input_file, "rb") as f:
		df = pickle.load(f)
		yield df
		yield load_pickle_file(input_file)


		def load_data(input_files: List[str],
		@@ -442,13 +458,7 @@ def load_from_disk(filename: str) -> Any:
		name = os.path.splitext(name)[0]
		extension = os.path.splitext(name)[1]
		if extension == ".pkl":
		if ".gz" in filename:
		with gzip.open(filename, "rb") as f:
		df = pickle.load(f)
		else:
		with open(filename, "rb") as f:
		df = pickle.load(f)
		return df
		return load_pickle_file(filename)
		elif extension == ".joblib":
		return joblib.load(filename)
		elif extension == ".csv":

docs/Makefile

+4 −0

Original line number	Diff line number	Diff line
		@@ -14,6 +14,10 @@ help:

		.PHONY: help Makefile

		doctest_examples:
		export PYTHONWARNINGS=
		@$(SPHINXBUILD) -M doctest "$(SOURCEDIR)" "$(BUILDDIR)" examples.rst;

		# Catch-all target: route all unknown targets to Sphinx using the new
		# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
		%: Makefile

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