From dddca1dd03b4d39012f74bcf80083a6e3fd48fef Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 30 Jan 2024 14:57:54 +0000
Subject: [PATCH] Update to black 2024 stable style

---
 planemo/autopygen/argument_parser_conversion.py                  | 1 +
 planemo/autopygen/commands/command_utils.py                      | 1 +
 planemo/autopygen/source_file_parsing/local_module_parsing.py    | 1 +
 .../autopygen/source_file_parsing/parser_discovery_and_init.py   | 1 +
 planemo/autopygen/source_file_parsing/parsing_commons.py         | 1 +
 planemo/autopygen/source_file_parsing/unknown_names_discovery.py | 1 +
 planemo/ci.py                                                    | 1 -
 planemo/cli.py                                                   | 1 +
 planemo/commands/cmd_autoupdate.py                               | 1 +
 planemo/commands/cmd_ci_setup.py                                 | 1 +
 planemo/commands/cmd_clone.py                                    | 1 +
 planemo/commands/cmd_conda_build.py                              | 1 +
 planemo/commands/cmd_conda_init.py                               | 1 +
 planemo/commands/cmd_conda_install.py                            | 1 +
 planemo/commands/cmd_config_init.py                              | 1 +
 planemo/commands/cmd_container_register.py                       | 1 +
 planemo/commands/cmd_create_alias.py                             | 1 +
 planemo/commands/cmd_create_gist.py                              | 1 +
 planemo/commands/cmd_delete_alias.py                             | 1 +
 planemo/commands/cmd_dockstore_init.py                           | 1 +
 planemo/commands/cmd_docs.py                                     | 1 +
 planemo/commands/cmd_lint.py                                     | 1 +
 planemo/commands/cmd_list_alias.py                               | 1 +
 planemo/commands/cmd_list_invocations.py                         | 1 +
 planemo/commands/cmd_merge_test_reports.py                       | 1 +
 planemo/commands/cmd_mull.py                                     | 1 +
 planemo/commands/cmd_mulled_init.py                              | 1 +
 planemo/commands/cmd_normalize.py                                | 1 +
 planemo/commands/cmd_open.py                                     | 1 +
 planemo/commands/cmd_project_init.py                             | 1 +
 planemo/commands/cmd_pull_request.py                             | 1 +
 planemo/commands/cmd_rerun.py                                    | 1 +
 planemo/commands/cmd_serve.py                                    | 1 +
 planemo/commands/cmd_share_test.py                               | 1 +
 planemo/commands/cmd_shed_create.py                              | 1 +
 planemo/commands/cmd_shed_diff.py                                | 1 +
 planemo/commands/cmd_shed_download.py                            | 1 +
 planemo/commands/cmd_shed_init.py                                | 1 +
 planemo/commands/cmd_shed_lint.py                                | 1 +
 planemo/commands/cmd_shed_serve.py                               | 1 +
 planemo/commands/cmd_shed_test.py                                | 1 +
 planemo/commands/cmd_shed_update.py                              | 1 +
 planemo/commands/cmd_shed_upload.py                              | 1 +
 planemo/commands/cmd_syntax.py                                   | 1 +
 planemo/commands/cmd_test.py                                     | 1 +
 planemo/commands/cmd_test_reports.py                             | 1 +
 planemo/commands/cmd_training_fill_data_library.py               | 1 +
 planemo/commands/cmd_workflow_convert.py                         | 1 +
 planemo/commands/cmd_workflow_edit.py                            | 1 +
 planemo/commands/cmd_workflow_job_init.py                        | 1 +
 planemo/commands/cmd_workflow_lint.py                            | 1 +
 planemo/commands/cmd_workflow_test_init.py                       | 1 +
 planemo/commands/cmd_workflow_test_on_invocation.py              | 1 +
 planemo/commands/cmd_workflow_upload.py                          | 1 +
 planemo/conda.py                                                 | 1 -
 planemo/context.py                                               | 1 +
 planemo/cwl/__init__.py                                          | 1 +
 planemo/cwl/run.py                                               | 1 +
 planemo/database/factory.py                                      | 1 +
 planemo/database/postgres_docker.py                              | 1 +
 planemo/deps.py                                                  | 1 +
 planemo/engine/toil.py                                           | 1 +
 planemo/galaxy/__init__.py                                       | 1 -
 planemo/galaxy/api.py                                            | 1 +
 planemo/galaxy/profiles.py                                       | 1 +
 planemo/galaxy/run.py                                            | 1 +
 planemo/galaxy/test/__init__.py                                  | 1 +
 planemo/galaxy/workflows.py                                      | 1 +
 planemo/linters/doi.py                                           | 1 +
 planemo/linters/xsd.py                                           | 1 +
 planemo/runnable.py                                              | 1 -
 planemo/shed/__init__.py                                         | 1 +
 planemo/templates.py                                             | 1 +
 planemo/test/results.py                                          | 1 +
 planemo/xml/validation.py                                        | 1 +
 tests/shed_app.py                                                | 1 +
 tests/test_cmd_autoupdate.py                                     | 1 +
 tests/test_cmd_dockstore_init.py                                 | 1 +
 tests/test_cmd_shed_test.py                                      | 1 +
 tests/test_cmd_test.py                                           | 1 +
 tests/test_cmd_test_conda.py                                     | 1 +
 tests/test_cmd_training_fill_data_library.py                     | 1 +
 tests/test_cmd_training_generate_from_wf.py                      | 1 +
 tests/test_cmd_training_init.py                                  | 1 +
 tests/test_cmd_workflow_convert.py                               | 1 +
 tests/test_cmd_workflow_job_init.py                              | 1 +
 tests/test_cmd_workflow_lint.py                                  | 1 +
 tests/test_cmd_workflow_test_init.py                             | 1 +
 tests/test_command_io.py                                         | 1 +
 tests/test_external_galaxy_commands.py                           | 1 +
 tests/test_galaxy_config.py                                      | 1 +
 tests/test_galaxy_serve.py                                       | 1 +
 tests/test_galaxy_workflow_utils.py                              | 1 +
 tests/test_git.py                                                | 1 +
 tests/test_io.py                                                 | 1 +
 tests/test_run.py                                                | 1 +
 tests/test_shed_upload.py                                        | 1 +
 tests/test_test_checker.py                                       | 1 +
 tests/test_training.py                                           | 1 +
 tests/test_training_tool_input.py                                | 1 +
 tests/test_training_topic.py                                     | 1 +
 tests/test_training_tutorial.py                                  | 1 +
 tests/test_training_utils.py                                     | 1 +
 tests/test_utils.py                                              | 1 +
 104 files changed, 100 insertions(+), 4 deletions(-)

diff --git a/planemo/autopygen/argument_parser_conversion.py b/planemo/autopygen/argument_parser_conversion.py
index b87d5e6d9..5ffd95ae2 100644
--- a/planemo/autopygen/argument_parser_conversion.py
+++ b/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
diff --git a/planemo/autopygen/commands/command_utils.py b/planemo/autopygen/commands/command_utils.py
index 4d20e57cd..db8c90192 100644
--- a/planemo/autopygen/commands/command_utils.py
+++ b/planemo/autopygen/commands/command_utils.py
@@ -10,6 +10,7 @@
 
 Elements can be nested
 """
+
 from typing import List
 
 from planemo.autopygen.param_info import (
diff --git a/planemo/autopygen/source_file_parsing/local_module_parsing.py b/planemo/autopygen/source_file_parsing/local_module_parsing.py
index 4b6dd0d7a..53ddc0def 100644
--- a/planemo/autopygen/source_file_parsing/local_module_parsing.py
+++ b/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 (
diff --git a/planemo/autopygen/source_file_parsing/parser_discovery_and_init.py b/planemo/autopygen/source_file_parsing/parser_discovery_and_init.py
index dc45b1529..de2555164 100644
--- a/planemo/autopygen/source_file_parsing/parser_discovery_and_init.py
+++ b/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 (
diff --git a/planemo/autopygen/source_file_parsing/parsing_commons.py b/planemo/autopygen/source_file_parsing/parsing_commons.py
index 7441c01a0..fe3b1e82a 100644
--- a/planemo/autopygen/source_file_parsing/parsing_commons.py
+++ b/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 (
diff --git a/planemo/autopygen/source_file_parsing/unknown_names_discovery.py b/planemo/autopygen/source_file_parsing/unknown_names_discovery.py
index ea2c53421..dcfafefd9 100644
--- a/planemo/autopygen/source_file_parsing/unknown_names_discovery.py
+++ b/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 (
diff --git a/planemo/ci.py b/planemo/ci.py
index 85c852a3d..2e1463b85 100644
--- a/planemo/ci.py
+++ b/planemo/ci.py
@@ -1,6 +1,5 @@
 """Utilities for dealing with continous integration systems."""
 
-
 import copy
 import math
 import os
diff --git a/planemo/cli.py b/planemo/cli.py
index 5b5fee4b7..6262881a3 100644
--- a/planemo/cli.py
+++ b/planemo/cli.py
@@ -1,4 +1,5 @@
 """The module describes a CLI framework extending ``click``."""
+
 import functools
 import os
 import sys
diff --git a/planemo/commands/cmd_autoupdate.py b/planemo/commands/cmd_autoupdate.py
index e4d7b5005..40c988810 100644
--- a/planemo/commands/cmd_autoupdate.py
+++ b/planemo/commands/cmd_autoupdate.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``autoupdate`` command."""
+
 import json
 from typing import Callable
 
diff --git a/planemo/commands/cmd_ci_setup.py b/planemo/commands/cmd_ci_setup.py
index 8f772ec1d..6c63a7df4 100644
--- a/planemo/commands/cmd_ci_setup.py
+++ b/planemo/commands/cmd_ci_setup.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``ci_setup`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_clone.py b/planemo/commands/cmd_clone.py
index 391d019e7..801ae8e6b 100644
--- a/planemo/commands/cmd_clone.py
+++ b/planemo/commands/cmd_clone.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``clone`` command."""
+
 from typing import Callable
 
 import click
diff --git a/planemo/commands/cmd_conda_build.py b/planemo/commands/cmd_conda_build.py
index 4b5aab13f..1463ee1dd 100644
--- a/planemo/commands/cmd_conda_build.py
+++ b/planemo/commands/cmd_conda_build.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``conda_build`` command."""
+
 from typing import (
     Tuple,
     TYPE_CHECKING,
diff --git a/planemo/commands/cmd_conda_init.py b/planemo/commands/cmd_conda_init.py
index 866aa1d7c..1bc31e1f0 100644
--- a/planemo/commands/cmd_conda_init.py
+++ b/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
 
diff --git a/planemo/commands/cmd_conda_install.py b/planemo/commands/cmd_conda_install.py
index 71801be95..7bb2b3759 100644
--- a/planemo/commands/cmd_conda_install.py
+++ b/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
 
diff --git a/planemo/commands/cmd_config_init.py b/planemo/commands/cmd_config_init.py
index 1d1b9d9b9..5affee41a 100644
--- a/planemo/commands/cmd_config_init.py
+++ b/planemo/commands/cmd_config_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``config_init`` command."""
+
 import os
 import sys
 
diff --git a/planemo/commands/cmd_container_register.py b/planemo/commands/cmd_container_register.py
index 685b0ceb5..41f700497 100644
--- a/planemo/commands/cmd_container_register.py
+++ b/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
diff --git a/planemo/commands/cmd_create_alias.py b/planemo/commands/cmd_create_alias.py
index 993ca5293..20ed45d31 100644
--- a/planemo/commands/cmd_create_alias.py
+++ b/planemo/commands/cmd_create_alias.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``create_alias`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_create_gist.py b/planemo/commands/cmd_create_gist.py
index 6d7cf3d72..90031d5e4 100644
--- a/planemo/commands/cmd_create_gist.py
+++ b/planemo/commands/cmd_create_gist.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``create_gist`` command."""
+
 import click
 
 from planemo import github_util
diff --git a/planemo/commands/cmd_delete_alias.py b/planemo/commands/cmd_delete_alias.py
index 577863f82..ba25e75f3 100644
--- a/planemo/commands/cmd_delete_alias.py
+++ b/planemo/commands/cmd_delete_alias.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``delete_alias`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_dockstore_init.py b/planemo/commands/cmd_dockstore_init.py
index 72ca1cb84..f1acc9ddd 100644
--- a/planemo/commands/cmd_dockstore_init.py
+++ b/planemo/commands/cmd_dockstore_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``dockstore_init`` command."""
+
 import os
 
 import click
diff --git a/planemo/commands/cmd_docs.py b/planemo/commands/cmd_docs.py
index fe2c85f02..4ca69ba63 100644
--- a/planemo/commands/cmd_docs.py
+++ b/planemo/commands/cmd_docs.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``docs`` command."""
+
 import click
 
 from planemo.cli import command_function
diff --git a/planemo/commands/cmd_lint.py b/planemo/commands/cmd_lint.py
index 23dcf4e06..c84f8f0b9 100644
--- a/planemo/commands/cmd_lint.py
+++ b/planemo/commands/cmd_lint.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``lint`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_list_alias.py b/planemo/commands/cmd_list_alias.py
index 16f21b750..86c3afd37 100644
--- a/planemo/commands/cmd_list_alias.py
+++ b/planemo/commands/cmd_list_alias.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``list_alias`` command."""
+
 import json
 
 import click
diff --git a/planemo/commands/cmd_list_invocations.py b/planemo/commands/cmd_list_invocations.py
index d1edc8755..46b8528e8 100644
--- a/planemo/commands/cmd_list_invocations.py
+++ b/planemo/commands/cmd_list_invocations.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``list_invocations`` command."""
+
 import json
 
 import click
diff --git a/planemo/commands/cmd_merge_test_reports.py b/planemo/commands/cmd_merge_test_reports.py
index 5d1ca4d9e..597d02980 100644
--- a/planemo/commands/cmd_merge_test_reports.py
+++ b/planemo/commands/cmd_merge_test_reports.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``merge_test_reports`` command."""
+
 import os
 
 import click
diff --git a/planemo/commands/cmd_mull.py b/planemo/commands/cmd_mull.py
index c87f7be8e..c55f24933 100644
--- a/planemo/commands/cmd_mull.py
+++ b/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
 
diff --git a/planemo/commands/cmd_mulled_init.py b/planemo/commands/cmd_mulled_init.py
index 9898ad5b3..5ea5ffbda 100644
--- a/planemo/commands/cmd_mulled_init.py
+++ b/planemo/commands/cmd_mulled_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``mulled_init`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_normalize.py b/planemo/commands/cmd_normalize.py
index 2c594e84d..a67093516 100644
--- a/planemo/commands/cmd_normalize.py
+++ b/planemo/commands/cmd_normalize.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``normalize`` command."""
+
 from xml.etree import ElementTree
 
 import click
diff --git a/planemo/commands/cmd_open.py b/planemo/commands/cmd_open.py
index 6db186231..93e421df2 100644
--- a/planemo/commands/cmd_open.py
+++ b/planemo/commands/cmd_open.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``open`` command."""
+
 import click
 
 from planemo.cli import command_function
diff --git a/planemo/commands/cmd_project_init.py b/planemo/commands/cmd_project_init.py
index 4175560c4..e29b7e869 100644
--- a/planemo/commands/cmd_project_init.py
+++ b/planemo/commands/cmd_project_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``project_init`` command."""
+
 import os
 import shutil
 import tempfile
diff --git a/planemo/commands/cmd_pull_request.py b/planemo/commands/cmd_pull_request.py
index 331387543..248cb0ccd 100644
--- a/planemo/commands/cmd_pull_request.py
+++ b/planemo/commands/cmd_pull_request.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``pull_request`` command."""
+
 import click
 
 from planemo import (
diff --git a/planemo/commands/cmd_rerun.py b/planemo/commands/cmd_rerun.py
index 984dd3194..0571f81b5 100644
--- a/planemo/commands/cmd_rerun.py
+++ b/planemo/commands/cmd_rerun.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``rerun`` command."""
+
 from typing import (
     Tuple,
     TYPE_CHECKING,
diff --git a/planemo/commands/cmd_serve.py b/planemo/commands/cmd_serve.py
index ba28f89fb..5711a8c6b 100644
--- a/planemo/commands/cmd_serve.py
+++ b/planemo/commands/cmd_serve.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``serve`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_share_test.py b/planemo/commands/cmd_share_test.py
index 39842ef39..a4b4c50e1 100644
--- a/planemo/commands/cmd_share_test.py
+++ b/planemo/commands/cmd_share_test.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``share_test`` command."""
+
 import click
 
 from planemo import (
diff --git a/planemo/commands/cmd_shed_create.py b/planemo/commands/cmd_shed_create.py
index 782792cf6..f5580276f 100644
--- a/planemo/commands/cmd_shed_create.py
+++ b/planemo/commands/cmd_shed_create.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_create`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_shed_diff.py b/planemo/commands/cmd_shed_diff.py
index be2c7fd97..c219449a5 100644
--- a/planemo/commands/cmd_shed_diff.py
+++ b/planemo/commands/cmd_shed_diff.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_diff`` command."""
+
 import shutil
 import sys
 import tempfile
diff --git a/planemo/commands/cmd_shed_download.py b/planemo/commands/cmd_shed_download.py
index 9d6133fc7..b42891f28 100644
--- a/planemo/commands/cmd_shed_download.py
+++ b/planemo/commands/cmd_shed_download.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_download`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_shed_init.py b/planemo/commands/cmd_shed_init.py
index 18cc9507e..b9b67a94b 100644
--- a/planemo/commands/cmd_shed_init.py
+++ b/planemo/commands/cmd_shed_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_init`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_shed_lint.py b/planemo/commands/cmd_shed_lint.py
index beb413580..b25ea5988 100644
--- a/planemo/commands/cmd_shed_lint.py
+++ b/planemo/commands/cmd_shed_lint.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_lint`` command."""
+
 import click
 
 from planemo import (
diff --git a/planemo/commands/cmd_shed_serve.py b/planemo/commands/cmd_shed_serve.py
index 19a531321..21d806cf1 100644
--- a/planemo/commands/cmd_shed_serve.py
+++ b/planemo/commands/cmd_shed_serve.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_serve`` command."""
+
 import click
 
 from planemo import (
diff --git a/planemo/commands/cmd_shed_test.py b/planemo/commands/cmd_shed_test.py
index 1833c04a3..3758230c0 100644
--- a/planemo/commands/cmd_shed_test.py
+++ b/planemo/commands/cmd_shed_test.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_test`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_shed_update.py b/planemo/commands/cmd_shed_update.py
index 69aac3d67..105e6556c 100644
--- a/planemo/commands/cmd_shed_update.py
+++ b/planemo/commands/cmd_shed_update.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_update`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_shed_upload.py b/planemo/commands/cmd_shed_upload.py
index 800207407..227c01c00 100644
--- a/planemo/commands/cmd_shed_upload.py
+++ b/planemo/commands/cmd_shed_upload.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``shed_upload`` command."""
+
 import sys
 
 import click
diff --git a/planemo/commands/cmd_syntax.py b/planemo/commands/cmd_syntax.py
index a64049137..152babc12 100644
--- a/planemo/commands/cmd_syntax.py
+++ b/planemo/commands/cmd_syntax.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``syntax`` command."""
+
 import click
 
 from planemo.cli import command_function
diff --git a/planemo/commands/cmd_test.py b/planemo/commands/cmd_test.py
index 765724127..4995d416e 100644
--- a/planemo/commands/cmd_test.py
+++ b/planemo/commands/cmd_test.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``test`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_test_reports.py b/planemo/commands/cmd_test_reports.py
index db034e13a..d972522f3 100644
--- a/planemo/commands/cmd_test_reports.py
+++ b/planemo/commands/cmd_test_reports.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``test_reports`` command."""
+
 import datetime
 import pathlib
 
diff --git a/planemo/commands/cmd_training_fill_data_library.py b/planemo/commands/cmd_training_fill_data_library.py
index f11acd567..d8a22abec 100644
--- a/planemo/commands/cmd_training_fill_data_library.py
+++ b/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
diff --git a/planemo/commands/cmd_workflow_convert.py b/planemo/commands/cmd_workflow_convert.py
index 34b7a2bae..b63630600 100644
--- a/planemo/commands/cmd_workflow_convert.py
+++ b/planemo/commands/cmd_workflow_convert.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_convert`` command."""
+
 import json
 import os
 
diff --git a/planemo/commands/cmd_workflow_edit.py b/planemo/commands/cmd_workflow_edit.py
index 8392040a3..e67ae877b 100644
--- a/planemo/commands/cmd_workflow_edit.py
+++ b/planemo/commands/cmd_workflow_edit.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_edit`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_workflow_job_init.py b/planemo/commands/cmd_workflow_job_init.py
index 5d3db9eb8..c3b8d6cbd 100644
--- a/planemo/commands/cmd_workflow_job_init.py
+++ b/planemo/commands/cmd_workflow_job_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_job_init`` command."""
+
 import os
 
 import click
diff --git a/planemo/commands/cmd_workflow_lint.py b/planemo/commands/cmd_workflow_lint.py
index 78e022c27..80085c46d 100644
--- a/planemo/commands/cmd_workflow_lint.py
+++ b/planemo/commands/cmd_workflow_lint.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_lint`` command."""
+
 import click
 
 from planemo import options
diff --git a/planemo/commands/cmd_workflow_test_init.py b/planemo/commands/cmd_workflow_test_init.py
index 94657cdd3..6c883eda7 100644
--- a/planemo/commands/cmd_workflow_test_init.py
+++ b/planemo/commands/cmd_workflow_test_init.py
@@ -1,4 +1,5 @@
 """Module describing the planemo ``workflow_test_init`` command."""
+
 import os
 
 import click
diff --git a/planemo/commands/cmd_workflow_test_on_invocation.py b/planemo/commands/cmd_workflow_test_on_invocation.py
index 7b5bcc8d5..8083e2a6a 100644
--- a/planemo/commands/cmd_workflow_test_on_invocation.py
+++ b/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
diff --git a/planemo/commands/cmd_workflow_upload.py b/planemo/commands/cmd_workflow_upload.py
index ef15a4df3..03776fb76 100644
--- a/planemo/commands/cmd_workflow_upload.py
+++ b/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
 
diff --git a/planemo/conda.py b/planemo/conda.py
index a338b2025..f21e8210b 100644
--- a/planemo/conda.py
+++ b/planemo/conda.py
@@ -3,7 +3,6 @@
 The extend galaxy-tool-util's features with planemo specific idioms.
 """
 
-
 import collections
 import os
 import threading
diff --git a/planemo/context.py b/planemo/context.py
index 3285e7576..fb5c5cd1f 100644
--- a/planemo/context.py
+++ b/planemo/context.py
@@ -3,6 +3,7 @@
 Abstractions for cross cutting concerns (logging, workspace management,
 etc.).
 """
+
 import abc
 import logging.config
 import os
diff --git a/planemo/cwl/__init__.py b/planemo/cwl/__init__.py
index 1e5eb09d2..b8314653b 100644
--- a/planemo/cwl/__init__.py
+++ b/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
 
diff --git a/planemo/cwl/run.py b/planemo/cwl/run.py
index bf22db886..e96b2959e 100644
--- a/planemo/cwl/run.py
+++ b/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 (
diff --git a/planemo/database/factory.py b/planemo/database/factory.py
index 6b24bf2c8..e90106247 100644
--- a/planemo/database/factory.py
+++ b/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
diff --git a/planemo/database/postgres_docker.py b/planemo/database/postgres_docker.py
index f5e6fd3b8..84cbed038 100644
--- a/planemo/database/postgres_docker.py
+++ b/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 (
diff --git a/planemo/deps.py b/planemo/deps.py
index 54f54291e..fdf81a5ab 100644
--- a/planemo/deps.py
+++ b/planemo/deps.py
@@ -1,4 +1,5 @@
 """Abstractions for building dependency resolution configurations."""
+
 import tempfile
 from string import Template
 
diff --git a/planemo/engine/toil.py b/planemo/engine/toil.py
index bf6b9160c..c3093651f 100644
--- a/planemo/engine/toil.py
+++ b/planemo/engine/toil.py
@@ -1,4 +1,5 @@
 """Module contianing the :class:`ToilEngine` implementation of :class:`Engine`."""
+
 from typing import (
     Callable,
     List,
diff --git a/planemo/galaxy/__init__.py b/planemo/galaxy/__init__.py
index 00a59a62e..4b7412d47 100644
--- a/planemo/galaxy/__init__.py
+++ b/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,
diff --git a/planemo/galaxy/api.py b/planemo/galaxy/api.py
index 23a3a7b32..6f4906f33 100644
--- a/planemo/galaxy/api.py
+++ b/planemo/galaxy/api.py
@@ -1,4 +1,5 @@
 """A high-level interface to local Galaxy instances using bioblend."""
+
 from io import StringIO
 from typing import Optional
 
diff --git a/planemo/galaxy/profiles.py b/planemo/galaxy/profiles.py
index 3582bcb55..f5e88066c 100644
--- a/planemo/galaxy/profiles.py
+++ b/planemo/galaxy/profiles.py
@@ -3,6 +3,7 @@
 This is a workspace with a specific default configuration and shed
 tool setup. It is meant to be used with various serve commands.
 """
+
 import json
 import os
 import shutil
diff --git a/planemo/galaxy/run.py b/planemo/galaxy/run.py
index 685a57f5b..8113a6f8a 100644
--- a/planemo/galaxy/run.py
+++ b/planemo/galaxy/run.py
@@ -1,4 +1,5 @@
 """Utilities for calling Galaxy scripts."""
+
 import os
 import shlex
 import string
diff --git a/planemo/galaxy/test/__init__.py b/planemo/galaxy/test/__init__.py
index 4a1260ce8..63682e95e 100644
--- a/planemo/galaxy/test/__init__.py
+++ b/planemo/galaxy/test/__init__.py
@@ -1,4 +1,5 @@
 """Entry point and interface for ``planemo.galaxy.test`` package."""
+
 from .actions import (
     handle_reports,
     handle_reports_and_summary,
diff --git a/planemo/galaxy/workflows.py b/planemo/galaxy/workflows.py
index 82ac66336..50bd8da54 100644
--- a/planemo/galaxy/workflows.py
+++ b/planemo/galaxy/workflows.py
@@ -1,4 +1,5 @@
 """Utilities for Galaxy workflows."""
+
 import json
 import os
 from collections import namedtuple
diff --git a/planemo/linters/doi.py b/planemo/linters/doi.py
index ea369b3a3..544eb590b 100644
--- a/planemo/linters/doi.py
+++ b/planemo/linters/doi.py
@@ -1,5 +1,6 @@
 """ Tool linting module that lints Galaxy tools for their DOIs (if a DOI type citation is present)
 """
+
 import planemo.lint
 
 
diff --git a/planemo/linters/xsd.py b/planemo/linters/xsd.py
index 71ebf7362..102e4a856 100644
--- a/planemo/linters/xsd.py
+++ b/planemo/linters/xsd.py
@@ -1,4 +1,5 @@
 """Tool linting module that lints Galaxy tool against experimental XSD."""
+
 import copy
 import os
 import tempfile
diff --git a/planemo/runnable.py b/planemo/runnable.py
index e852836d1..e9867864e 100644
--- a/planemo/runnable.py
+++ b/planemo/runnable.py
@@ -1,6 +1,5 @@
 """Describe artifacts that can be run, tested, and linted."""
 
-
 import abc
 import os
 from enum import (
diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py
index fd0965099..f546418c7 100644
--- a/planemo/shed/__init__.py
+++ b/planemo/shed/__init__.py
@@ -1,4 +1,5 @@
 """Abstractions for shed related interactions used by the rest of planemo."""
+
 import contextlib
 import copy
 import fnmatch
diff --git a/planemo/templates.py b/planemo/templates.py
index 1b362d55e..6d071734b 100644
--- a/planemo/templates.py
+++ b/planemo/templates.py
@@ -1,4 +1,5 @@
 """Templating abstraction around jinja2 for Planemo."""
+
 try:
     from jinja2 import Template
 except ImportError:
diff --git a/planemo/test/results.py b/planemo/test/results.py
index b53627fe4..50bb4bcf1 100644
--- a/planemo/test/results.py
+++ b/planemo/test/results.py
@@ -2,6 +2,7 @@
 
 Is a JSON.
 """
+
 import json
 import os
 
diff --git a/planemo/xml/validation.py b/planemo/xml/validation.py
index d2f312769..417d3bc58 100644
--- a/planemo/xml/validation.py
+++ b/planemo/xml/validation.py
@@ -1,4 +1,5 @@
 """Module describing abstractions for validating XML content."""
+
 import abc
 import subprocess
 from collections import namedtuple
diff --git a/tests/shed_app.py b/tests/shed_app.py
index c843a4c5d..66ec0f6b8 100644
--- a/tests/shed_app.py
+++ b/tests/shed_app.py
@@ -1,6 +1,7 @@
 """ Test app to emulate planemo-relevant portions of the
 the ToolShed API... for now :).
 """
+
 import json
 import os
 import tarfile
diff --git a/tests/test_cmd_autoupdate.py b/tests/test_cmd_autoupdate.py
index f3667b18b..da4a90dfb 100644
--- a/tests/test_cmd_autoupdate.py
+++ b/tests/test_cmd_autoupdate.py
@@ -1,4 +1,5 @@
 """Tests for the ``autoupdate`` command."""
+
 import json
 import os
 import tempfile
diff --git a/tests/test_cmd_dockstore_init.py b/tests/test_cmd_dockstore_init.py
index f1eab3e36..1938ac54e 100644
--- a/tests/test_cmd_dockstore_init.py
+++ b/tests/test_cmd_dockstore_init.py
@@ -1,4 +1,5 @@
 """Tests for the ``dockstore_init`` command."""
+
 import os
 from typing import Optional
 
diff --git a/tests/test_cmd_shed_test.py b/tests/test_cmd_shed_test.py
index 1a1db8e0f..83547a992 100644
--- a/tests/test_cmd_shed_test.py
+++ b/tests/test_cmd_shed_test.py
@@ -1,4 +1,5 @@
 """Module contains :class:`CmdTestTestCase` - integration tests for the ``test`` command."""
+
 from .test_utils import (
     CliTestCase,
     run_verbosely,
diff --git a/tests/test_cmd_test.py b/tests/test_cmd_test.py
index 0101c027a..7d0475f33 100644
--- a/tests/test_cmd_test.py
+++ b/tests/test_cmd_test.py
@@ -1,4 +1,5 @@
 """Module contains :class:`CmdTestTestCase` - integration tests for the ``test`` command."""
+
 import json
 import os
 import shutil
diff --git a/tests/test_cmd_test_conda.py b/tests/test_cmd_test_conda.py
index f3fa88a6e..2824693ae 100644
--- a/tests/test_cmd_test_conda.py
+++ b/tests/test_cmd_test_conda.py
@@ -1,4 +1,5 @@
 """Module contains :class:`CmdTestTestCase` - integration tests for the ``test`` command."""
+
 import os
 
 from .test_utils import (
diff --git a/tests/test_cmd_training_fill_data_library.py b/tests/test_cmd_training_fill_data_library.py
index 0af07a427..6da48f559 100644
--- a/tests/test_cmd_training_fill_data_library.py
+++ b/tests/test_cmd_training_fill_data_library.py
@@ -1,4 +1,5 @@
 """Tests for the ``training_fill_data_library`` command."""
+
 from .test_cmd_training_generate_from_wf import create_tutorial_dir
 from .test_utils import CliTestCase
 
diff --git a/tests/test_cmd_training_generate_from_wf.py b/tests/test_cmd_training_generate_from_wf.py
index fd600563a..b28831c10 100644
--- a/tests/test_cmd_training_generate_from_wf.py
+++ b/tests/test_cmd_training_generate_from_wf.py
@@ -1,4 +1,5 @@
 """Tests for the ``training_generate_from_wf`` command."""
+
 import os
 import shutil
 
diff --git a/tests/test_cmd_training_init.py b/tests/test_cmd_training_init.py
index 75b866252..e78ed5e5a 100644
--- a/tests/test_cmd_training_init.py
+++ b/tests/test_cmd_training_init.py
@@ -1,4 +1,5 @@
 """Tests for the ``training_init`` command."""
+
 import os
 
 from .test_utils import (
diff --git a/tests/test_cmd_workflow_convert.py b/tests/test_cmd_workflow_convert.py
index a2bd4e7f7..bfd6cd946 100644
--- a/tests/test_cmd_workflow_convert.py
+++ b/tests/test_cmd_workflow_convert.py
@@ -1,4 +1,5 @@
 """Tests for the ``workflow_test_init`` command."""
+
 import json
 import os
 
diff --git a/tests/test_cmd_workflow_job_init.py b/tests/test_cmd_workflow_job_init.py
index 5bdfed37c..dfd4d54b1 100644
--- a/tests/test_cmd_workflow_job_init.py
+++ b/tests/test_cmd_workflow_job_init.py
@@ -1,4 +1,5 @@
 """Tests for the ``workflow_test_init`` command."""
+
 import os
 
 import yaml
diff --git a/tests/test_cmd_workflow_lint.py b/tests/test_cmd_workflow_lint.py
index 77e438cd2..02d38c2e7 100644
--- a/tests/test_cmd_workflow_lint.py
+++ b/tests/test_cmd_workflow_lint.py
@@ -1,4 +1,5 @@
 """Tests for the ``workflow_lint`` command."""
+
 import glob
 import os
 
diff --git a/tests/test_cmd_workflow_test_init.py b/tests/test_cmd_workflow_test_init.py
index 4c0295d0c..fb34fa03b 100644
--- a/tests/test_cmd_workflow_test_init.py
+++ b/tests/test_cmd_workflow_test_init.py
@@ -1,4 +1,5 @@
 """Tests for the ``workflow_test_init`` command."""
+
 import os
 
 import yaml
diff --git a/tests/test_command_io.py b/tests/test_command_io.py
index 45decc94f..e8d40d5f8 100644
--- a/tests/test_command_io.py
+++ b/tests/test_command_io.py
@@ -1,4 +1,5 @@
 """Test cases for the CommandIO abstraction in tool_builder."""
+
 import os
 
 from planemo.tool_builder import CommandIO
diff --git a/tests/test_external_galaxy_commands.py b/tests/test_external_galaxy_commands.py
index b1fa3133b..9db9076ec 100644
--- a/tests/test_external_galaxy_commands.py
+++ b/tests/test_external_galaxy_commands.py
@@ -1,5 +1,6 @@
 """Tests for planemo commands relating to external Galaxy instances
 """
+
 import os
 
 import yaml
diff --git a/tests/test_galaxy_config.py b/tests/test_galaxy_config.py
index c8cf7442f..a4724dce6 100644
--- a/tests/test_galaxy_config.py
+++ b/tests/test_galaxy_config.py
@@ -1,4 +1,5 @@
 """Unit tests for ``planemo.galaxy.config``."""
+
 import contextlib
 import os
 
diff --git a/tests/test_galaxy_serve.py b/tests/test_galaxy_serve.py
index bdc77bfa7..382ac2301 100644
--- a/tests/test_galaxy_serve.py
+++ b/tests/test_galaxy_serve.py
@@ -3,6 +3,7 @@
 This tests this as a library functionality - additional integration
 style tests are available in ``test_cmd_serve.py``.
 """
+
 import os
 
 from planemo import network_util
diff --git a/tests/test_galaxy_workflow_utils.py b/tests/test_galaxy_workflow_utils.py
index 763c557ac..f0e885227 100644
--- a/tests/test_galaxy_workflow_utils.py
+++ b/tests/test_galaxy_workflow_utils.py
@@ -1,4 +1,5 @@
 """Test utilities for dealing with Galaxy workflows."""
+
 import os
 
 from planemo.galaxy.workflows import describe_outputs
diff --git a/tests/test_git.py b/tests/test_git.py
index 7b34bc087..4237f5136 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -1,4 +1,5 @@
 """Test git library functions in ``planemo.git``."""
+
 import contextlib
 import os
 
diff --git a/tests/test_io.py b/tests/test_io.py
index 542b40087..baeb03aeb 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -1,4 +1,5 @@
 """Test utilities from :module:`planemo.io`."""
+
 import tempfile
 
 from planemo import io
diff --git a/tests/test_run.py b/tests/test_run.py
index f5a65926e..51ff42271 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -1,4 +1,5 @@
 """The module contains a class to test the ``cwl_run`` command."""
+
 import os
 
 from .test_utils import (
diff --git a/tests/test_shed_upload.py b/tests/test_shed_upload.py
index 091d7204d..d1ef07e49 100644
--- a/tests/test_shed_upload.py
+++ b/tests/test_shed_upload.py
@@ -3,6 +3,7 @@
 Specifically, tests for shed_upload, shed_download, and shed_create.
 commands.
 """
+
 import contextlib
 import os
 import shutil
diff --git a/tests/test_test_checker.py b/tests/test_test_checker.py
index 2edfafa25..b5b6ccc1c 100644
--- a/tests/test_test_checker.py
+++ b/tests/test_test_checker.py
@@ -1,4 +1,5 @@
 """Unit tests for runnable test case checking and related functionality."""
+
 import os
 
 from planemo.runnable import (
diff --git a/tests/test_training.py b/tests/test_training.py
index 2ace2f58d..1539036a9 100644
--- a/tests/test_training.py
+++ b/tests/test_training.py
@@ -1,4 +1,5 @@
 """Training training functions."""
+
 import json
 import os
 import shutil
diff --git a/tests/test_training_tool_input.py b/tests/test_training_tool_input.py
index 722be50a4..3ee81aead 100644
--- a/tests/test_training_tool_input.py
+++ b/tests/test_training_tool_input.py
@@ -1,4 +1,5 @@
 """Training:tool_input functions."""
+
 import json
 import os
 
diff --git a/tests/test_training_topic.py b/tests/test_training_topic.py
index a3654ec22..a887d8a5f 100644
--- a/tests/test_training_topic.py
+++ b/tests/test_training_topic.py
@@ -1,4 +1,5 @@
 """Training:topic functions."""
+
 import os
 import shutil
 
diff --git a/tests/test_training_tutorial.py b/tests/test_training_tutorial.py
index a65be4cb8..2dfaafa44 100644
--- a/tests/test_training_tutorial.py
+++ b/tests/test_training_tutorial.py
@@ -1,4 +1,5 @@
 """Training:tutorial functions."""
+
 import os
 import shutil
 
diff --git a/tests/test_training_utils.py b/tests/test_training_utils.py
index 72b8df6e2..e0c43d592 100644
--- a/tests/test_training_utils.py
+++ b/tests/test_training_utils.py
@@ -1,4 +1,5 @@
 """Training:utils functions."""
+
 import os
 
 from planemo.training.utils import (
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 88363b4da..17d8b4288 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,4 +1,5 @@
 """Provide abstractions over click testing of the app and unittest."""
+
 import ast
 import contextlib
 import functools