Update to black 2024 stable style

bioblend/_tests/TestGalaxyGroups.py

@@ -1,6 +1,7 @@
 """
 WARNING: only admins can operate on groups!
 """
+
 import uuid
 
 from . import GalaxyTestBase

bioblend/_tests/TestGalaxyHistories.py

@@ -1,5 +1,6 @@
 """
 """
+
 import os
 import shutil
 import tarfile

bioblend/_tests/TestGalaxyInstance.py

@@ -1,6 +1,7 @@
 """
 Tests on the GalaxyInstance object itself.
 """
+
 import os
 import time
 import unittest

bioblend/_tests/TestGalaxyToolContainerResolution.py

@@ -1,6 +1,7 @@
 """
 Test functions in bioblend.galaxy.container_resolution
 """
+
 from . import (
     GalaxyTestBase,
     test_util,

bioblend/_tests/TestGalaxyToolDependencies.py

@@ -1,6 +1,7 @@
 """
 Test functions in bioblend.galaxy.tool_dependencies
 """
+
 from . import (
     GalaxyTestBase,
     test_util,

bioblend/_tests/TestGalaxyTools.py

@@ -1,5 +1,6 @@
 """
 """
+
 import os
 from typing import (
     Any,

bioblend/_tests/test_util.py

@@ -1,5 +1,6 @@
 """ General support infrastructure not tied to any particular test.
 """
+
 import os
 import random
 import string

bioblend/galaxy/__init__.py

@@ -1,6 +1,7 @@
 """
 A base representation of an instance of Galaxy
 """
+
 from typing import Optional
 
 from bioblend.galaxy import (

bioblend/galaxy/config/__init__.py

@@ -2,6 +2,7 @@
 Contains possible interaction dealing with Galaxy configuration.
 
 """
+
 from typing import TYPE_CHECKING
 
 from bioblend.galaxy.client import Client

bioblend/galaxy/container_resolution/__init__.py

@@ -2,6 +2,7 @@
 Contains interactions dealing with Galaxy container resolvers.
 Works only with Galaxy > 22.01
 """
+
 from typing import (
     List,
     Optional,

bioblend/galaxy/datasets/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Datasets
 """
+
 import logging
 import os
 import shlex
@@ -99,8 +100,7 @@ def download_dataset(
         use_default_filename: bool = True,
         require_ok_state: bool = True,
         maxwait: float = 12000,
-    ) -> bytes:
-        ...
+    ) -> bytes: ...
 
     @overload
     def download_dataset(
@@ -110,8 +110,7 @@ def download_dataset(
         use_default_filename: bool = True,
         require_ok_state: bool = True,
         maxwait: float = 12000,
-    ) -> str:
-        ...
+    ) -> str: ...
 
     def download_dataset(
         self,

bioblend/galaxy/datatypes/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Datatype
 """
+
 from typing import (
     Dict,
     List,

bioblend/galaxy/folders/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy library folders
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/forms/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Forms
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/ftpfiles/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy FTP Files
 """
+
 from typing import (
     List,
     TYPE_CHECKING,

bioblend/galaxy/genomes/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Histories
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/groups/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Groups
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/histories/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Histories
 """
+
 import logging
 import re
 import sys
@@ -270,8 +271,7 @@ def show_history(
         self,
         history_id: str,
         contents: Literal[False] = False,
-    ) -> Dict[str, Any]:
-        ...
+    ) -> Dict[str, Any]: ...
 
     @overload
     def show_history(
@@ -282,8 +282,7 @@ def show_history(
         visible: Optional[bool] = None,
         details: Optional[str] = None,
         types: Optional[List[str]] = None,
-    ) -> List[Dict[str, Any]]:
-        ...
+    ) -> List[Dict[str, Any]]: ...
 
     # Fallback in case the caller provides a regular bool as contents
     @overload

bioblend/galaxy/invocations/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy workflow invocations
 """
+
 import logging
 import time
 from typing import (

bioblend/galaxy/jobs/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Jobs
 """
+
 import logging
 import time
 from typing import (

bioblend/galaxy/libraries/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Data Libraries
 """
+
 import logging
 import time
 from typing import (

bioblend/galaxy/objects/client.py

@@ -4,6 +4,7 @@
 Classes in this module should not be instantiated directly, but used
 via their handles in :class:`~.galaxy_instance.GalaxyInstance`.
 """
+
 import abc
 import json
 from collections.abc import Sequence
@@ -498,12 +499,10 @@ class ObjDatasetClient(ObjClient):
     """
 
     @overload
-    def get(self, id_: str, hda_ldda: Literal["hda"] = "hda") -> wrappers.HistoryDatasetAssociation:
-        ...
+    def get(self, id_: str, hda_ldda: Literal["hda"] = "hda") -> wrappers.HistoryDatasetAssociation: ...
 
     @overload
-    def get(self, id_: str, hda_ldda: Literal["ldda"]) -> wrappers.LibraryDatasetDatasetAssociation:
-        ...
+    def get(self, id_: str, hda_ldda: Literal["ldda"]) -> wrappers.LibraryDatasetDatasetAssociation: ...
 
     def get(self, id_: str, hda_ldda: HdaLdda = "hda") -> wrappers.Dataset:
         """

bioblend/galaxy/roles/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Roles
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/tool_data/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Tool data tables
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/tool_dependencies/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains interactions dealing with Galaxy dependency resolvers.
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/tools/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interaction dealing with Galaxy tools.
 """
+
 from os.path import basename
 from typing import (
     Any,

bioblend/galaxy/users/__init__.py

@@ -3,6 +3,7 @@
 
 Most of these methods must be executed by a registered Galaxy admin user.
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/visual/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy visualization
 """
+
 from typing import (
     Any,
     Dict,

bioblend/galaxy/workflows/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains possible interactions with the Galaxy Workflows
 """
+
 import json
 import os
 from typing import (

bioblend/galaxyclient.py

@@ -5,6 +5,7 @@
 should not use it directly.
 A base representation of an instance
 """
+
 import base64
 import contextlib
 import json

bioblend/toolshed/__init__.py

@@ -1,6 +1,7 @@
 """
 A base representation of an instance of Tool Shed
 """
+
 from typing import Optional
 
 from bioblend.galaxyclient import GalaxyClient

bioblend/toolshed/categories/__init__.py

@@ -1,6 +1,7 @@
 """
 Interaction with a Tool Shed instance categories
 """
+
 from typing import (
     Any,
     Dict,

bioblend/toolshed/repositories/__init__.py

@@ -1,6 +1,7 @@
 """
 Interaction with a Tool Shed instance repositories
 """
+
 from typing import (
     Any,
     Dict,

bioblend/toolshed/tools/__init__.py

@@ -1,6 +1,7 @@
 """
 Interaction with a Tool Shed instance tools
 """
+
 from typing import (
     Any,
     Dict,

setup.cfg

@@ -10,8 +10,10 @@ exclude =
     build
 # 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
 # E501 is line length, managed by 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
+# SFS3 is string literal formatting using f-strings
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
-ignore = E203,E501,E741,SFS3,W503
+ignore = E203,E501,E701,E704,SFS3,W503
 
 [metadata]
 author = Enis Afgan