Update to black 2024 stable style

.flake8

@@ -4,7 +4,8 @@
 # E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length (delegated to black)
+# E701,E704 are multiple statements on one line; we follow black's formatting here. See https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#configuration
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E203,E402,E501,E701,E704,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/tool_shed/test/test_data/repos

.github/workflows/lint.yaml

@@ -55,6 +55,4 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
-        with:
-          version: "23.3.0"
       - uses: isort/isort-action@master

lib/galaxy/actions/library.py

@@ -1,6 +1,7 @@
 """
 Contains library functions
 """
+
 import json
 import logging
 import os.path

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -1,6 +1,7 @@
 """
 Mock infrastructure for testing ModelManagers.
 """
+
 import os
 import shutil
 import tempfile

lib/galaxy/auth/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains implementations of the authentication logic.
 """
+
 import logging
 
 from galaxy.auth.util import (

lib/galaxy/auth/providers/__init__.py

@@ -3,6 +3,7 @@ Created on 15/07/2014
 
 @author: Andrew Robinson
 """
+
 import abc
 
 

lib/galaxy/auth/providers/alwaysreject.py

@@ -3,6 +3,7 @@ Created on 16/07/2014
 
 @author: Andrew Robinson
 """
+
 import logging
 
 from . import AuthProvider

lib/galaxy/auth/providers/ldap_ad.py

@@ -89,7 +89,6 @@ def _parse_ldap_options(options_unparsed):
 
 
 class LDAP(AuthProvider):
-
     """
     Attempts to authenticate users against an LDAP server.
 

lib/galaxy/auth/providers/localdb.py

@@ -3,6 +3,7 @@ Created on 16/07/2014
 
 @author: Andrew Robinson
 """
+
 import logging
 
 from . import AuthProvider

lib/galaxy/auth/providers/pam_auth.py

@@ -3,6 +3,7 @@ Created on 13/07/2015
 
 Author Peter van Heusden (pvh@sanbi.ac.za)
 """
+
 import logging
 import shlex
 

lib/galaxy/config/__init__.py

@@ -1,6 +1,7 @@
 """
 Universe configuration builder.
 """
+
 # absolute_import needed for tool_shed package.
 
 import configparser
@@ -231,9 +232,9 @@ class BaseAppConfiguration(HasDynamicProperties):
     # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path
     renamed_options: Optional[Dict[str, str]] = None
     deprecated_dirs: Dict[str, str] = {}
-    paths_to_check_against_root: Set[
-        str
-    ] = set()  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
+    paths_to_check_against_root: Set[str] = (
+        set()
+    )  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
     add_sample_file_to_defaults: Set[str] = set()  # for these options, add sample config files to their defaults
     listify_options: Set[str] = set()  # values for these options are processed as lists of values
     object_store_store_by: str

lib/galaxy/datatypes/anvio.py

@@ -2,6 +2,7 @@
 Datatypes for Anvi'o
 https://github.com/merenlab/anvio
 """
+
 import glob
 import logging
 import os

lib/galaxy/datatypes/checkers.py

@@ -2,6 +2,7 @@
 
 External datatypes may make use of these functions.
 """
+
 from galaxy.util.checkers import (
     check_binary,
     check_bz2,

lib/galaxy/datatypes/constructive_solid_geometry.py

@@ -193,6 +193,7 @@ class Vtk:
     TODO: only legacy formats are currently supported and support for XML formats
     should be added.
     """
+
     subtype = ""
     # Add metadata elements.
     MetadataElement(name="vtk_version", default=None, desc="Vtk version", readonly=True, optional=True, visible=True)

lib/galaxy/datatypes/converters/interval_to_fli.py

@@ -13,6 +13,7 @@ where location is formatted as:
 
 and symbols are sorted in lexigraphical order.
 """
+
 import optparse
 
 from bx.tabular.io import (

lib/galaxy/datatypes/data.py

@@ -425,9 +425,9 @@ class Data(metaclass=DataMeta):
         self, dataset: DatasetHasHidProtocol, to_ext: Optional[str], headers: Headers, **kwd
     ) -> Tuple[IO, Headers]:
         headers["Content-Length"] = str(os.stat(dataset.get_file_name()).st_size)
-        headers[
-            "content-type"
-        ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+        headers["content-type"] = (
+            "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+        )
         filename = self._download_filename(
             dataset,
             to_ext,
@@ -476,9 +476,9 @@ class Data(metaclass=DataMeta):
                 element_identifier=kwd.get("element_identifier"),
                 filename_pattern=kwd.get("filename_pattern"),
             )
-            headers[
-                "content-type"
-            ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+            headers["content-type"] = (
+                "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+            )
             headers["Content-Disposition"] = f'attachment; filename="{filename}"'
             return open(data.get_file_name(), "rb"), headers
 

lib/galaxy/datatypes/dataproviders/base.py

@@ -1,6 +1,7 @@
 """
 Base class(es) for all DataProviders.
 """
+
 # there's a blurry line between functionality here and functionality in datatypes module
 # attempting to keep parsing to a minimum here and focus on chopping/pagination/reformat(/filtering-maybe?)
 #   and using as much pre-computed info/metadata from the datatypes module as possible

lib/galaxy/datatypes/dataproviders/chunk.py

@@ -4,6 +4,7 @@ Chunk (N number of bytes at M offset to a source's beginning) provider.
 Primarily for file sources but usable by any iterator that has both
 seek and read( N ).
 """
+
 import base64
 import logging
 import os

lib/galaxy/datatypes/dataproviders/column.py

@@ -2,6 +2,7 @@
 Providers that provide lists of lists generally where each line of a source
 is further subdivided into multiple data (e.g. columns from a line).
 """
+
 import logging
 import re
 from urllib.parse import unquote_plus

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -5,6 +5,7 @@ Dataproviders that use either:
     - or provide data in some way relevant to bioinformatic data
         (e.g. parsing genomic regions from their source)
 """
+
 import logging
 import sys
 

lib/galaxy/datatypes/dataproviders/external.py

@@ -2,6 +2,7 @@
 Data providers that iterate over a source that is not in memory
 or not in a file.
 """
+
 import gzip
 import logging
 import subprocess

lib/galaxy/datatypes/dataproviders/hierarchy.py

@@ -1,6 +1,7 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
+
 import logging
 
 from galaxy.util import (

lib/galaxy/datatypes/dataproviders/line.py

@@ -1,6 +1,7 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
+
 import collections
 import logging
 import re

lib/galaxy/datatypes/genetics.py

@@ -11,6 +11,7 @@ subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or
 ross lazarus for rgenetics
 august 20 2007
 """
+
 import logging
 import os
 import re

lib/galaxy/datatypes/gis.py

@@ -1,6 +1,7 @@
 """
 GIS classes
 """
+
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.protocols import (
     DatasetProtocol,

lib/galaxy/datatypes/goldenpath.py

@@ -365,7 +365,6 @@ class AGPLine(metaclass=abc.ABCMeta):
 
 
 class AGPSeqLine(AGPLine):
-
     """
     A subclass of AGPLine specifically for AGP lines that represent sequences.
     """
@@ -462,7 +461,6 @@ class AGPSeqLine(AGPLine):
 
 
 class AGPGapLine(AGPLine):
-
     """
     A subclass of AGPLine specifically for AGP lines that represent sequence gaps.
     """

lib/galaxy/datatypes/graph.py

@@ -1,6 +1,7 @@
 """
 Graph content classes.
 """
+
 import logging
 from typing import List
 

lib/galaxy/datatypes/hdf5.py

@@ -2,6 +2,7 @@
 
 This datatype was created for use with the iSEE interactive tool.
 """
+
 from typing import Optional
 
 from galaxy.datatypes.data import Data

lib/galaxy/datatypes/images.py

@@ -1,6 +1,7 @@
 """
 Image classes
 """
+
 import base64
 import json
 import logging

lib/galaxy/datatypes/interval.py

@@ -1,6 +1,7 @@
 """
 Interval datatypes
 """
+
 import logging
 import sys
 import tempfile

lib/galaxy/datatypes/media.py

@@ -1,4 +1,5 @@
 """Video classes"""
+
 import json
 import subprocess
 import wave

lib/galaxy/datatypes/mothur.py

@@ -1,6 +1,7 @@
 """
 Mothur Metagenomics Datatypes
 """
+
 import logging
 import re
 from typing import (

lib/galaxy/datatypes/neo4j.py

@@ -1,6 +1,7 @@
 """
 Neo4j Composite Dataset
 """
+
 import logging
 
 from galaxy.datatypes.data import Data

lib/galaxy/datatypes/ngsindex.py

@@ -1,6 +1,7 @@
 """
 NGS indexes
 """
+
 import logging
 import os
 

lib/galaxy/datatypes/phylip.py

@@ -7,6 +7,7 @@ Created on January. 05, 2018
 @githuborganization: C3BI
 Phylip datatype sniffer
 """
+
 from typing import TYPE_CHECKING
 
 from galaxy import util

lib/galaxy/datatypes/proteomics.py

@@ -1,6 +1,7 @@
 """
 Proteomics Datatypes
 """
+
 import logging
 import re
 from typing import (

lib/galaxy/datatypes/protocols.py

@@ -1,37 +1,33 @@
 """
 Location of protocols used in datatypes
 """
+
 from typing import Any
 
 from typing_extensions import Protocol
 
 
 class HasClearAssociatedFiles(Protocol):
-    def clear_associated_files(self, metadata_safe: bool = False, purge: bool = False) -> None:
-        ...
+    def clear_associated_files(self, metadata_safe: bool = False, purge: bool = False) -> None: ...
 
 
 class HasCreatingJob(Protocol):
     @property
-    def creating_job(self):
-        ...
+    def creating_job(self): ...
 
 
 class HasExt(Protocol):
     @property
-    def ext(self):
-        ...
+    def ext(self): ...
 
 
 class HasExtraFilesPath(Protocol):
     @property
-    def extra_files_path(self):
-        ...
+    def extra_files_path(self): ...
 
 
 class HasFileName(Protocol):
-    def get_file_name(self, sync_cache=True) -> str:
-        ...
+    def get_file_name(self, sync_cache=True) -> str: ...
 
 
 class HasHid(Protocol):
@@ -54,8 +50,7 @@ class HasName(Protocol):
     name: str
 
 
-class HasExtraFilesAndMetadata(HasExtraFilesPath, HasMetadata, Protocol):
-    ...
+class HasExtraFilesAndMetadata(HasExtraFilesPath, HasMetadata, Protocol): ...
 
 
 class DatasetProtocol(
@@ -78,24 +73,17 @@ class DatasetProtocol(
     states: Any
 
     @property
-    def datatype(self):
-        ...
+    def datatype(self): ...
 
-    def get_converted_files_by_type(self, file_type):
-        ...
+    def get_converted_files_by_type(self, file_type): ...
 
-    def get_mime(self) -> str:
-        ...
+    def get_mime(self) -> str: ...
 
-    def get_size(self) -> int:
-        ...
+    def get_size(self) -> int: ...
 
-    def has_data(self) -> bool:
-        ...
+    def has_data(self) -> bool: ...
 
-    def set_peek(self) -> None:
-        ...
+    def set_peek(self) -> None: ...
 
 
-class DatasetHasHidProtocol(DatasetProtocol, HasHid, Protocol):
-    ...
+class DatasetHasHidProtocol(DatasetProtocol, HasHid, Protocol): ...

lib/galaxy/datatypes/qualityscore.py

@@ -1,6 +1,7 @@
 """
 Qualityscore class
 """
+
 import logging
 
 from galaxy.datatypes.protocols import DatasetProtocol

lib/galaxy/datatypes/registry.py

@@ -356,9 +356,9 @@ class Registry:
                             compressed_datatype_instance = compressed_datatype_class()
                             self.datatypes_by_extension[compressed_extension] = compressed_datatype_instance
                             for suffix in infer_from_suffixes:
-                                self.datatypes_by_suffix_inferences[
-                                    f"{suffix}.{auto_compressed_type}"
-                                ] = compressed_datatype_instance
+                                self.datatypes_by_suffix_inferences[f"{suffix}.{auto_compressed_type}"] = (
+                                    compressed_datatype_instance
+                                )
                             if display_in_upload and compressed_extension not in self.upload_file_formats:
                                 self.upload_file_formats.append(compressed_extension)
                             self.datatype_info_dicts.append(

lib/galaxy/datatypes/sniff.py

@@ -91,8 +91,7 @@ class ConvertResult(NamedTuple):
 class ConvertFunction(Protocol):
     def __call__(
         self, fname: str, in_place: bool = True, tmp_dir: Optional[str] = None, tmp_prefix: Optional[str] = "gxupload"
-    ) -> ConvertResult:
-        ...
+    ) -> ConvertResult: ...
 
 
 def convert_newlines(

lib/galaxy/datatypes/tracks.py

@@ -1,6 +1,7 @@
 """
 Datatype classes for tracks/track views within galaxy.
 """
+
 import logging
 
 from galaxy.datatypes.protocols import (

lib/galaxy/datatypes/triples.py

@@ -1,6 +1,7 @@
 """
 Triple format classes
 """
+
 import logging
 import re
 

lib/galaxy/datatypes/util/gff_util.py

@@ -1,6 +1,7 @@
 """
 Provides utilities for working with GFF files.
 """
+
 import copy
 
 from bx.intervals.io import (

lib/galaxy/datatypes/xml.py

@@ -1,6 +1,7 @@
 """
 XML format classes
 """
+
 import logging
 import re
 from typing import List

lib/galaxy/dependencies/dev-requirements.txt

@@ -11,7 +11,7 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-black==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
+black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
 build==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/di.py

@@ -1,4 +1,5 @@
 """Dependency injection framework for Galaxy-type apps."""
+
 from typing import (
     Optional,
     Type,

lib/galaxy/exceptions/error_codes.py

@@ -2,6 +2,7 @@
 
 See the file error_codes.json for actual error code descriptions.
 """
+
 from json import loads
 from typing import Dict
 

lib/galaxy/forms/forms.py

@@ -1,6 +1,7 @@
 """
 FormDefinition and field factories
 """
+
 # TODO: A FormDefinitionField is closely linked to a form_builder result.
 # Can this functionality be further abstracted and merged with form_builder?
 from galaxy.model import (

lib/galaxy/job_execution/actions/post.py

@@ -2,6 +2,7 @@
 Actions to be run at job completion (or output hda creation, as in the case of
 immediate_actions listed below.
 """
+
 import datetime
 
 from markupsafe import escape

lib/galaxy/job_execution/datasets.py

@@ -1,6 +1,7 @@
 """
 Utility classes allowing Job interface to reason about datasets.
 """
+
 import os.path
 from abc import (
     ABCMeta,

lib/galaxy/job_execution/output_collect.py

@@ -1,5 +1,6 @@
 """ Code allowing tools to define extra files associated with an output datset.
 """
+
 import logging
 import operator
 import os

lib/galaxy/job_execution/setup.py

@@ -1,4 +1,5 @@
 """Utilities to help job and tool code setup jobs."""
+
 import json
 import os
 import threading

lib/galaxy/job_metrics/__init__.py

@@ -10,6 +10,7 @@ Each :class:`JobInstrumenter` plugin object describes how to inject a bits
 of shell code into a job scripts (before and after tool commands run) and then
 collect the output of these from a job directory.
 """
+
 import collections
 import logging
 import os

lib/galaxy/job_metrics/formatting.py

@@ -1,4 +1,5 @@
 """Utilities related to formatting job metrics for human consumption."""
+
 from typing import (
     Any,
     NamedTuple,

lib/galaxy/job_metrics/instrumenters/__init__.py

@@ -2,6 +2,7 @@
 
 These are responsible for collecting and formatting a coherent set of metrics.
 """
+
 import os.path
 from abc import (
     ABCMeta,

lib/galaxy/job_metrics/instrumenters/cgroup.py

@@ -1,4 +1,5 @@
 """The module describes the ``cgroup`` job metrics plugin."""
+
 import decimal
 import logging
 import numbers

lib/galaxy/job_metrics/instrumenters/core.py

@@ -1,4 +1,5 @@
 """The module describes the ``core`` job metrics plugin."""
+
 import logging
 import time
 from typing import (

lib/galaxy/job_metrics/instrumenters/cpuinfo.py

@@ -1,4 +1,5 @@
 """The module describes the ``cpuinfo`` job metrics plugin."""
+
 import logging
 import re
 from typing import Any

lib/galaxy/job_metrics/instrumenters/env.py

@@ -1,4 +1,5 @@
 """The module describes the ``env`` job metrics plugin."""
+
 import logging
 import re
 from typing import (

lib/galaxy/job_metrics/instrumenters/hostname.py

@@ -1,4 +1,5 @@
 """The module describes the ``hostname`` job metrics plugin."""
+
 import logging
 
 from . import InstrumentPlugin

lib/galaxy/job_metrics/instrumenters/meminfo.py

@@ -1,4 +1,5 @@
 """The module describes the ``meminfo`` job metrics plugin."""
+
 import re
 
 from galaxy import util

lib/galaxy/job_metrics/instrumenters/uname.py

@@ -1,4 +1,5 @@
 """The module describes the ``uname`` job metrics plugin."""
+
 from . import InstrumentPlugin
 from .. import formatting
 

lib/galaxy/jobs/__init__.py

@@ -1,6 +1,7 @@
 """
 Support for running a tool in Galaxy via an internal job management system
 """
+
 import copy
 import datetime
 import errno

lib/galaxy/jobs/handler.py

@@ -1,6 +1,7 @@
 """
 Galaxy job handler, prepares, runs, tracks, and finishes Galaxy jobs
 """
+
 import datetime
 import os
 import time

lib/galaxy/jobs/manager.py

@@ -1,6 +1,7 @@
 """
 Top-level Galaxy job manager, moves jobs to handler(s)
 """
+
 import logging
 from functools import partial
 

lib/galaxy/jobs/runners/__init__.py

@@ -1,6 +1,7 @@
 """
 Base classes for job runner plugins.
 """
+
 import datetime
 import os
 import string

lib/galaxy/jobs/runners/aws.py

@@ -1,5 +1,6 @@
 """ Galaxy job runners to use Amazon AWS native compute resources, such as AWS Batch.
 """
+
 import bisect
 import hashlib
 import json

lib/galaxy/jobs/runners/condor.py

@@ -10,6 +10,7 @@ greater reuse of the DRM specific hooks you'll need to write. Ideally this plugi
 have been written to target that framework, but we don't have the bandwidth to rewrite
 it at this time.
 """
+
 import logging
 import os
 import subprocess

lib/galaxy/jobs/runners/local.py

@@ -1,6 +1,7 @@
 """
 Job runner plugin for executing jobs on the local system via the command line.
 """
+
 import datetime
 import logging
 import os

lib/galaxy/jobs/runners/pulsar.py

@@ -2,6 +2,7 @@
 
 More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
 """
+
 import copy
 import errno
 import logging

lib/galaxy/jobs/runners/slurm.py

@@ -1,6 +1,7 @@
 """
 SLURM job control via the DRMAA API.
 """
+
 import os
 import time
 

lib/galaxy/jobs/runners/univa.py

@@ -28,6 +28,7 @@ known bugs/problems:
       cases 10.
     * The sheduler logs contains quite useful information.
 """
+
 import logging
 import re
 import signal

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

@@ -3,6 +3,7 @@ This module and its submodules contains utilities for running external
 processes and interfacing with job managers. This module should contain
 functionality shared between Galaxy and the Pulsar.
 """
+
 from galaxy.util.bunch import Bunch
 from .kill import kill_pid
 

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

@@ -1,5 +1,6 @@
 """
 """
+
 import json
 
 from galaxy.util.plugin_config import plugins_dict

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

@@ -1,6 +1,7 @@
 """
 Abstract base class for cli job plugins.
 """
+
 from abc import (
     ABCMeta,
     abstractmethod,

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

@@ -1,6 +1,7 @@
 """
 Abstract base class for runners which execute commands via a shell.
 """
+
 from abc import (
     ABCMeta,
     abstractmethod,

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

@@ -1,6 +1,7 @@
 """
 Condor helper utilities.
 """
+
 from subprocess import (
     CalledProcessError,
     check_call,

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

@@ -1,4 +1,5 @@
 """Interface layer for pykube library shared between Galaxy and Pulsar."""
+
 import logging
 import os
 import re

lib/galaxy/main_config.py

@@ -2,6 +2,7 @@
 
 This is for use by web framework code and scripts (e.g. scripts/galaxy_main.py).
 """
+
 import os
 from typing import (
     List,

lib/galaxy/managers/annotatable.py

@@ -39,8 +39,7 @@ class AnnotatableManagerMixin:
     annotation_assoc: type
 
     @abc.abstractmethod
-    def session(self) -> scoped_session:
-        ...
+    def session(self) -> scoped_session: ...
 
     def annotation(self, item) -> Optional[str]:
         """

lib/galaxy/managers/base.py

@@ -21,6 +21,7 @@ and allow both predefined and user controlled key sets.
 ModelDeserializers control how a model validates and process an incoming
 attribute change to a model object.
 """
+
 # TODO: it may be there's a better way to combine the above three classes
 #   such as: a single flat class, serializers being singletons in the manager, etc.
 #   instead of the three separate classes. With no 'apparent' perfect scheme
@@ -594,8 +595,7 @@ class SkipAttribute(Exception):
 
 
 class Serializer(Protocol):
-    def __call__(self, item: Any, key: str, **context) -> Any:
-        ...
+    def __call__(self, item: Any, key: str, **context) -> Any: ...
 
 
 # TODO: eventually all urls should be generated by the url builder and this can be safely removed.
@@ -883,8 +883,7 @@ class ModelValidator:
 
 
 class Deserializer(Protocol):
-    def __call__(self, item: Any, key: Any, val: Any, **kwargs) -> Any:
-        ...
+    def __call__(self, item: Any, key: Any, val: Any, **kwargs) -> Any: ...
 
 
 class ModelDeserializer(HasAModelManager[T]):

lib/galaxy/managers/cloudauthzs.py

@@ -61,9 +61,9 @@ class CloudAuthzsSerializer(base.ModelSerializer):
             "user_id": lambda item, key, **context: self.app.security.encode_id(item.user_id),
             "provider": lambda item, key, **context: str(item.provider),
             "config": lambda item, key, **context: item.config,
-            "authn_id": lambda item, key, **context: self.app.security.encode_id(item.authn_id)
-            if item.authn_id
-            else None,
+            "authn_id": lambda item, key, **context: (
+                self.app.security.encode_id(item.authn_id) if item.authn_id else None
+            ),
             "last_update": lambda item, key, **context: str(item.last_update),
             "last_activity": lambda item, key, **context: str(item.last_activity),
             "create_time": lambda item, key, **context: item.create_time.isoformat(),

lib/galaxy/managers/collections.py

@@ -671,14 +671,12 @@ class DatasetCollectionManager:
     @overload
     def get_dataset_collection_instance(
         self, trans: ProvidesHistoryContext, instance_type: Literal["history"], id, **kwds: Any
-    ) -> model.HistoryDatasetCollectionAssociation:
-        ...
+    ) -> model.HistoryDatasetCollectionAssociation: ...
 
     @overload
     def get_dataset_collection_instance(
         self, trans: ProvidesHistoryContext, instance_type: Literal["library"], id, **kwds: Any
-    ) -> model.LibraryDatasetCollectionAssociation:
-        ...
+    ) -> model.LibraryDatasetCollectionAssociation: ...
 
     def get_dataset_collection_instance(
         self, trans: ProvidesHistoryContext, instance_type: DatasetCollectionInstanceType, id, **kwds: Any

lib/galaxy/managers/configuration.py

@@ -4,6 +4,7 @@ and a more expanded set of data for admin in AdminConfigSerializer.
 
 Used by both the API and bootstrapped data.
 """
+
 import logging
 import sys
 from typing import (

lib/galaxy/managers/context.py

@@ -28,6 +28,7 @@ should annotate their dependency on the narrowest context they require.
 A method that requires a user but not a history should declare its
 ``trans`` argument as requiring type :class:`galaxy.managers.context.ProvidesUserContext`.
 """
+
 # TODO: Refactor this class so that galaxy.managers depends on a package
 # containing this.
 # TODO: Provide different classes for real users and potentially bootstrapped

lib/galaxy/managers/datasets.py

@@ -1,6 +1,7 @@
 """
 Manager and Serializer for Datasets.
 """
+
 import glob
 import logging
 import os

lib/galaxy/managers/dbkeys.py

@@ -1,6 +1,7 @@
 """
 Functionality for dealing with dbkeys.
 """
+
 import logging
 import os.path
 import re

lib/galaxy/managers/deletable.py

@@ -8,6 +8,7 @@ models have some backing/supporting resources that can be removed as well
 the supporting resources as well. These models also have the boolean
 attribute 'purged'.
 """
+
 from typing import (
     Any,
     Dict,
@@ -32,8 +33,7 @@ class DeletableManagerMixin:
     removed by an admin/script.
     """
 
-    def _session_setattr(self, item: Base, attr: str, val: Any, flush: bool = True):
-        ...
+    def _session_setattr(self, item: Base, attr: str, val: Any, flush: bool = True): ...
 
     def delete(self, item, flush=True, **kwargs):
         """
@@ -91,8 +91,7 @@ class PurgableManagerMixin(DeletableManagerMixin):
     file).
     """
 
-    def _session_setattr(self, item: Base, attr: str, val: Any, flush: bool = True):
-        ...
+    def _session_setattr(self, item: Base, attr: str, val: Any, flush: bool = True): ...
 
     def purge(self, item, flush=True, **kwargs):
         """

lib/galaxy/managers/executables.py

@@ -1,4 +1,5 @@
 """Utilities for loading tools and workflows from paths for admin user requests."""
+
 from typing import (
     Any,
     Dict,

lib/galaxy/managers/folders.py

@@ -1,6 +1,7 @@
 """
 Manager and Serializer for Library Folders.
 """
+
 import logging
 from dataclasses import dataclass
 from typing import (

lib/galaxy/managers/hdas.py

@@ -4,6 +4,7 @@ Manager and Serializer for HDAs.
 HistoryDatasetAssociations (HDAs) are datasets contained or created in a
 history.
 """
+
 import gettext
 import logging
 import os

lib/galaxy/managers/hdcas.py

@@ -4,6 +4,7 @@ Manager and Serializer for HDCAs.
 HistoryDatasetCollectionAssociations (HDCAs) are datasets contained or created in a
 history.
 """
+
 import logging
 from typing import Dict
 

lib/galaxy/managers/histories.py

@@ -4,6 +4,7 @@ Manager and Serializer for histories.
 Histories are containers for datasets or dataset collections
 created (or copied) by users over the course of an analysis.
 """
+
 import logging
 from typing import (
     Any,
@@ -853,9 +854,9 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
             "contents_active": self.serialize_contents_active,
             #  TODO: Use base manager's serialize_id for user_id (and others)
             #  after refactoring hierarchy here?
-            "user_id": lambda item, key, encode_id=True, **context: self.app.security.encode_id(item.user_id)
-            if item.user_id is not None and encode_id
-            else item.user_id,
+            "user_id": lambda item, key, encode_id=True, **context: (
+                self.app.security.encode_id(item.user_id) if item.user_id is not None and encode_id else item.user_id
+            ),
         }
         self.serializers.update(serializers)
 

lib/galaxy/managers/history_contents.py

@@ -2,6 +2,7 @@
 Heterogenous lists/contents are difficult to query properly since unions are
 not easily made.
 """
+
 import json
 import logging
 from typing import (

lib/galaxy/managers/libraries.py

@@ -1,6 +1,7 @@
 """
 Manager and Serializer for libraries.
 """
+
 import logging
 from typing import (
     Dict,

lib/galaxy/managers/library_datasets.py

@@ -1,4 +1,5 @@
 """Manager and Serializer for library datasets."""
+
 import logging
 
 from sqlalchemy import select

lib/galaxy/managers/markdown_parse.py

@@ -5,6 +5,7 @@ This file is meant to be relatively self contained and just used to "parse" and
 Galaxy Markdown. Keeping things isolated to allow re-use of these utilities in other
 projects (e.g. gxformat2).
 """
+
 import re
 from typing import (
     cast,

lib/galaxy/managers/markdown_util.py

@@ -10,6 +10,7 @@ potential history flavor would allow objects to be referenced by HID. This
 second idea is unimplemented, it is just an example of the general concept of
 context specific processing.
 """
+
 import abc
 import base64
 import codecs

lib/galaxy/managers/pages.py

@@ -5,6 +5,7 @@ Pages are markup created and saved by users that can contain Galaxy objects
 (such as datasets) and are often used to describe or present an analysis
 from within Galaxy.
 """
+
 import logging
 import re
 from html.entities import name2codepoint

lib/galaxy/managers/quotas.py

@@ -3,6 +3,7 @@ Manager and Serializers for Quotas.
 
 For more information about quotas: https://galaxyproject.org/admin/disk-quotas/
 """
+
 import logging
 from typing import (
     cast,