Added flake8 testing and fixed lint errors

Author: nuwang

.travis.yml

@@ -1,23 +1,25 @@
 language: python
-python: 3.5
 os:
   - linux
-#  - osx
-env:
-  - TOX_ENV=py27-aws
-  - TOX_ENV=py27-openstack
-  - TOX_ENV=py35-aws
-  - TOX_ENV=py35-openstack
-  - TOX_ENV=pypy-aws
-  - TOX_ENV=pypy-openstack
 matrix:
   fast_finish: true
-  allow_failures:
-    - os: osx
+  include:
+    - python: 2.7
+      env: TOXENV=py27-aws
+    - python: 3.5
+      env: TOXENV=py35-aws
+    - python: pypy
+      env: TOXENV=pypy-aws
+    - python: 2.7
+      env: TOXENV=py27-openstack
+    - python: 3.5
+      env: TOXENV=py35-openstack
+    - python: pypy
+      env: TOXENV=pypy-openstack
 install:
   - pip install tox
   - pip install coveralls
 script:
-  - tox -e $TOX_ENV
+  - tox -e $TOXENV
 after_success:
   - coveralls

genomespaceclient/__init__.py

@@ -1,4 +1,4 @@
-from .client import GenomeSpaceClient
-from .client import GSFileMetadata
-from .client import GSDataFormat
-from .shell import main
+from .client import GSDataFormat  # noqa
+from .client import GSFileMetadata  # noqa
+from .client import GenomeSpaceClient  # noqa
+from .shell import main  # noqa

genomespaceclient/client.py

@@ -1,11 +1,11 @@
 import errno
-import logging
-import re
 import glob
+import logging
 import os
+import re
 
-from genomespaceclient import storage_handlers
 from genomespaceclient import gs_glob
+from genomespaceclient import storage_handlers
 from genomespaceclient.exceptions import GSClientException
 
 import requests
@@ -462,9 +462,9 @@ def copy(self, source, destination, recurse=False):
         Copies a file to/from/within GenomeSpace.
 
         E.g.
-
-        client.copy("/tmp/local_file.txt",
-        "https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt")
+        .. code-block:: python
+            client.copy("/tmp/local_file.txt",
+                    "https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt")
 
         :type source: :class:`str`
         :param source: Local filename or GenomeSpace URL of source file.
@@ -495,9 +495,9 @@ def move(self, source, destination):
         Moves a file within GenomeSpace.
 
         E.g.
-
-        client.move("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt",
-        "https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
+        .. code-block:: python
+            client.move("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt",
+                        "https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
 
         :type source: :str:
         :param source: GenomeSpace URL of source file. Cannot be a local file.
@@ -521,8 +521,8 @@ def list(self, genomespace_url):
         Returns a list of files within a GenomeSpace folder.
 
         E.g.
-
-        client.list("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/")
+        .. code-block:: python
+            client.list("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/")
 
         :type genomespace_url: :class:`str`
         :param genomespace_url: GenomeSpace URL of folder to list.
@@ -540,8 +540,8 @@ def delete(self, genomespace_url, recurse=False):
         Deletes a file within a GenomeSpace folder.
 
         E.g.
-
-        client.delete("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
+        .. code-block:: python
+            client.delete("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
 
         :type genomespace_url: :class:`str`
         :param genomespace_url: GenomeSpace URL of file to delete.
@@ -592,7 +592,8 @@ def mkdir(self, genomespace_url, create_path=True):
         Creates a folder at a given location.
 
         E.g.
-        client.mkdir("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/Folder1")
+        .. code-block:: python
+            client.mkdir("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/Folder1")
 
         :type genomespace_url: :class:`str`
         :param genomespace_url: GenomeSpace URL of file to delete.
@@ -618,7 +619,9 @@ def get_metadata(self, genomespace_url):
 
         E.g.
 
-        client.get_metadata("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
+        .. code-block:: python
+
+            client.get_metadata("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")
 
         :type genomespace_url: :class:`str`
         :param genomespace_url: GenomeSpace URL of file to delete.
@@ -639,14 +642,16 @@ def get_remaining_token_time(self, genomespace_url):
         If you don't have one, will return 0, as the non existent token has
         no time left to live. See:
         http://www.genomespace.org/support/api/restful-access-to-identity-server#get_token_time
-          
-        E.g. 
-        
-        client.get_remaining_token_time('https://genomespace.genome.edu.au/')
-        
+
+        E.g.
+
+        .. code-block:: python
+
+            client.get_remaining_token_time('https://genomespace.genome.edu.au/')
+
         :type genomespace_url: :class:`str`
         :param genomespace_url: GenomeSpace URL.
-        
+
         :rtype: :class:`int`
         :return: the time the token has left to live in milliseconds.
         """

genomespaceclient/shell.py

@@ -178,5 +178,6 @@ def main():
     finally:
         logging.shutdown()
 
+
 if __name__ == "__main__":
     sys.exit(main())

genomespaceclient/storage_handlers.py

@@ -1,20 +1,18 @@
-from __future__ import print_function
-
-from abc import ABCMeta, abstractmethod
 import logging
 import os
+from abc import ABCMeta, abstractmethod
 
 from cloudbridge.cloud.factory import CloudProviderFactory, ProviderList
+
 from genomespaceclient import util
-import requests
 
+import requests
 
 try:
     from urllib.parse import urlparse
 except ImportError:
     from urlparse import urlparse
 
-
 log = logging.getLogger(__name__)
 
 
@@ -73,8 +71,7 @@ def download(self, download_info, destination):
                           " copied".format(
                               progress=util.format_file_size(bytes_copied),
                               total=util.format_file_size(int(total_length))
-                              if total_length else "unknown size"),
-                          end='\r')
+                              if total_length else "unknown size", end='\r'))
             if log.isEnabledFor(logging.INFO):
                 print("\n")
 

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 setup(name='python-genomespaceclient',
       version="0.2",
@@ -9,7 +9,7 @@
       url='http://python-genomespaceclient.readthedocs.org/',
       install_requires=['cloudbridge>=0.3,<0.4', 'requests'],
       extras_require={
-          'dev': ['tox', 'sphinx']
+          'dev': ['tox', 'sphinx', 'flake8', 'flake8-import-order']
       },
       packages=find_packages(),
       license='MIT',

test/helpers.py

@@ -14,6 +14,7 @@
 except ImportError:
     from urlparse import urlparse
 
+
 def get_test_username():
     return os.environ["GENOMESPACE_USERNAME"]
 
@@ -33,8 +34,8 @@ def get_remote_test_folder():
 
 def get_genomespace_url():
     """
-    :return: the scheme and net location of the remote test folder in the form of
-             a url. E.g. https://genomespace.genome.edu.au
+    :return: the scheme and net location of the remote test folder in the form
+             of a url. E.g. https://genomespace.genome.edu.au
     :rtype: :class:`str`
     """
     url_components = urlparse(get_remote_test_folder())

test/test_genomespace_client.py

@@ -2,13 +2,13 @@
 import os
 import shutil
 import tempfile
-
-from test.helpers import get_test_username
-
-from test import helpers
 import unittest
 import uuid
-from genomespaceclient import GSFileMetadata, GSDataFormat
+from test import helpers
+from test.helpers import get_test_username
+
+from genomespaceclient import GSDataFormat, GSFileMetadata
+
 try:
     from urllib.parse import urljoin
 except ImportError:

test/test_genomespace_shell.py

@@ -1,10 +1,10 @@
 import filecmp
 import os
+import shutil
 import tempfile
-from test import helpers
 import unittest
 import uuid
-import shutil
+from test import helpers
 
 from genomespaceclient import main
 

tox.ini

@@ -7,7 +7,8 @@
 envlist = {py27,py35,pypy}-{aws,openstack}
 
 [testenv]
-commands = {envpython} -m coverage run --branch --source=genomespaceclient setup.py test {posargs}
+commands = flake8 genomespaceclient test setup.py
+           {envpython} -m coverage run --branch --source=genomespaceclient setup.py test {posargs}
 setenv =
     aws: GENOMESPACE_TEST_FOLDER={env:GENOMESPACE_TEST_FOLDER_AWS}
     openstack: GENOMESPACE_TEST_FOLDER={env:GENOMESPACE_TEST_FOLDER_OS}