Merge pull request #92 from nsoranzo/python3_fixes

Python3 fixes

Author: jmchilton

galaxy/tools/deps/conda_util.py

@@ -12,6 +12,7 @@
 import six
 from six.moves import shlex_quote
 
+from galaxy.util import unicodify
 from . import (
     commands,
     installable
@@ -165,6 +166,7 @@ def ensure_conda_build_installed_if_needed(self):
     def conda_info(self):
         if self.conda_exec is not None:
             info_out = commands.execute([self.conda_exec, "info", "--json"])
+            info_out = unicodify(info_out)
             info = json.loads(info_out)
             return info
         else:
@@ -494,6 +496,7 @@ def best_search_result(conda_target, conda_context, channels_override=None, offl
         search_cmd.extend(conda_context._override_channels_args)
     search_cmd.append(conda_target.package)
     res = commands.execute(search_cmd)
+    res = unicodify(res)
     hits = json.loads(res).get(conda_target.package, [])
     hits = sorted(hits, key=lambda hit: packaging.version.parse(hit['version']), reverse=True)
 

galaxy/tools/deps/containers.py

@@ -8,9 +8,15 @@
 
 import six
 
-from galaxy.util import asbool
-from galaxy.util import in_directory
-from galaxy.util import plugin_config
+from galaxy.util import (
+    asbool,
+    in_directory,
+    plugin_config
+)
+from . import (
+    docker_util,
+    singularity_util
+)
 from .container_resolvers.explicit import ExplicitContainerResolver
 from .container_resolvers.mulled import (
     BuildMulledDockerContainerResolver,
@@ -19,10 +25,11 @@
     CachedMulledSingularityContainerResolver,
     MulledDockerContainerResolver,
 )
-from .requirements import ContainerDescription
-from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL
-from ..deps import docker_util
-from ..deps import singularity_util
+from .requirements import (
+    ContainerDescription,
+    DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES,
+    DEFAULT_CONTAINER_SHELL
+)
 
 log = logging.getLogger(__name__)