Improved python 3 compatibility

patric_tools/config.py

@@ -14,11 +14,9 @@
 
 """
 try:
-    from urlparse import urlsplit, urljoin
-    from urllib import unquote, urlretrieve
-except ImportError: # Python 3
-    from urllib.parse import urlsplit, unquote  # TODO: include urljoin
-    from urllib.request import urlretrieve
+    from urlparse import urljoin
+except ImportError:  # Python 3
+    from urllib.parse import urljoin
 
 
 PATRIC_FTP_BASE_URL = "ftp://ftp.patricbrc.org"

patric_tools/genomes.py

@@ -17,8 +17,8 @@
 import os
 try:
     from urlparse import urljoin
-except ImportError: # Python 3
-    pass  # TODO: include urljoin
+except ImportError:  # Python 3
+    from urllib.parse import urljoin
 
 from time import sleep
 

patric_tools/tests/test_config.py

@@ -18,13 +18,16 @@
 from unittest import TestCase
 
 try:
+    from urllib2 import urlopen
     from urlparse import urljoin
-except ImportError: # Python 3
-    pass  # TODO: include urljoin
+except ImportError:  # Python 3
+    from urllib.parse import urljoin
+    from urllib.request import urlopen
 
 from ..config import PATRIC_FTP_BASE_URL, PATRIC_FTP_AMR_METADATA_URL, \
     PATRIC_FTP_GENOMES_URL, PATRIC_FTP_GENOMES_METADATA_URL
 
+
 class UtilityTests(TestCase):
     def setUp(self):
         """
@@ -34,9 +37,8 @@ def setUp(self):
         pass
 
     def _test_url(self, url):
-        import urllib2
         try:
-            urllib2.urlopen(url, timeout=10)
+            urlopen(url, timeout=10)
         except:
             self.fail("Could not reach {0!s}".format(url))
 

patric_tools/utils.py

@@ -17,11 +17,10 @@
 import posixpath
 
 try:
-    from urlparse import urlsplit, urljoin
-    from urllib import unquote, urlretrieve
-except ImportError: # Python 3
-    from urllib.parse import urlsplit, unquote  #TODO: include urljoin
-    from urllib.request import urlretrieve
+    from urlparse import urlsplit
+    from urllib import unquote
+except ImportError:  # Python 3
+    from urllib.parse import urlsplit, unquote
 
 
 def download_file_from_url(url, outdir):
@@ -51,7 +50,7 @@ def download_file_from_url(url, outdir):
         system("wget --quiet -o /dev/null -O {0!s} --continue --timeout 20 {1!s}".format(os.path.join(outdir, url_extract_file_name(url)), url))
         return ""
     except Exception as e:
-        print e
+        print(e)
         return url + str(e)
 
 

setup.py

@@ -25,7 +25,7 @@
 
 setup(
     name='PATRIC Tools',
-    version='1.0.0',
+    version='1.1.0',
 
     description='A Python package to interact with the PATRIC database (https://www.patricbrc.org)',
     long_description=long_description,