From 74b0ba0e4784275ec61e3008099bbf3292612963 Mon Sep 17 00:00:00 2001
From: Simon Bray <sbray1371@gmail.com>
Date: Fri, 27 May 2022 13:00:12 +0200
Subject: [PATCH] fix bad merge and run black and isort

---
 planemo/engine/galaxy.py    |  2 +-
 planemo/engine/test.py      | 10 +++++-----
 planemo/options.py          |  4 +++-
 planemo/runnable.py         |  2 +-
 tests/test_cmd_serve.py     |  8 +++++---
 tests/test_galaxy_config.py |  5 -----
 6 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/planemo/engine/galaxy.py b/planemo/engine/galaxy.py
index 6b571b27b..8d72fb869 100644
--- a/planemo/engine/galaxy.py
+++ b/planemo/engine/galaxy.py
@@ -80,7 +80,7 @@ def _register_job_data(job_data):
                         interactor.VERBOSE_GALAXY_ERRORS = True
 
                     # on an external Galaxy it makes sense to keep test histories
-                    no_history_cleanup = config._kwds.get('engine') == 'external_galaxy'
+                    no_history_cleanup = config._kwds.get("engine") == "external_galaxy"
 
                     interactor.verify_tool(
                         tool_id,
diff --git a/planemo/engine/test.py b/planemo/engine/test.py
index d8a721081..034235af9 100644
--- a/planemo/engine/test.py
+++ b/planemo/engine/test.py
@@ -1,11 +1,11 @@
 import os
 
 from planemo.engine import engine_context
-from planemo.galaxy import galaxy_config
-from planemo.galaxy import galaxy_serve
-from planemo.galaxy.api import (
-    DEFAULT_ADMIN_API_KEY
+from planemo.galaxy import (
+    galaxy_config,
+    galaxy_serve,
 )
+from planemo.galaxy.api import DEFAULT_ADMIN_API_KEY
 from planemo.galaxy.config import _find_test_data
 from planemo.galaxy.ephemeris_sleep import sleep
 from planemo.galaxy.test import (
@@ -24,7 +24,7 @@ def test_runnables(ctx, runnables, original_paths=None, **kwds):
     if kwds.get("serve"):
         if "galaxy" not in kwds["engine"]:
             raise ValueError("The serve option is only supported by Galaxy-based engines.")
-        kwds["galaxy_url"] = kwds["galaxy_url"] or ''.join(("http://", kwds["host"], ":", str(kwds["port"])))
+        kwds["galaxy_url"] = kwds["galaxy_url"] or "".join(("http://", kwds["host"], ":", str(kwds["port"])))
         kwds["galaxy_admin_key"] = kwds["galaxy_admin_key"] or DEFAULT_ADMIN_API_KEY
         pid = os.fork()
         if pid == 0:
diff --git a/planemo/options.py b/planemo/options.py
index 7142b9dcc..9d72f3251 100644
--- a/planemo/options.py
+++ b/planemo/options.py
@@ -887,7 +887,9 @@ def serve_option():
         "--serve",
         is_flag=True,
         default=False,
-        help=("Continue serving Galaxy instance after testing. Like the serve command itself, this is only compatible with Galaxy-based engines.")
+        help=(
+            "Continue serving Galaxy instance after testing. Like the serve command itself, this is only compatible with Galaxy-based engines."
+        ),
     )
 
 
diff --git a/planemo/runnable.py b/planemo/runnable.py
index 523d6afb4..1b52a73b9 100644
--- a/planemo/runnable.py
+++ b/planemo/runnable.py
@@ -494,7 +494,7 @@ def flatten_to_single_artifacts(runnables):
         if runnable.type.is_single_artifact:
             single_runnables.append(runnable)
         else:
-            paths = glob.glob(f'{runnable.path}/*')
+            paths = glob.glob(f"{runnable.path}/*")
             for path in paths:
                 if os.path.isdir(path):
                     continue
diff --git a/tests/test_cmd_serve.py b/tests/test_cmd_serve.py
index e90faba15..3bb7a0527 100644
--- a/tests/test_cmd_serve.py
+++ b/tests/test_cmd_serve.py
@@ -173,9 +173,11 @@ def test_workflow_test_with_serve(self):
         extra_args = [
             "--serve",
             test_artifact,
-            "--port", str(self._port),
+            "--port",
+            str(self._port),
             "--no_dependency_resolution",
-            "--extra_tools", cat,
+            "--extra_tools",
+            cat,
         ]
         self._launch_thread_and_wait(self._run_test, extra_args)
         time.sleep(30)
@@ -184,7 +186,7 @@ def test_workflow_test_with_serve(self):
         user_gi = self._user_gi
         workflows = user_gi.workflows.get_workflows()
         assert len(workflows) == 1
-        assert workflows[0]['name'] == 'TestWorkflow1'
+        assert workflows[0]["name"] == "TestWorkflow1"
         histories = user_gi.histories.get_histories(name="CWL Target History")
         assert len(histories) == 1
 
diff --git a/tests/test_galaxy_config.py b/tests/test_galaxy_config.py
index 505300f75..c8cf7442f 100644
--- a/tests/test_galaxy_config.py
+++ b/tests/test_galaxy_config.py
@@ -48,13 +48,8 @@ def test_refgenie_config_version():
         version_path = os.path.join(galaxy_lib_path, "version.py")
         with open(version_path, "w") as version_fh:
             version_fh.write('VERSION_MAJOR = "21.05"')
-<<<<<<< HEAD
-        refgenie_config = get_refgenie_config(galaxy_root=tdc.temp_directory, refgenie_dir='/')
-    assert yaml.load(refgenie_config, Loader=yaml.SafeLoader)['config_version'] == 0.3
-=======
         refgenie_config = get_refgenie_config(galaxy_root=tdc.temp_directory, refgenie_dir="/")
     assert yaml.load(refgenie_config, Loader=yaml.SafeLoader)["config_version"] == 0.3
->>>>>>> upstream/master
 
 
 def _assert_property_is(config, prop, value):