Bring in Galaxy dev branch updates.

Raise max-complexity for tool output verification code.

Author: jmchilton

galaxy/exceptions/__init__.py

@@ -170,17 +170,17 @@ class ConfigurationError(Exception):
     err_code = error_codes.CONFIG_ERROR
 
 
-class InconsistentDatabase (MessageException):
+class InconsistentDatabase(MessageException):
     status_code = 500
     err_code = error_codes.INCONSISTENT_DATABASE
 
 
-class InternalServerError (MessageException):
+class InternalServerError(MessageException):
     status_code = 500
     err_code = error_codes.INTERNAL_SERVER_ERROR
 
 
-class NotImplemented (MessageException):
+class NotImplemented(MessageException):
     status_code = 501
     err_code = error_codes.NOT_IMPLEMENTED
 

galaxy/tools/cwl/util.py

@@ -9,7 +9,11 @@
 import tempfile
 from collections import namedtuple
 
-from six import BytesIO, iteritems, python_2_unicode_compatible
+from six import (
+    BytesIO,
+    iteritems,
+    python_2_unicode_compatible
+)
 
 STORE_SECONDARY_FILES_WITH_BASENAME = True
 SECONDARY_FILES_EXTRA_PREFIX = "__secondary_files__"
@@ -36,7 +40,7 @@ def output_properties(path=None, content=None, basename=None, pseduo_location=Fa
     try:
         contents = f.read(1024 * 1024)
         filesize = 0
-        while len(contents) > 0:
+        while contents:
             checksum.update(contents)
             filesize += len(contents)
             contents = f.read(1024 * 1024)

galaxy/tools/deps/container_resolvers/__init__.py

@@ -12,7 +12,7 @@
 
 @six.python_2_unicode_compatible
 @six.add_metaclass(ABCMeta)
-class ContainerResolver(Dictifiable, object):
+class ContainerResolver(Dictifiable):
     """Description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.

galaxy/tools/deps/containers.py

@@ -386,7 +386,7 @@ def preprocess_volumes(volumes_raw_str, container_type):
     return ",".join([":".join(v) for v in volumes])
 
 
-class HasDockerLikeVolumes:
+class HasDockerLikeVolumes(object):
     """Mixin to share functionality related to Docker volume handling.
 
     Singularity seems to have a fairly compatible syntax for volume handling.

galaxy/tools/deps/mulled/util.py

@@ -209,7 +209,7 @@ def v2_image_name(targets, image_build=None, name_override=None):
         return "mulled-v2-%s%s" % (package_hash.hexdigest(), suffix)
 
 
-class PrintProgress:
+class PrintProgress(object):
     def __init__(self):
         self.thread = threading.Thread(target=self.progress)
         self.stop = False

galaxy/tools/deps/resolvers/__init__.py

@@ -14,7 +14,7 @@
 
 
 @six.add_metaclass(ABCMeta)
-class DependencyResolver(Dictifiable, object):
+class DependencyResolver(Dictifiable):
     """Abstract description of a technique for resolving container images for tool execution."""
 
     # Keys for dictification.
@@ -43,7 +43,7 @@ def resolve(self, requirement, **kwds):
         """
 
 
-class MultipleDependencyResolver:
+class MultipleDependencyResolver(object):
     """Variant of DependencyResolver that can optionally resolve multiple dependencies together."""
 
     @abstractmethod
@@ -62,7 +62,7 @@ def resolve_all(self, requirements, **kwds):
 
 
 @six.add_metaclass(ABCMeta)
-class ListableDependencyResolver:
+class ListableDependencyResolver(object):
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can iterate over its dependencies and generate
     requirements.
@@ -78,7 +78,7 @@ def _to_requirement(self, name, version=None):
         return ToolRequirement(name=name, type="package", version=version)
 
 
-class MappableDependencyResolver:
+class MappableDependencyResolver(object):
     """Mix this into a ``DependencyResolver`` to allow mapping files.
 
     Mapping files allow adapting generic requirements to specific local implementations.
@@ -176,7 +176,7 @@ def from_dict(raw_mapping):
 
 
 @six.add_metaclass(ABCMeta)
-class SpecificationAwareDependencyResolver:
+class SpecificationAwareDependencyResolver(object):
     """Mix this into a :class:`DependencyResolver` to implement URI specification matching.
 
     Allows adapting generic requirements to more specific URIs - to tailor name
@@ -188,7 +188,7 @@ def _expand_specs(self, requirement):
         """Find closest matching specification for discovered resolver and return new concrete requirement."""
 
 
-class SpecificationPatternDependencyResolver:
+class SpecificationPatternDependencyResolver(SpecificationAwareDependencyResolver):
     """Implement the :class:`SpecificationAwareDependencyResolver` with a regex pattern."""
 
     @abstractproperty
@@ -220,7 +220,7 @@ def _expand_specs(self, requirement):
 
 
 @six.add_metaclass(ABCMeta)
-class InstallableDependencyResolver:
+class InstallableDependencyResolver(object):
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can attempt to install new dependencies.
     """
@@ -233,7 +233,7 @@ def install_dependency(self, name, version, type, **kwds):
 
 
 @six.add_metaclass(ABCMeta)
-class Dependency(Dictifiable, object):
+class Dependency(Dictifiable):
     dict_collection_visible_keys = ['dependency_type', 'exact', 'name', 'version', 'cacheable']
     cacheable = False
 

galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py

@@ -7,12 +7,15 @@
 import os
 from xml.etree import ElementTree as ET
 
+from . import (
+    DependencyResolver,
+    NullDependency
+)
 from .resolver_mixins import (
     UsesHomebrewMixin,
     UsesInstalledRepositoriesMixin,
     UsesToolDependencyDirMixin,
 )
-from ..resolvers import DependencyResolver, NullDependency
 
 log = logging.getLogger(__name__)
 

galaxy/tools/deps/resolvers/conda.py

@@ -9,6 +9,17 @@
 
 import galaxy.tools.deps.installable
 import galaxy.tools.deps.requirements
+from . import (
+    Dependency,
+    DependencyException,
+    DependencyResolver,
+    InstallableDependencyResolver,
+    ListableDependencyResolver,
+    MappableDependencyResolver,
+    MultipleDependencyResolver,
+    NullDependency,
+    SpecificationPatternDependencyResolver,
+)
 from ..conda_util import (
     build_isolated_environment,
     cleanup_failed_install,
@@ -23,17 +34,6 @@
     is_conda_target_installed,
     USE_PATH_EXEC_DEFAULT,
 )
-from ..resolvers import (
-    Dependency,
-    DependencyException,
-    DependencyResolver,
-    InstallableDependencyResolver,
-    ListableDependencyResolver,
-    MappableDependencyResolver,
-    MultipleDependencyResolver,
-    NullDependency,
-    SpecificationPatternDependencyResolver,
-)
 
 
 DEFAULT_BASE_PATH_DIRECTORY = "_conda"

galaxy/tools/deps/resolvers/galaxy_packages.py

@@ -9,14 +9,14 @@
     realpath,
 )
 
-from .resolver_mixins import UsesToolDependencyDirMixin
-from ..resolvers import (
+from . import (
     Dependency,
     DependencyResolver,
     ListableDependencyResolver,
     MappableDependencyResolver,
     NullDependency,
 )
+from .resolver_mixins import UsesToolDependencyDirMixin
 
 log = logging.getLogger(__name__)
 

galaxy/tools/deps/resolvers/homebrew.py

@@ -12,9 +12,11 @@
 incompatible changes coming.
 """
 
-
+from . import (
+    DependencyResolver,
+    NullDependency
+)
 from .resolver_mixins import UsesHomebrewMixin
-from ..resolvers import DependencyResolver, NullDependency
 
 # TODO: Implement prefer version linked...
 PREFER_VERSION_LINKED = 'linked'