Format code with black 25.1.0

lib/galaxy/app_unittest_utils/tools_support.py

@@ -1,4 +1,4 @@
-""" Module contains test fixtures meant to aide in the testing of jobs and
+"""Module contains test fixtures meant to aide in the testing of jobs and
 tool evaluation. Such extensive "fixtures" are something of an anti-pattern
 so use of this should be limited to tests of very 'extensive' classes.
 """

lib/galaxy/datatypes/metadata.py

@@ -1,4 +1,4 @@
-""" Expose the model metadata module as a datatype module also,
+"""Expose the model metadata module as a datatype module also,
 allowing it to live in galaxy.model means the model module doesn't
 have any dependencies on th datatypes module. This module will need
 to remain here for datatypes living in the tool shed so we might as

lib/galaxy/datatypes/text.py

@@ -1,5 +1,4 @@
-""" Clearing house for generic text datatypes that are not XML or tabular.
-"""
+"""Clearing house for generic text datatypes that are not XML or tabular."""
 
 import gzip
 import json

lib/galaxy/job_execution/output_collect.py

@@ -1,5 +1,4 @@
-""" Code allowing tools to define extra files associated with an output datset.
-"""
+"""Code allowing tools to define extra files associated with an output datset."""
 
 import logging
 import operator

lib/galaxy/jobs/runners/aws.py

@@ -1,5 +1,4 @@
-""" Galaxy job runners to use Amazon AWS native compute resources, such as AWS Batch.
-"""
+"""Galaxy job runners to use Amazon AWS native compute resources, such as AWS Batch."""
 
 import bisect
 import hashlib

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

@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import json
 

lib/galaxy/jobs/stock_rules.py

@@ -1,4 +1,4 @@
-""" Stock job 'dynamic' rules for use in the job config file - these may cover some
+"""Stock job 'dynamic' rules for use in the job config file - these may cover some
 simple use cases but will just proxy into functions in rule_helper so similar
 functionality - but more tailored and composable can be utilized in custom
 rules.

lib/galaxy/model/dataset_collections/structure.py

@@ -1,5 +1,4 @@
-""" Module for reasoning about structure of and matching hierarchical collections of data.
-"""
+"""Module for reasoning about structure of and matching hierarchical collections of data."""
 
 import logging
 

lib/galaxy/objectstore/caching.py

@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import logging
 import os

lib/galaxy/objectstore/s3_boto3.py

@@ -1,5 +1,4 @@
-"""A more modern version of the S3 object store based on boto3 instead of boto.
-"""
+"""A more modern version of the S3 object store based on boto3 instead of boto."""
 
 import logging
 import os

lib/galaxy/short_term_storage/__init__.py

@@ -1,4 +1,4 @@
-""" Short Term Storage service for Galaxy.
+"""Short Term Storage service for Galaxy.
 
 This service is used to store files for a short period of time (e.g. a few minutes, hours or days)
 and then serve them to the client. This is useful for large files that take a long time to

lib/galaxy/tool_util/cwl/parser.py

@@ -1,4 +1,4 @@
-""" This module provides proxy objects around objects from the common
+"""This module provides proxy objects around objects from the common
 workflow language reference implementation library cwltool. These proxies
 adapt cwltool to Galaxy features and abstract the library away from the rest
 of the framework.

lib/galaxy/tool_util/cwl/representation.py

@@ -1,5 +1,5 @@
-""" This module is responsible for converting between Galaxy's tool
-input description and the CWL description for a job json. """
+"""This module is responsible for converting between Galaxy's tool
+input description and the CWL description for a job json."""
 
 import json
 import logging

lib/galaxy/tool_util/deps/brew_util.py

@@ -1,4 +1,4 @@
-""" brew_exts defines generic extensions to Homebrew this file
+"""brew_exts defines generic extensions to Homebrew this file
 builds on those abstraction and provides Galaxy specific functionality
 not useful to the brew external commands.
 """

lib/galaxy/tool_util/deps/containers.py

@@ -149,7 +149,7 @@ def __destination_container(
             return container
 
         def container_from_description_from_dicts(
-            destination_container_dicts: List[Dict[str, Any]]
+            destination_container_dicts: List[Dict[str, Any]],
         ) -> Optional[Container]:
             for destination_container_dict in destination_container_dicts:
                 container_description = ContainerDescription.from_dict(destination_container_dict)

lib/galaxy/tool_util/parameters/convert.py

@@ -1,5 +1,4 @@
-"""Utilities for converting between request states.
-"""
+"""Utilities for converting between request states."""
 
 import logging
 from typing import (

lib/galaxy/tool_util/parameters/models.py

@@ -1056,7 +1056,7 @@ def request_requires_value(self) -> bool:
 
 
 def cond_test_parameter_default_value(
-    test_parameter: Union["BooleanParameterModel", "SelectParameterModel"]
+    test_parameter: Union["BooleanParameterModel", "SelectParameterModel"],
 ) -> Optional[DiscriminatorType]:
     default_value: Optional[DiscriminatorType] = None
     if isinstance(test_parameter, BooleanParameterModel):

lib/galaxy/tool_util/parser/__init__.py

@@ -1,5 +1,4 @@
-""" Package responsible for parsing tools from files/abstract tool sources.
-"""
+"""Package responsible for parsing tools from files/abstract tool sources."""
 
 from .factory import (
     get_input_source,

lib/galaxy/tool_util/parser/interface.py

@@ -766,7 +766,7 @@ def element_to_dict(element_dict):
 
     @staticmethod
     def from_dict(
-        as_dict: Union[AnyTestCollectionDefDict, JsonTestCollectionDefCollectionElementDict]
+        as_dict: Union[AnyTestCollectionDefDict, JsonTestCollectionDefCollectionElementDict],
     ) -> "TestCollectionDef":
         if "model_class" in as_dict:
             xml_as_dict = cast(XmlTestCollectionDefDict, as_dict)

lib/galaxy/tool_util/parser/output_collection_def.py

@@ -1,4 +1,4 @@
-""" This module define an abstract class for reasoning about Galaxy's
+"""This module define an abstract class for reasoning about Galaxy's
 dataset collection after jobs are finished.
 """
 

lib/galaxy/tool_util/verify/__init__.py

@@ -544,7 +544,7 @@ def _parse_label_list(label_list_str: Optional[str]) -> List[int]:
 
 
 def get_image_metric(
-    attributes: Dict[str, Any]
+    attributes: Dict[str, Any],
 ) -> Callable[["numpy.typing.NDArray", "numpy.typing.NDArray"], "numpy.floating"]:
     metric_name = attributes.get("metric", DEFAULT_METRIC)
     pin_labels = _parse_label_list(attributes.get("pin_labels", DEFAULT_PIN_LABELS))

lib/galaxy/tools/error_reports/__init__.py

@@ -1,5 +1,4 @@
-"""This module defines the error reporting framework for Galaxy jobs.
-"""
+"""This module defines the error reporting framework for Galaxy jobs."""
 
 import collections
 import logging

lib/galaxy/tools/error_reports/plugins/base_git.py

@@ -1,5 +1,4 @@
-"""This module defines the common functions for error reporting for Galaxy jobs towards Git applications (e.g. Github/GitLab).
-"""
+"""This module defines the common functions for error reporting for Galaxy jobs towards Git applications (e.g. Github/GitLab)."""
 
 import logging
 from abc import (

lib/galaxy/tools/recommendations.py

@@ -1,4 +1,4 @@
-""" Compute tool recommendations """
+"""Compute tool recommendations"""
 
 import json
 import logging

lib/galaxy/tools/wrappers.py

@@ -560,7 +560,7 @@ def to_wrapper(
                 DatasetInstance,
                 DatasetCollectionInstance,
                 DatasetCollectionElement,
-            ]
+            ],
         ) -> DatasetFilenameWrapper:
             if isinstance(dataset, DatasetCollectionElement):
                 dataset2 = dataset.dataset_instance

lib/galaxy/util/facts.py

@@ -1,5 +1,4 @@
-"""Return various facts for string formatting.
-"""
+"""Return various facts for string formatting."""
 
 import socket
 from collections.abc import MutableMapping

lib/galaxy/util/path/__init__.py

@@ -1,5 +1,4 @@
-"""Path manipulation functions.
-"""
+"""Path manipulation functions."""
 
 import errno
 import importlib

lib/galaxy/util/path/ntpath.py

@@ -1,5 +1,4 @@
-"""Galaxy "safe" path functions forced to work with Windows-style paths regardless of current platform
-"""
+"""Galaxy "safe" path functions forced to work with Windows-style paths regardless of current platform"""
 
 import ntpath
 import sys

lib/galaxy/util/path/posixpath.py

@@ -1,5 +1,4 @@
-"""Galaxy "safe" path functions forced to work with POSIX-style paths regardless of current platform
-"""
+"""Galaxy "safe" path functions forced to work with POSIX-style paths regardless of current platform"""
 
 import posixpath
 import sys

lib/galaxy/util/permutations.py

@@ -1,4 +1,4 @@
-""" There is some shared logic between matching/multiplying inputs in workflows
+"""There is some shared logic between matching/multiplying inputs in workflows
 and tools. This module is meant to capture some general permutation logic that
 can be applicable for both cases but will only be used in the newer tools case
 first.

lib/galaxy/util/properties.py

@@ -1,4 +1,4 @@
-""" Module used to blend ini, environment, and explicit dictionary properties
+"""Module used to blend ini, environment, and explicit dictionary properties
 to determine application configuration. Some hard coded defaults for Galaxy but
 this should be reusable by tool shed and pulsar as well.
 """

lib/galaxy/util/resources.py

@@ -1,5 +1,4 @@
-"""Provide a consistent interface into and utilities for importlib file resources.
-"""
+"""Provide a consistent interface into and utilities for importlib file resources."""
 
 import sys
 

lib/galaxy/util/script.py

@@ -1,5 +1,4 @@
-"""Utilities for Galaxy scripts
-"""
+"""Utilities for Galaxy scripts"""
 
 import argparse
 import logging

lib/galaxy/util/validation.py

@@ -1,4 +1,4 @@
-""" Module for validation of incoming inputs.
+"""Module for validation of incoming inputs.
 
 TODO: Refactor BaseController references to similar methods to use this module.
 """

lib/galaxy/visualization/data_providers/phyloviz/__init__.py

@@ -1,4 +1,4 @@
-""" Data providers code for PhyloViz """
+"""Data providers code for PhyloViz"""
 
 from typing import (
     Any,

lib/galaxy/visualization/tracks/__init__.py

@@ -1 +1 @@
-""" Summary.py required to be in this module due to pickling. """
+"""Summary.py required to be in this module due to pickling."""

lib/galaxy/web_stack/transport.py

@@ -1,5 +1,4 @@
-"""Web application stack operations
-"""
+"""Web application stack operations"""
 
 import logging
 import threading

lib/galaxy/webapps/base/webapp.py

@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import datetime
 import inspect

lib/galaxy/webapps/galaxy/api/job_files.py

@@ -1,4 +1,4 @@
-""" API for asynchronous job running mechanisms can use to fetch or put files
+"""API for asynchronous job running mechanisms can use to fetch or put files
 related to running and queued jobs.
 """
 

lib/galaxy/webapps/galaxy/api/job_ports.py

@@ -1,4 +1,4 @@
-""" API for asynchronous job running mechanisms can use to fetch or put files
+"""API for asynchronous job running mechanisms can use to fetch or put files
 related to running and queued jobs.
 """
 

lib/galaxy/webapps/galaxy/api/job_tokens.py

@@ -1,5 +1,4 @@
-""" API asynchronous job running mechanisms can use to get a fresh OIDC token.
-"""
+"""API asynchronous job running mechanisms can use to get a fresh OIDC token."""
 
 import logging
 

lib/galaxy/webapps/galaxy/api/tool_entry_points.py

@@ -1,4 +1,4 @@
-""" API for asynchronous job running mechanisms can use to fetch or put files
+"""API for asynchronous job running mechanisms can use to fetch or put files
 related to running and queued jobs.
 """
 

lib/galaxy/webapps/reports/controllers/query.py

@@ -1,5 +1,4 @@
-""" Mixin to help build advanced queries for reports interface.
-"""
+"""Mixin to help build advanced queries for reports interface."""
 
 import sqlalchemy as sa
 

lib/galaxy/workflow/extract.py

@@ -1,4 +1,4 @@
-""" This module contains functionality to aid in extracting workflows from
+"""This module contains functionality to aid in extracting workflows from
 histories.
 """
 

lib/galaxy/workflow/reports/generators/__init__.py

@@ -1,5 +1,4 @@
-"""Module containing Galaxy workflow report generator plugins.
-"""
+"""Module containing Galaxy workflow report generator plugins."""
 
 from abc import (
     ABCMeta,

lib/galaxy/workflow/reports/generators/markdown.py

@@ -1,5 +1,4 @@
-"""The class defines the default stock Galaxy workflow reporting plugin
-"""
+"""The class defines the default stock Galaxy workflow reporting plugin"""
 
 import logging
 import string

lib/galaxy/workflow/schedulers/__init__.py

@@ -1,4 +1,4 @@
-""" Module containing Galaxy workflow scheduling plugins. Galaxy's interface
+"""Module containing Galaxy workflow scheduling plugins. Galaxy's interface
 for workflow scheduling is highly experimental and the interface required for
 scheduling plugins will almost certainly change.
 """

lib/galaxy/workflow/schedulers/core.py

@@ -1,4 +1,4 @@
-""" The class defines the stock Galaxy workflow scheduling plugin - currently
+"""The class defines the stock Galaxy workflow scheduling plugin - currently
 it simply schedules the whole workflow up front when offered.
 """
 

lib/galaxy/workflow/steps.py

@@ -1,4 +1,4 @@
-""" This module contains utility methods for reasoning about and ordering
+"""This module contains utility methods for reasoning about and ordering
 workflow steps.
 """
 

lib/galaxy_ext/__init__.py

@@ -1,4 +1,4 @@
-""" Package for things which are loaded from outside Galaxy and which we can be
+"""Package for things which are loaded from outside Galaxy and which we can be
 sure will not conflict with the `galaxy` namespace, which may be provided by
 other packages (e.g. galaxy_ops in the toolshed).
 """

lib/galaxy_ext/metadata/__init__.py

@@ -1 +1 @@
-""" Work with Galaxy metadata"""
+"""Work with Galaxy metadata"""

lib/galaxy_test/base/api_asserts.py

@@ -1,5 +1,4 @@
-"""Utility methods for making assertions about Galaxy API responses, etc...
-"""
+"""Utility methods for making assertions about Galaxy API responses, etc..."""
 
 from typing import (
     Any,

lib/galaxy_test/base/env.py

@@ -1,5 +1,4 @@
-"""Base utilities for working Galaxy test environments.
-"""
+"""Base utilities for working Galaxy test environments."""
 
 import fcntl
 import os

lib/tool_shed/test/base/driver.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
-"""Test driver for tool shed functional tests.
-"""
+"""Test driver for tool shed functional tests."""
 
 import os
 import string

scripts/apply_tags.py

@@ -1,4 +1,4 @@
-""" Apply tags to the inherited history items of Galaxy """
+"""Apply tags to the inherited history items of Galaxy"""
 
 import sys
 import time

scripts/galaxy_main.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-""" Entry point for starting Galaxy without starting as part of a web server.
+"""Entry point for starting Galaxy without starting as part of a web server.
 
 Example Usage: Start a job/workflow handler without a web server and with
 a given name using.

test/integration/test_scripts.py

@@ -1,5 +1,4 @@
-"""Integration tests for various scripts in scripts/.
-"""
+"""Integration tests for various scripts in scripts/."""
 
 import json
 import os

test/unit/app/managers/base.py

@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import json
 from typing import cast

test/unit/app/managers/test_CollectionManager.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
-"""
-"""
+""" """
 from galaxy import model
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.datasets import DatasetManager