Python 3 all the stuff.

Fixes #62.

.travis.yml

@@ -8,6 +8,7 @@ env:
   - TOX_ENV=lint-docs
   - TOX_ENV=py26 SETUP=true
   - TOX_ENV=py27 SETUP=true
+  - TOX_ENV=py34 SETUP=true
 
 install:
   - pip install tox

CONTRIBUTING.rst

@@ -117,7 +117,7 @@ Before you submit a pull request, check that it meets these guidelines:
 1. If the pull request adds functionality, the docs should ideally be updated.
    Put your new functionality into a function with a docstring. (Until the
    @jmchilton learns to do this consistently this is only a suggestion though.)
-2. The pull request should work for Python 2.6 and 2.7. Check
+2. The pull request should work for Python 2.6, 2.7, and 3.4. Check
    https://travis-ci.org/galaxyproject/planemo/pull_requests
    and make sure that the tests pass for all supported Python versions. The
    tests are imperfect and Travis sometimes fails in a transient fashion so

HISTORY.rst

@@ -7,6 +7,7 @@ History
 0.4.0.dev0
 ------------------------
 
+* Python 3 support.
 
 ------------------------
 0.3.0 (2015-04-12)

galaxy/objectstore/__init__.py

@@ -184,7 +184,7 @@ class DiskObjectStore(ObjectStore):
     >>> import tempfile
     >>> file_path=tempfile.mkdtemp()
     >>> obj = Bunch(id=1)
-    >>> s = DiskObjectStore(Bunch(umask=077, job_working_directory=file_path, new_file_path=file_path, object_store_check_old_style=False), file_path=file_path)
+    >>> s = DiskObjectStore(Bunch(umask=0o077, job_working_directory=file_path, new_file_path=file_path, object_store_check_old_style=False), file_path=file_path)
     >>> s.create(obj)
     >>> s.exists(obj)
     True
@@ -287,7 +287,7 @@ def create(self, obj, **kwargs):
             # Create the file if it does not exist
             if not dir_only:
                 open(path, 'w').close()  # Should be rb?
-                umask_fix_perms(path, self.config.umask, 0666)
+                umask_fix_perms(path, self.config.umask, 0o666)
 
     def empty(self, obj, **kwargs):
         return os.path.getsize(self.get_filename(obj, **kwargs)) == 0
@@ -311,7 +311,7 @@ def delete(self, obj, entire_dir=False, **kwargs):
             if self.exists(obj, **kwargs):
                 os.remove(path)
                 return True
-        except OSError, ex:
+        except OSError as ex:
             log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex))
         return False
 
@@ -344,7 +344,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
                     force_symlink( os.readlink( file_name ), self.get_filename( obj, **kwargs ) )
                 else:
                     shutil.copy( file_name, self.get_filename( obj, **kwargs ) )
-            except IOError, ex:
+            except IOError as ex:
                 log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex))
                 raise ex
 

galaxy/objectstore/rods.py

@@ -152,7 +152,7 @@ def create(self, obj, **kwargs):
                 # that we can prevent overwriting
                 doi = irods.dataObjInp_t()
                 doi.objPath = rods_path
-                doi.createMode = 0640
+                doi.createMode = 0o640
                 doi.dataSize = 0  # 0 actually means "unknown", although literally 0 would be preferable
                 irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource )
                 status = irods.rcDataObjCreate( self.rods_conn, doi )
@@ -195,7 +195,7 @@ def delete( self, obj, entire_dir=False, **kwargs ):
             return True
         except AttributeError:
             log.warning( 'delete(): operation failed: object does not exist: %s', rods_path )
-        except AssertionError, e:
+        except AssertionError as e:
             # delete() does not raise on deletion failure
             log.error( 'delete(): operation failed: %s', e )
         finally:
@@ -281,7 +281,7 @@ def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         # put will create if necessary
         doi = irods.dataObjInp_t()
         doi.objPath = self.__get_rods_path( obj, **kwargs )
-        doi.createMode = 0640
+        doi.createMode = 0o640
         doi.dataSize = os.stat( file_name ).st_size
         doi.numThreads = 0
         irods.addKeyVal( doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource )

galaxy/objectstore/s3.py

@@ -192,13 +192,13 @@ def _get_bucket(self, bucket_name):
     def _fix_permissions(self, rel_path):
         """ Set permissions on rel_path"""
         for basedir, _, files in os.walk(rel_path):
-            umask_fix_perms(basedir, self.config.umask, 0777, self.config.gid)
+            umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
             for filename in files:
                 path = os.path.join(basedir, filename)
                 # Ignore symlinks
                 if os.path.islink(path):
                     continue
-                umask_fix_perms( path, self.config.umask, 0666, self.config.gid )
+                umask_fix_perms( path, self.config.umask, 0o666, self.config.gid )
 
     def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs):
         rel_path = os.path.join(*directory_hash_id(obj.id))
@@ -439,7 +439,7 @@ def size(self, obj, **kwargs):
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
-            except OSError, ex:
+            except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
         elif self.exists(obj, **kwargs):
             return self._get_size_in_s3(rel_path)

galaxy/tools/deps/resolvers/modules.py

@@ -8,7 +8,7 @@
 """
 from os import environ, pathsep
 from os.path import exists, isdir, join
-from StringIO import StringIO
+from six import StringIO
 from subprocess import Popen, PIPE
 
 from ..resolvers import DependencyResolver, INDETERMINATE_DEPENDENCY, Dependency
@@ -107,13 +107,13 @@ def has_module(self, module, version):
 
         for module_name, module_version in module_generator:
             names_match = module == module_name
-            module_match = names_match and (version == None or module_version == version)
+            module_match = names_match and (version is None or module_version == version)
             if module_match:
                 return True
         return False
 
     def __modules(self):
-        raw_output = self.__module_avail_output()
+        raw_output = self.__module_avail_output().decode("utf-8")
         for line in StringIO(raw_output):
             line = line and line.strip()
             if not line or line.startswith("-"):

galaxy/util/odict.py

@@ -2,7 +2,14 @@
 Ordered dictionary implementation.
 """
 
-from UserDict import UserDict
+try:
+    from galaxy import eggs
+    eggs.require("six")
+except ImportError:
+    # Allow code to operate outside Galaxy.
+    pass
+
+from six.moves import UserDict
 
 
 class odict(UserDict):