Merge pull request #1425 from nsoranzo/black_2024

Update to black 2024 stable style

planemo/autopygen/argument_parser_conversion.py

@@ -3,6 +3,7 @@
 and to transform it into easily usable ParamInfo class containing
 all the necessary info for 'inputs' element initialization
 """
+
 import ast
 import logging
 import math

planemo/autopygen/commands/command_utils.py

@@ -10,6 +10,7 @@
 
 Elements can be nested
 """
+
 from typing import List
 
 from planemo.autopygen.param_info import (

planemo/autopygen/source_file_parsing/local_module_parsing.py

@@ -2,6 +2,7 @@
 Module responsible for resolving assignments and constant list comprehensives
 used in argument parser
 """
+
 import ast
 import logging
 from typing import (

planemo/autopygen/source_file_parsing/parser_discovery_and_init.py

@@ -2,6 +2,7 @@
 Module responsible for discovery of import statements importing Argument parser
 and discovery of the statements initializing the parser itself
 """
+
 import ast
 import logging
 from typing import (

planemo/autopygen/source_file_parsing/parsing_commons.py

@@ -1,6 +1,7 @@
 """
 Module containing the parent class of Dicovery classes
 """
+
 import abc
 import ast
 from typing import (

planemo/autopygen/source_file_parsing/unknown_names_discovery.py

@@ -2,6 +2,7 @@
 Module containing discovery classes used to find names
 (assignments to variables) that have not been extracted yet
 """
+
 import ast
 import builtins
 from typing import (

planemo/ci.py

@@ -1,6 +1,5 @@
 """Utilities for dealing with continous integration systems."""
 
-
 import copy
 import math
 import os

planemo/cli.py

@@ -1,4 +1,5 @@
 """The module describes a CLI framework extending ``click``."""
+
 import functools
 import os
 import sys

planemo/commands/cmd_autoupdate.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``autoupdate`` command."""
+
 import json
 from typing import Callable
 

planemo/commands/cmd_ci_setup.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``ci_setup`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_clone.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``clone`` command."""
+
 from typing import Callable
 
 import click

planemo/commands/cmd_conda_build.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``conda_build`` command."""
+
 from typing import (
     Tuple,
     TYPE_CHECKING,

planemo/commands/cmd_conda_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``conda_init`` command."""
+
 import click
 from galaxy.tool_util.deps import conda_util
 

planemo/commands/cmd_conda_install.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``conda_install`` command."""
+
 import click
 from galaxy.tool_util.deps import conda_util
 

planemo/commands/cmd_config_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``config_init`` command."""
+
 import os
 import sys
 

planemo/commands/cmd_container_register.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``container_register`` command."""
+
 import os
 import string
 from typing import List

planemo/commands/cmd_create_alias.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``create_alias`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_create_gist.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``create_gist`` command."""
+
 import click
 
 from planemo import github_util

planemo/commands/cmd_delete_alias.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``delete_alias`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_dockstore_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``dockstore_init`` command."""
+
 import os
 
 import click

planemo/commands/cmd_docs.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``docs`` command."""
+
 import click
 
 from planemo.cli import command_function

planemo/commands/cmd_lint.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``lint`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_list_alias.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``list_alias`` command."""
+
 import json
 
 import click

planemo/commands/cmd_list_invocations.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``list_invocations`` command."""
+
 import json
 
 import click

planemo/commands/cmd_merge_test_reports.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``merge_test_reports`` command."""
+
 import os
 
 import click

planemo/commands/cmd_mull.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``mull`` command."""
+
 import click
 from galaxy.tool_util.deps.mulled.mulled_build import mull_targets
 

planemo/commands/cmd_mulled_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``mulled_init`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_normalize.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``normalize`` command."""
+
 from xml.etree import ElementTree
 
 import click

planemo/commands/cmd_open.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``open`` command."""
+
 import click
 
 from planemo.cli import command_function

planemo/commands/cmd_project_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``project_init`` command."""
+
 import os
 import shutil
 import tempfile

planemo/commands/cmd_pull_request.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``pull_request`` command."""
+
 import click
 
 from planemo import (

planemo/commands/cmd_rerun.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``rerun`` command."""
+
 from typing import (
     Tuple,
     TYPE_CHECKING,

planemo/commands/cmd_serve.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``serve`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_share_test.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``share_test`` command."""
+
 import click
 
 from planemo import (

planemo/commands/cmd_shed_create.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_create`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_shed_diff.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_diff`` command."""
+
 import shutil
 import sys
 import tempfile

planemo/commands/cmd_shed_download.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_download`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_shed_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_init`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_shed_lint.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_lint`` command."""
+
 import click
 
 from planemo import (

planemo/commands/cmd_shed_serve.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_serve`` command."""
+
 import click
 
 from planemo import (

planemo/commands/cmd_shed_test.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_test`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_shed_update.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_update`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_shed_upload.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_upload`` command."""
+
 import sys
 
 import click

planemo/commands/cmd_syntax.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``syntax`` command."""
+
 import click
 
 from planemo.cli import command_function

planemo/commands/cmd_test.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``test`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_test_reports.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``test_reports`` command."""
+
 import datetime
 import pathlib
 

planemo/commands/cmd_training_fill_data_library.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``training_fill_data_library`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_workflow_convert.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_convert`` command."""
+
 import json
 import os
 

planemo/commands/cmd_workflow_edit.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_edit`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_workflow_job_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_job_init`` command."""
+
 import os
 
 import click

planemo/commands/cmd_workflow_lint.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_lint`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_workflow_test_init.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_test_init`` command."""
+
 import os
 
 import click

planemo/commands/cmd_workflow_test_on_invocation.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_test_check`` command."""
+
 import click
 
 from planemo import options

planemo/commands/cmd_workflow_upload.py

@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_upload`` command."""
+
 from collections import defaultdict
 from pathlib import Path
 

planemo/conda.py

@@ -3,7 +3,6 @@
 The extend galaxy-tool-util's features with planemo specific idioms.
 """
 
-
 import collections
 import os
 import threading

planemo/context.py

@@ -3,6 +3,7 @@
 Abstractions for cross cutting concerns (logging, workspace management,
 etc.).
 """
+
 import abc
 import logging.config
 import os

planemo/cwl/__init__.py

@@ -1,4 +1,5 @@
 """Entry point for modules describing abstractions for dealing with CWL artifacts."""
+
 from .run import run_cwltool
 from .toil import run_toil
 

planemo/cwl/run.py

@@ -4,6 +4,7 @@
 Peter Amstutz and serves the reference implementation for the CWL.
 It can be found at https://github.com/common-workflow-language/cwltool,
 """
+
 import json
 import tempfile
 from typing import (

planemo/database/factory.py

@@ -1,4 +1,5 @@
 """Create a DatabaseSource from supplied planemo configuration."""
+
 from galaxy.util.commands import which
 
 from .interface import DatabaseSource

planemo/database/postgres_docker.py

@@ -1,4 +1,5 @@
 """Module describes a :class:`DatabaseSource` for managed, dockerized postgres databases."""
+
 import time
 
 from galaxy.tool_util.deps import (

planemo/deps.py

@@ -1,4 +1,5 @@
 """Abstractions for building dependency resolution configurations."""
+
 import tempfile
 from string import Template
 

planemo/engine/toil.py

@@ -1,4 +1,5 @@
 """Module contianing the :class:`ToilEngine` implementation of :class:`Engine`."""
+
 from typing import (
     Callable,
     List,

planemo/galaxy/__init__.py

@@ -1,6 +1,5 @@
 """Entry-point for Galaxy specific functionality in Planemo."""
 
-
 from .config import galaxy_config
 from .run import (
     run_galaxy_command,