Merge pull request #3491 from nsoranzo/python3

Python3: use @six.add_metaclass() decorator

.ci/flake8_lint_include_list.txt

@@ -14,6 +14,7 @@ lib/galaxy/dataset_collections/__init__.py
 lib/galaxy/dataset_collections/structure.py
 lib/galaxy/dataset_collections/subcollections.py
 lib/galaxy/dataset_collections/type_description.py
+lib/galaxy/dataset_collections/types/__init__.py
 lib/galaxy/datatypes/assembly.py
 lib/galaxy/datatypes/binary.py
 lib/galaxy/datatypes/checkers.py
@@ -93,16 +94,7 @@ lib/galaxy/jobs/runners/pulsar.py
 lib/galaxy/jobs/runners/slurm.py
 lib/galaxy/jobs/runners/state_handlers/
 lib/galaxy/jobs/runners/tasks.py
-lib/galaxy/jobs/runners/util/cli/factory.py
-lib/galaxy/jobs/runners/util/cli/job/__init__.py
-lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
-lib/galaxy/jobs/runners/util/cli/job/torque.py
-lib/galaxy/jobs/runners/util/cli/shell/__init__.py
-lib/galaxy/jobs/runners/util/drmaa/
-lib/galaxy/jobs/runners/util/env.py
-lib/galaxy/jobs/runners/util/external.py
-lib/galaxy/jobs/runners/util/__init__.py
-lib/galaxy/jobs/runners/util/job_script/
+lib/galaxy/jobs/runners/util/
 lib/galaxy/jobs/splitters/basic.py
 lib/galaxy/jobs/splitters/__init__.py
 lib/galaxy/jobs/stock_rules.py
@@ -266,16 +258,7 @@ lib/galaxy/security/validate_user_input.py
 lib/galaxy/tags/
 lib/galaxy/tools/
 lib/galaxy/util/
-lib/galaxy_utils/__init__.py
-lib/galaxy/util/sleeper.py
-lib/galaxy/util/specs.py
-lib/galaxy_utils/sequence/fasta.py
-lib/galaxy_utils/sequence/fastq.py
-lib/galaxy_utils/sequence/__init__.py
-lib/galaxy_utils/sequence/transform.py
-lib/galaxy_utils/sequence/vcf.py
-lib/galaxy/util/template.py
-lib/galaxy/util/ucsc.py
+lib/galaxy_utils/
 lib/galaxy/version.py
 lib/galaxy/visualization/data_providers/basic.py
 lib/galaxy/visualization/data_providers/cigar.py

.ci/py3_sources.txt

@@ -65,7 +65,7 @@ lib/galaxy/webapps/tool_shed/util/ratings_util.py
 lib/galaxy/work/
 lib/galaxy/workflow/extract.py
 lib/galaxy/workflow/run.py
-lib/galaxy/workflow/schedulers/core.py
+lib/galaxy/workflow/schedulers/
 lib/galaxy/workflow/steps.py
 lib/galaxy_ext/
 lib/galaxy_utils/

lib/galaxy/auth/providers/__init__.py

@@ -3,13 +3,14 @@ Created on 15/07/2014
 
 @author: Andrew Robinson
 """
-
 import abc
 
+import six
 
+
+@six.add_metaclass(abc.ABCMeta)
 class AuthProvider(object):
     """A base class for all Auth Providers."""
-    __metaclass__ = abc.ABCMeta
 
     @abc.abstractproperty
     def plugin_type(self):

lib/galaxy/dataset_collections/types/__init__.py

@@ -1,13 +1,18 @@
-from galaxy import exceptions
-from abc import ABCMeta
-from abc import abstractmethod
-
 import logging
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
+
+from galaxy import exceptions
+
 log = logging.getLogger( __name__ )
 
 
+@six.add_metaclass(ABCMeta)
 class DatasetCollectionType(object):
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def generate_elements( self, dataset_instances ):

lib/galaxy/jobs/datasets.py

@@ -2,13 +2,17 @@
 Utility classes allowing Job interface to reason about datasets.
 """
 import os.path
-from abc import ABCMeta
-from abc import abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
 
 
 def dataset_path_rewrites( dataset_paths ):
-    dataset_paths_with_rewrites = filter( lambda path: getattr( path, "false_path", None ), dataset_paths )
-    return dict( [ ( dp.real_path, dp ) for dp in dataset_paths_with_rewrites ] )
+    dataset_paths_with_rewrites = [path for path in dataset_paths if getattr(path, "false_path", None)]
+    return dict( ( dp.real_path, dp ) for dp in dataset_paths_with_rewrites )
 
 
 class DatasetPath( object ):
@@ -49,9 +53,9 @@ class DatasetPath( object ):
         return dataset_path
 
 
+@six.add_metaclass(ABCMeta)
 class DatasetPathRewriter( object ):
     """ Used by runner to rewrite paths. """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def rewrite_dataset_path( self, dataset, dataset_type ):

lib/galaxy/jobs/metrics/instrumenters/__init__.py

@@ -3,19 +3,21 @@
 These are responsible for collecting and formatting a coherent set of metrics.
 """
 import os.path
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
 
-from abc import ABCMeta
-from abc import abstractmethod
+import six
 
 from ...metrics import formatting
 
-
 INSTRUMENT_FILE_PREFIX = "__instrument"
 
 
+@six.add_metaclass(ABCMeta)
 class InstrumentPlugin( object ):
     """Describes how to instrument job scripts and retrieve collected metrics."""
-    __metaclass__ = ABCMeta
     formatter = formatting.JobMetricFormatter()
 
     @property

lib/galaxy/jobs/runners/util/cli/__init__.py

@@ -1,8 +1,11 @@
 """
 """
 from glob import glob
-from os.path import basename, join
 from os import getcwd
+from os.path import (
+    basename,
+    join
+)
 
 DEFAULT_SHELL_PLUGIN = 'LocalShell'
 
@@ -61,7 +64,7 @@ class CliInterface(object):
             raise ValueError(ERROR_MESSAGE_NO_JOB_PLUGIN)
         job_plugin_class = self.cli_job_interfaces.get(job_plugin, None)
         if not job_plugin_class:
-            raise ValueError(ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN % (job_plugin, self.cli_job_interfaces.keys()))
+            raise ValueError(ERROR_MESSAGE_NO_SUCH_JOB_PLUGIN % (job_plugin, list(self.cli_job_interfaces.keys())))
         job_interface = job_plugin_class(**job_params)
 
         return job_interface

lib/galaxy/jobs/runners/util/cli/job/__init__.py

@@ -1,11 +1,16 @@
 """
 Abstract base class for cli job plugins.
 """
-from abc import ABCMeta, abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
 
 
+@six.add_metaclass(ABCMeta)
 class BaseJobExec(object):
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def __init__(self, **params):

lib/galaxy/jobs/runners/util/cli/job/slurm.py

@@ -1,10 +1,9 @@
 # A simple CLI runner for slurm that can be used when running Galaxy from a
 # non-submit host and using a Slurm cluster.
+from logging import getLogger
 
 from ..job import BaseJobExec
 
-from logging import getLogger
-
 try:
     from galaxy.model import Job
     job_states = Job.states

lib/galaxy/jobs/runners/util/cli/shell/__init__.py

@@ -1,11 +1,16 @@
 """
 Abstract base class for runners which execute commands via a shell.
 """
-from abc import ABCMeta, abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
 
 
+@six.add_metaclass(ABCMeta)
 class BaseShellExec(object):
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def __init__(self, *args, **kwargs):

lib/galaxy/jobs/runners/util/cli/shell/local.py

@@ -1,11 +1,17 @@
+from logging import getLogger
+from subprocess import (
+    PIPE,
+    Popen
+)
 from tempfile import TemporaryFile
 from time import sleep
-from subprocess import Popen, PIPE
 
 from ..shell import BaseShellExec
-from ....util import Bunch, kill_pid
+from ....util import (
+    Bunch,
+    kill_pid
+)
 
-from logging import getLogger
 log = getLogger(__name__)
 
 TIMEOUT_ERROR_MESSAGE = u'Execution timed out'

lib/galaxy/jobs/runners/util/cli/shell/rsh.py

@@ -1,6 +1,7 @@
+from logging import getLogger
+
 from .local import LocalShell
 
-from logging import getLogger
 log = getLogger(__name__)
 
 __all__ = ('RemoteShell', 'SecureShell', 'GlobusSecureShell')

lib/galaxy/jobs/runners/util/condor/__init__.py

@@ -1,7 +1,14 @@
 """
 Condor helper utilities.
 """
-from subprocess import Popen, PIPE, STDOUT, check_call, CalledProcessError
+from subprocess import (
+    CalledProcessError,
+    check_call,
+    PIPE,
+    Popen,
+    STDOUT
+)
+
 from ..external import parse_external_id
 
 DEFAULT_QUERY_CLASSAD = dict(

lib/galaxy/jobs/runners/util/kill.py

@@ -1,10 +1,10 @@
 import os
 from platform import system
-from time import sleep
 from subprocess import Popen
+from time import sleep
 
 try:
-    from psutil import Process, NoSuchProcess
+    from psutil import NoSuchProcess, Process
 except ImportError:
     """ Don't make psutil a strict requirement, but use if available. """
     Process = None

lib/galaxy/jobs/runners/util/retry.py

@@ -1,7 +1,7 @@
+import logging
 from itertools import count
 from time import sleep
 
-import logging
 log = logging.getLogger(__name__)
 
 DEFAULT_MAX_RETRIES = -1  # By default don't retry.

lib/galaxy/jobs/runners/util/sudo.py

@@ -1,6 +1,8 @@
 import logging
-
-from subprocess import Popen, PIPE
+from subprocess import (
+    PIPE,
+    Popen
+)
 
 SUDO_PATH = '/usr/bin/sudo'
 SUDO_PRESERVE_ENVIRONMENT_ARG = '-E'

lib/galaxy/tools/deps/container_resolvers/__init__.py

@@ -5,17 +5,18 @@ from abc import (
     abstractproperty,
 )
 
+import six
+
 from galaxy.util.dictifiable import Dictifiable
 
 
+@six.add_metaclass(ABCMeta)
 class ContainerResolver(Dictifiable, object):
     """Description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.
     dict_collection_visible_keys = ['resolver_type']
 
-    __metaclass__ = ABCMeta
-
     def __init__(self, app_info=None, **kwds):
         """Default initializer for ``ContainerResolver`` subclasses."""
         self.app_info = app_info

lib/galaxy/tools/deps/containers.py

@@ -279,8 +279,8 @@ class JobInfo(object):
         self.job_directory_type = job_directory_type  # "galaxy" or "pulsar"
 
 
+@six.add_metaclass(ABCMeta)
 class Container( object ):
-    __metaclass__ = ABCMeta
 
     def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description):
         self.container_id = container_id
@@ -445,8 +445,9 @@ class NullContainer(object):
     def __init__(self):
         pass
 
-    def __nonzero__(self):
+    def __bool__(self):
         return False
+    __nonzero__ = __bool__
 
 
 NULL_CONTAINER = NullContainer()

lib/galaxy/tools/deps/installable.py

@@ -2,13 +2,14 @@
 
 import logging
 import os
-
 from abc import (
     ABCMeta,
     abstractmethod,
     abstractproperty,
 )
 
+import six
+
 from galaxy.util.filelock import (
     FileLock,
     FileLockException
@@ -17,11 +18,10 @@ from galaxy.util.filelock import (
 log = logging.getLogger(__name__)
 
 
+@six.add_metaclass(ABCMeta)
 class InstallableContext(object):
     """Represent a directory/configuration of something that can be installed."""
 
-    __metaclass__ = ABCMeta
-
     @abstractmethod
     def is_installed(self):
         """Return bool indicating if the configured software is installed."""

lib/galaxy/tools/deps/resolvers/__init__.py

@@ -5,6 +5,7 @@ from abc import (
     abstractproperty,
 )
 
+import six
 import yaml
 
 from galaxy.util import listify
@@ -13,6 +14,7 @@ from galaxy.util.dictifiable import Dictifiable
 from ..requirements import ToolRequirement
 
 
+@six.add_metaclass(ABCMeta)
 class DependencyResolver(Dictifiable, object):
     """Abstract description of a technique for resolving container images for tool execution."""
 
@@ -26,7 +28,6 @@ class DependencyResolver(Dictifiable, object):
     disabled = False
     resolves_simple_dependencies = True
     config_options = {}
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def resolve( self, requirement, **kwds ):
@@ -51,12 +52,12 @@ class MultipleDependencyResolver:
         """
 
 
+@six.add_metaclass(ABCMeta)
 class ListableDependencyResolver:
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can iterate over its dependencies and generate
     requirements.
     """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def list_dependencies(self):
@@ -87,7 +88,7 @@ class MappableDependencyResolver:
     def _mapping_file_to_list(mapping_file):
         with open(mapping_file, "r") as f:
             raw_mapping = yaml.load(f) or []
-            return map(RequirementMapping.from_dict, raw_mapping)
+        return map(RequirementMapping.from_dict, raw_mapping)
 
     def _expand_mappings(self, requirement):
         for mapping in self._mappings:
@@ -134,13 +135,13 @@ class RequirementMapping(object):
         return RequirementMapping(from_name, from_version, to_name, to_version)
 
 
+@six.add_metaclass(ABCMeta)
 class SpecificationAwareDependencyResolver:
     """Mix this into a :class:`DependencyResolver` to implement URI specification matching.
 
     Allows adapting generic requirements to more specific URIs - to tailor name
     or version to specified resolution system.
     """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def _expand_specs(self, requirement):
@@ -178,11 +179,11 @@ class SpecificationPatternDependencyResolver:
         return requirement
 
 
+@six.add_metaclass(ABCMeta)
 class InstallableDependencyResolver:
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can attempt to install new dependencies.
     """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def install_dependency(self, name, version, type, **kwds):
@@ -191,9 +192,9 @@ class InstallableDependencyResolver:
         """
 
 
+@six.add_metaclass(ABCMeta)
 class Dependency(Dictifiable, object):
     dict_collection_visible_keys = ['dependency_type', 'exact', 'name', 'version', 'cacheable']
-    __metaclass__ = ABCMeta
     cacheable = False
 
     @abstractmethod

lib/galaxy/tools/parser/interface.py

@@ -1,17 +1,19 @@
-from abc import ABCMeta
-from abc import abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
 
 import six
 
 NOT_IMPLEMENTED_MESSAGE = "Galaxy tool format does not yet support this tool feature."
 
 
+@six.add_metaclass(ABCMeta)
 @six.python_2_unicode_compatible
 class ToolSource(object):
     """ This interface represents an abstract source to parse tool
     information from.
     """
-    __metaclass__ = ABCMeta
     default_is_multi_byte = False
 
     @abstractmethod
@@ -202,8 +204,8 @@ class PagesSource(object):
         return True
 
 
+@six.add_metaclass(ABCMeta)
 class PageSource(object):
-    __metaclass__ = ABCMeta
 
     def parse_display(self):
         return None
@@ -213,8 +215,8 @@ class PageSource(object):
         """ Return a list of InputSource objects. """
 
 
+@six.add_metaclass(ABCMeta)
 class InputSource(object):
-    __metaclass__ = ABCMeta
     default_optional = False
 
     def elem(self):

lib/galaxy/tools/toolbox/lineages/interface.py

@@ -1,11 +1,15 @@
-from abc import ABCMeta
-from abc import abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
 
 
+@six.add_metaclass(ABCMeta)
 class ToolLineage(object):
     """
     """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def get_versions( self, reverse=False ):

lib/galaxy/tools/toolbox/tags.py

@@ -1,9 +1,12 @@
 """ Handle details of tool tagging - perhaps a deprecated feature.
 """
 import logging
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
 
-from abc import ABCMeta
-from abc import abstractmethod
+import six
 
 log = logging.getLogger( __name__ )
 
@@ -18,8 +21,8 @@ def tool_tag_manager( app ):
         return NullToolTagManager()
 
 
+@six.add_metaclass(ABCMeta)
 class AbstractToolTagManager( object ):
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def reset_tags( self ):

lib/galaxy/util/object_wrapper.py

@@ -6,8 +6,8 @@ import inspect
 import logging
 import string
 import sys
-
 from numbers import Number
+
 try:
     from types import NoneType
 except ImportError:
@@ -56,6 +56,7 @@ from types import (
     ModuleType,
     TracebackType,
 )
+
 from six.moves import (
     copyreg as copy_reg,
     UserDict
@@ -307,7 +308,7 @@ class SafeStringWrapper( object ):
 
     # Skip __slots__
 
-    # Don't need __metaclass__, we'll use the helper function to handle with subclassing for e.g. isinstance()
+    # Don't need to define a metaclass, we'll use the helper function to handle with subclassing for e.g. isinstance()
 
     # Revisit:
     # __instancecheck__

lib/galaxy/workflow/schedulers/__init__.py

@@ -2,10 +2,15 @@
 for workflow scheduling is highly experimental and the interface required for
 scheduling plugins will almost certainly change.
 """
-from abc import ABCMeta
-from abc import abstractmethod
+from abc import (
+    ABCMeta,
+    abstractmethod
+)
+
+import six
 
 
+@six.add_metaclass(ABCMeta)
 class WorkflowSchedulingPlugin( object ):
     """ A plugin defining how Galaxy should schedule plugins. By default
     plugins are passive and should monitor Galaxy's work queue for
@@ -13,7 +18,6 @@ class WorkflowSchedulingPlugin( object ):
     the scheduling plugin should be forced (i.e. if scheduling happen all at
     once or the request will be stored and monitored outside of Galaxy.)
     """
-    __metaclass__ = ABCMeta
 
     @property
     @abstractmethod
@@ -30,8 +34,8 @@ class WorkflowSchedulingPlugin( object ):
         """
 
 
+@six.add_metaclass(ABCMeta)
 class ActiveWorkflowSchedulingPlugin( WorkflowSchedulingPlugin ):
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def schedule( self, workflow_invocation ):

lib/galaxy_utils/sequence/sequence.py

@@ -1,8 +1,9 @@
 # Dan Blankenberg
-import transform
 import string
 from copy import deepcopy
 
+from . import transform
+
 
 class SequencingRead( object ):
     color_space_converter = transform.ColorSpaceConverter()