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Add .deepsource.toml, Fix issues raised by DeepSource #163

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reece merged 1 commit into from
Dec 17, 2019
Merged

Add .deepsource.toml, Fix issues raised by DeepSource #163

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10 changes: 10 additions & 0 deletions .deepsource.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
version = 1

test_patterns = [
'tests/test_*.py'
]

[[analyzers]]
name = 'python'
enabled = true
runtime_version = '2.x.x'
7 changes: 3 additions & 4 deletions eutils/_internal/xmlfacades/entrezgene.py
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Expand Up @@ -76,7 +76,6 @@ def type(self):

if __name__ == "__main__":
import os
import lxml.etree
from .xmlfacades.entrezgeneset import EntrezgeneSet
data_dir = os.path.join(os.path.dirname(__file__), '..', '..', 'tests', 'data')
data_file = os.path.join(data_dir, 'entrezgeneset.xml.gz')
Expand All @@ -85,13 +84,13 @@ def type(self):

# <LICENSE>
# Copyright 2015 eutils Committers
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
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20 changes: 10 additions & 10 deletions eutils/_internal/xmlfacades/gbseq.py
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Expand Up @@ -51,7 +51,7 @@ def gene(self):
if not gene:
return None
return gene.qualifiers['gene']

@property
def genes(self):
raise RuntimeError("The genes property is obsolete; use gene instead")
Expand All @@ -62,7 +62,7 @@ def gi(self):
d = {t: l.rstrip('|').split('|')
for t, _, l in [si.partition('|') for si in seqids]}
gis = d['gi']
assert 1 == len(gis), "expected exactly one gi in XML"
assert len(gis) == 1, "expected exactly one gi in XML"
return int(gis[0])

@property
Expand Down Expand Up @@ -118,7 +118,7 @@ class GBFeatureTable(Base):

GBFeatureTable provides an iterator over all features, and returns
GBFeature instances.

In addition, when selecting features for specific types, the
features are instantiated as their type-specific subclasses. This
is the preferred selection mechanism for these feature types.
Expand All @@ -129,13 +129,13 @@ class GBFeatureTable(Base):

def __iter__(self):
return (GBFeature(n) for n in self._xml_root.iterfind('GBFeature'))

@property
def cds(self):
key = 'CDS'
nodes = self._get_nodes_with_key(key)
assert len(nodes) <= 1, "Node has {n=n} {key} features! (expected <= 1)".format(n=len(nodes), key=key)
return None if len(nodes) == 0 else GBFeatureCDS(nodes[0])
return None if not nodes else GBFeatureCDS(nodes[0])

@property
def exons(self):
Expand All @@ -148,7 +148,7 @@ def gene(self):
key = 'gene'
nodes = self._get_nodes_with_key(key)
assert len(nodes) <= 1, "Node has {n=n} {key} features! (expected <= 1)".format(n=len(nodes), key=key)
return None if len(nodes) == 0 else GBFeature(nodes[0])
return None if not nodes else GBFeature(nodes[0])

@property
def source(self):
Expand Down Expand Up @@ -192,7 +192,7 @@ def get_qualifiers(self, name):
def get_qualifier(self, name):
nodes = self.get_qualifiers(name)
assert len(nodes) <= 1, "Node has {n=n} {key} features! (expected <= 1 when using get_qualifier)".format(n=len(nodes), key=name)
if len(nodes)==0:
if not nodes:
return None
return self.get_qualifiers(name)[0]

Expand Down Expand Up @@ -237,13 +237,13 @@ def inference(self):

# <LICENSE>
# Copyright 2015 eutils Committers
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
Expand Down
15 changes: 10 additions & 5 deletions setup.py
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Expand Up @@ -3,8 +3,13 @@
from setuptools import setup, find_packages

package_name = "eutils"
short_description = open("doc/short-description.txt").read()
long_description = open("README.rst").read()

with open("doc/short-description.txt") as short_desc:
short_description = short_desc.read()

with open("README.rst") as long_desc:
long_description = long_desc.read()


setup(
author = package_name + " Committers",
Expand Down Expand Up @@ -62,13 +67,13 @@

# <LICENSE>
# Copyright 2016 Source Code Committers
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
Expand Down
13 changes: 6 additions & 7 deletions tests/test_eutils_queryservice.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
"""Performs a query using every form of eutils fcgi that this python
"""Performs a query using every form of eutils fcgi that this python
library should support.

"If you liked it, then you shoulda put a test on it." --Beyonce
Expand All @@ -21,7 +21,7 @@


def assert_in_xml(xml, item):
if six.PY3 and type(xml) == six.binary_type:
if six.PY3 and isinstance(xml, six.binary_type):
xml = xml.decode()
assert item in xml

Expand Down Expand Up @@ -77,18 +77,17 @@ def test_esearch(self):

@vcr.use_cassette
def test_elink(self):
'''Testing elink.fcgi by looking up related pmids in pubmed.'''
'''Testing elink.fcgi by looking up related pmids in pubmed.'''
# Expected response should contain the following information:

# * pubmed (all related links)
# * citedin (papers that cited this paper)
# * five (the "five" that pubmed displays as the top related results)
# * reviews (review papers that cite this paper)
# * combined (?)

expected_keys = ['pubmed', 'citedin', 'five', 'reviews', 'combined']
xmlstr = self.qs.elink( { 'dbfrom': 'pubmed', 'id': 1234567, 'cmd': 'neighbor' } )

xmlstr = self.qs.elink({'dbfrom': 'pubmed', 'id': 1234567, 'cmd': 'neighbor'})

resd = parse_related_pmids_result(xmlstr)
assert 'pubmed' in resd.keys()

Expand Down