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Merged
abradle merged 2 commits into from
Dec 17, 2017
Merged

use contextmanager to open/close files #32

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12662c9
use contextmanager to open/close files
kain88-de Dec 16, 2017
25a3754
update CHANGELOG
kain88-de Dec 16, 2017
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -61,3 +61,7 @@ All notable changes to this project will be documented in this file, following t
## v1.0.8 - 2017-08-17
### Fixed
- Changing ascii to utf8 #29

## v1.0.x - 20XX-XX-XX
### Fixed
- Don't leak open file handles #32
3 changes: 2 additions & 1 deletion mmtf/api/default_api.py
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Expand Up @@ -87,7 +87,8 @@ def parse(file_path):
:param file_path: the input file path. Data is not entropy compressed (e.g. gzip)
:return an API to decoded data """
newDecoder = MMTFDecoder()
newDecoder.decode_data(msgpack.unpackb(open(file_path, "rb").read()))
with open(file_path, "rb") as fh:
newDecoder.decode_data(msgpack.unpackb(fh.read()))
return newDecoder


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4 changes: 2 additions & 2 deletions mmtf/api/mmtf_writer.py
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Expand Up @@ -256,8 +256,8 @@ def get_msgpack(self):


def write_file(self, file_path):
out_f = open(file_path, "wb")
out_f.write(self.get_msgpack())
with open(file_path, "wb") as out_f:
out_f.write(self.get_msgpack())


def init_structure(self, total_num_bonds, total_num_atoms,
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3 changes: 2 additions & 1 deletion mmtf/tests/codec_tests.py
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Expand Up @@ -190,7 +190,8 @@ def test_round_trip(self):
decoded.decode_data(msgpack.unpackb(packed))

def test_gzip_open(self):
ungzip_data(open("mmtf/tests/testdatastore/4CUP.mmtf.gz","rb").read())
with open("mmtf/tests/testdatastore/4CUP.mmtf.gz","rb") as fh:
ungzip_data(fh.read())

def test_fetch(self):
if _internet_on(BASE_URL):
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