Apply 2026 black style

scripts/api/copy_hda_to_library_folder.py

@@ -26,7 +26,7 @@ if __name__ == "__main__":
         print(usage, file=sys.stderr)
         sys.exit(1)
 
-    (base_url, key, hda_id, library_id, folder_id) = sys.argv[1:6]
+    base_url, key, hda_id, library_id, folder_id = sys.argv[1:6]
 
     message = ""
     if num_args >= 7:

scripts/api/create.py

@@ -4,6 +4,7 @@ Generic POST/create script
 
 usage: create.py key url [key=value ...]
 """
+
 import sys
 
 from common import submit

scripts/api/data_manager_example_execute.py

@@ -87,7 +87,7 @@ if __name__ == "__main__":
         default=DEFAULT_SLEEP_TIME,
         help="How long to sleep between check loops",
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     # check options
     assert options.api_key is not None, ValueError("You must specify an API key.")

scripts/api/delete.py

@@ -4,6 +4,7 @@ Generic DELETE/delete script
 
 usage: delete.py key url
 """
+
 import sys
 
 from common import delete

scripts/api/library_upload_dir.py

@@ -115,7 +115,7 @@ class Uploader:
         all_files = [x.strip() for x in list(sys.stdin.readlines())]
 
         for idx, path in enumerate(all_files):
-            (dirName, fname) = path.rsplit(os.path.sep, 1)
+            dirName, fname = path.rsplit(os.path.sep, 1)
             if not os.path.exists(os.path.join(dirName, fname)):
                 continue
             # Figure out what the memo key will be early

scripts/api/reset_metadata_on_installed_repositories.py

@@ -8,6 +8,7 @@ usage: reset_metadata_on_installed_repositories.py key
 Here is a working example of how to use this script.
 python ./reset_metadata_on_installed_repositories.py -a 22be3b -u http://localhost:8763/
 """
+
 import argparse
 
 from common import submit

scripts/api/update.py

@@ -4,6 +4,7 @@ Generic PUT/update script
 
 usage: create.py key url [key=value ...]
 """
+
 import sys
 
 from common import update

scripts/cwl_conformance_to_test_cases.py

@@ -8,8 +8,7 @@ THIS_DIRECTORY = os.path.dirname(os.path.realpath(__file__))
 GALAXY_ROOT_DIR = os.path.abspath(os.path.join(THIS_DIRECTORY, os.pardir))
 CWL_API_TESTS_DIRECTORY = os.path.join(GALAXY_ROOT_DIR, "lib", "galaxy_test", "api", "cwl")
 
-TEST_FILE_TEMPLATE = string.Template(
-    '''"""Test CWL conformance for version ${version}."""
+TEST_FILE_TEMPLATE = string.Template('''"""Test CWL conformance for version ${version}."""
 
 import pytest
 
@@ -18,11 +17,9 @@ from ..test_workflows_cwl import BaseCwlWorkflowsApiTestCase
 
 class TestCwlConformance(BaseCwlWorkflowsApiTestCase):
     """Test case mapping to CWL conformance tests for version ${version}."""
-$tests'''
-)
+$tests''')
 
-TEST_TEMPLATE = string.Template(
-    '''
+TEST_TEMPLATE = string.Template('''
 ${marks}    def test_conformance_${version_simple}_${id_}(self):
         """${doc}
 
@@ -31,8 +28,7 @@ ${marks}    def test_conformance_${version_simple}_${id_}(self):
 ${cwl_test_def}
         """  # noqa: W293
         self.cwl_populator.run_conformance_test("""${version}""", """${doc}""")
-'''
-)
+''')
 
 RED_TESTS = {
     "v1.0": [

scripts/external_chown_script.py

@@ -41,7 +41,7 @@ def main():
     path, galaxy_user_name, gid = validate_parameters()
     for cmd in [["chown", "-Rh", galaxy_user_name, path], ["chgrp", "-Rh", gid, path]]:
         p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        (stdoutdata, stderrdata) = p.communicate()
+        stdoutdata, stderrdata = p.communicate()
         exitcode = p.returncode
         if exitcode != 0:
             sys.exit("external_chown_script: could not chown\ncmd was {}\n".format(" ".join(cmd)))

scripts/galaxy_main.py

@@ -17,6 +17,7 @@ defaults logging to a single file with the following:
 galaxy-main -d --server-name handler0 --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --log-file handler0.log
 
 """
+
 import functools
 import logging
 import os

scripts/grt/export.py

@@ -3,6 +3,7 @@
 
 See doc/source/admin/grt.rst for more detailed usage information.
 """
+
 import argparse
 import json
 import logging

scripts/grt/upload.py

@@ -3,6 +3,7 @@
 
 See doc/source/admin/grt.rst for more detailed usage information.
 """
+
 import argparse
 import logging
 import os

scripts/loc_files/create_all_fasta_loc.py

@@ -245,7 +245,7 @@ def __main__():
         default="True",
         help="Copy over text from all_fasta.loc.sample file (false if set to append)",
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     exemptions = [e.strip() for e in options.exemptions.split(",")]
     fasta_exts = [x.strip() for x in options.fasta_exts.split(",")]

scripts/release-diff.py

@@ -152,7 +152,7 @@ def main(old_revision, new_revision=None):
             old_contents = yaml.load(load_at_time(real_path, old_revision), Loader=MockOrderedLoader)
             new_contents = yaml.load(load_at_time(real_path, new_revision), Loader=MockOrderedLoader)
 
-            (a, r, c) = diff_files(old_contents, new_contents)
+            a, r, c = diff_files(old_contents, new_contents)
             if a:
                 added[filename] = sorted(a)
 

scripts/secret_decoder_ring.py

@@ -2,6 +2,7 @@
 """
 Script to encode/decode the IDs that galaxy exposes to users and admins.
 """
+
 import argparse
 import logging
 import os

scripts/tool_shed/deprecate_repositories_without_metadata.py

@@ -67,7 +67,7 @@ def main():
         help="verbose mode, print the name of each repository",
         default=False,
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     try:
         ini_file = args[0]
     except IndexError:

scripts/tools/re_escape_output.py

@@ -5,6 +5,7 @@ Escapes a file into a form suitable for use with tool tests using re_match or re
 usage: re_escape_output.py [options] input_file [output_file]
     -m: Use Multiline Matching
 """
+
 import optparse
 import re
 
@@ -14,7 +15,7 @@ def __main__():
     parser.add_option(
         "-m", "--multiline", action="store_true", dest="multiline", default=False, help="Use Multiline Matching"
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     input = open(args[0], "rb")
     if len(args) > 1:
         output = open(args[1], "wb")