diff --git a/contrib/galaxy_config_merger.py b/contrib/galaxy_config_merger.py
index cedacbb44ef..880bfe3bff6 100644
--- a/contrib/galaxy_config_merger.py
+++ b/contrib/galaxy_config_merger.py
@@ -26,7 +26,7 @@ def main():
     parser.add_option(
         "-o", "--output", dest="output", action="store", help="path to the new merged galaxy.ini.new file"
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     for option in ["sample", "config"]:
         if getattr(options, option) is None:
diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
index e143c649fd5..70704a43111 100644
--- a/doc/parse_gx_xsd.py
+++ b/doc/parse_gx_xsd.py
@@ -106,11 +106,9 @@ def _build_tag(tag, hide_attributes):
     tag_help.write(text)
     if best_practices := _get_bp_link(annotation_el):
         tag_help.write("\n\n### Best Practices\n")
-        tag_help.write(
-            f"""
+        tag_help.write(f"""
 Find the Intergalactic Utilities Commission suggested best practices for this
-element [here]({best_practices})."""
-        )
+element [here]({best_practices}).""")
     tag_help.write(_build_attributes_table(tag, attributes, hide_attributes))
 
     return tag_help.getvalue()
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index 75ae2aa088d..4f5f902d8b6 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -209,7 +209,7 @@ class LibraryActions:
     def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, response_code, message):
         preserve_dirs = util.string_as_bool(params.get("preserve_dirs", False))
         uploaded_datasets = []
-        (files_and_folders, _response_code, _message) = self._get_path_files_and_folders(params, preserve_dirs)
+        files_and_folders, _response_code, _message = self._get_path_files_and_folders(params, preserve_dirs)
         if _response_code:
             return (uploaded_datasets, _response_code, _message)
         for path, name, folder in files_and_folders:
diff --git a/lib/galaxy/auth/providers/pam_auth.py b/lib/galaxy/auth/providers/pam_auth.py
index 349d291d36d..ec9acce01e0 100644
--- a/lib/galaxy/auth/providers/pam_auth.py
+++ b/lib/galaxy/auth/providers/pam_auth.py
@@ -71,7 +71,7 @@ class PAM(AuthProvider):
         # we will be given the "public name" as username
         if string_as_bool(options.get("login-use-email", False)) and email is not None:
             if "@" in email:
-                (email_user, email_domain) = email.split("@")
+                email_user, email_domain = email.split("@")
                 pam_username = email_user
                 if email_domain == options.get("maildomain", None):
                     auto_register_email = email
diff --git a/lib/galaxy/celery/base_task.py b/lib/galaxy/celery/base_task.py
index 31d35a7e8e1..62db58124b3 100644
--- a/lib/galaxy/celery/base_task.py
+++ b/lib/galaxy/celery/base_task.py
@@ -94,7 +94,7 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
         if not result:
             sched_time = now + datetime.timedelta(seconds=task_interval_secs)
             upsert_stmt = (
-                ps_insert(CeleryUserRateLimit)  # type:ignore[attr-defined]
+                ps_insert(CeleryUserRateLimit)  # type: ignore[attr-defined]
                 .values(user_id=user_id, last_scheduled_time=now)
                 .returning(CeleryUserRateLimit.last_scheduled_time)
                 .on_conflict_do_update(index_elements=["user_id"], set_=dict(last_scheduled_time=sched_time))
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index ed343110dce..416fcc85568 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -2913,7 +2913,7 @@ class BlibSQlite(SQlite):
             conn = sqlite.connect(dataset.get_file_name())
             c = conn.cursor()
             tables_query = "SELECT majorVersion,minorVersion FROM LibInfo"
-            (majorVersion, minorVersion) = c.execute(tables_query).fetchall()[0]
+            majorVersion, minorVersion = c.execute(tables_query).fetchall()[0]
             dataset.metadata.blib_version = f"{majorVersion}.{minorVersion}"
         except Exception as e:
             log.warning("%s, set_meta Exception: %s", self, e)
diff --git a/lib/galaxy/datatypes/blast.py b/lib/galaxy/datatypes/blast.py
index fbcf447f559..2336e3fdf8f 100644
--- a/lib/galaxy/datatypes/blast.py
+++ b/lib/galaxy/datatypes/blast.py
@@ -30,6 +30,7 @@
 
 Covers the ``blastxml`` format and the BLAST databases.
 """
+
 import logging
 import os
 from collections.abc import Callable
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py
index 489f242c6cc..f738f4d1e43 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -4,6 +4,7 @@ Input: fasta, int
 Output: tabular
 Return titles with lengths of corresponding seq
 """
+
 import sys
 
 
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
index 45ba059dd35..1ad7d1ea747 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -10,6 +10,7 @@
 Input: fasta
 Output: tabular
 """
+
 import os
 import sys
 
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
index 2b69080a848..b3ea10bc9df 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
@@ -13,6 +13,7 @@ the order should be:
 Usage:
 %python fastqsolexa_to_fasta_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
 """
+
 import sys
 
 
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
index 0b6a79c2f3d..12b11ca9b12 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
@@ -13,6 +13,7 @@ the order should be:
 Usage:
 %python fastqsolexa_to_qual_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
 """
+
 import sys
 
 
diff --git a/lib/galaxy/datatypes/converters/interval_to_fli.py b/lib/galaxy/datatypes/converters/interval_to_fli.py
index 78ba26256d3..f2b22ebf90f 100644
--- a/lib/galaxy/datatypes/converters/interval_to_fli.py
+++ b/lib/galaxy/datatypes/converters/interval_to_fli.py
@@ -32,7 +32,7 @@ def main():
     # Process arguments.
     parser = optparse.OptionParser()
     parser.add_option("-F", "--format", dest="input_format")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     in_fname, out_fname = args
     input_format = options.input_format.lower()
 
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index bc96047f9d5..610b079a420 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -20,7 +20,7 @@ def main():
     parser.add_option("-c", "--chr-col", type="int", dest="chrom_col", default=1)
     parser.add_option("-s", "--start-col", type="int", dest="start_col", default=2)
     parser.add_option("-e", "--end-col", type="int", dest="end_col", default=3)
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     input_fname, output_fname = args
 
     # Make column indices 0-based.
diff --git a/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py b/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
index 6646e7a9533..298abd1fb32 100644
--- a/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
+++ b/lib/galaxy/datatypes/converters/parquet_to_csv_converter.py
@@ -3,6 +3,7 @@
 Input: parquet
 Output: csv
 """
+
 import os
 import sys
 
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
index 5c991c88440..ce159562cd3 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
@@ -14,7 +14,7 @@ from bx.interval_index_file import Indexes
 def main():
     # Read options, args.
     parser = optparse.OptionParser()
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     input_fname, output_fname = args
 
     # Do conversion.
diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
index 097459048de..abf44d9423e 100644
--- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
+++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
@@ -4,6 +4,7 @@ convert a ref.taxonomy file to a seq.taxonomy file
 Usage:
 %python ref_to_seq_taxonomy_converter.py <ref.taxonom> <seq.taxonomy>
 """
+
 import re
 import sys
 
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
index 873d4393091..7aa7449791f 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
@@ -12,7 +12,7 @@ from bx.interval_index_file import Indexes
 def main():
     # Read options, args.
     parser = optparse.OptionParser()
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     in_file, out_file = args
 
     # Do conversion.
diff --git a/lib/galaxy/datatypes/dataproviders/__init__.py b/lib/galaxy/datatypes/dataproviders/__init__.py
index b18734eda2c..3cf8f787608 100644
--- a/lib/galaxy/datatypes/dataproviders/__init__.py
+++ b/lib/galaxy/datatypes/dataproviders/__init__.py
@@ -15,6 +15,7 @@ can be piped from one to the other.
     keywords to the proper (often final) provider. These errors that result
     can be hard to diagnose.
 """
+
 from . import (
     base,
     chunk,
diff --git a/lib/galaxy/datatypes/dataproviders/line.py b/lib/galaxy/datatypes/dataproviders/line.py
index ac2dc3a51f3..71cd2f37fbb 100644
--- a/lib/galaxy/datatypes/dataproviders/line.py
+++ b/lib/galaxy/datatypes/dataproviders/line.py
@@ -163,7 +163,7 @@ class BlockDataProvider(base.LimitedOffsetDataProvider):
         """
         # composition - not inheritance
         # TODO: not a fan of this:
-        (filter_fn, limit, offset) = (kwargs.pop("filter_fn", None), kwargs.pop("limit", None), kwargs.pop("offset", 0))
+        filter_fn, limit, offset = (kwargs.pop("filter_fn", None), kwargs.pop("limit", None), kwargs.pop("offset", 0))
         line_provider = FilteredLineDataProvider(source, **kwargs)
         super().__init__(line_provider, filter_fn=filter_fn, limit=limit, offset=offset)
 
diff --git a/lib/galaxy/datatypes/media.py b/lib/galaxy/datatypes/media.py
index a695e119de9..ba5d39156a8 100644
--- a/lib/galaxy/datatypes/media.py
+++ b/lib/galaxy/datatypes/media.py
@@ -257,7 +257,7 @@ class Video(Binary):
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
         if which("ffprobe"):
             metadata, streams = ffprobe(dataset.get_file_name())
-            (w, h, fps) = self._get_resolution(streams)
+            w, h, fps = self._get_resolution(streams)
             dataset.metadata.resolution_w = w
             dataset.metadata.resolution_h = h
             dataset.metadata.fps = fps
diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py
index 0d6fec174de..29a53f6face 100644
--- a/lib/galaxy/datatypes/neo4j.py
+++ b/lib/galaxy/datatypes/neo4j.py
@@ -29,10 +29,8 @@ class Neo4j(Html):
         cannot rename the datasets here - they come with the default unfortunately
         """
         # self.regenerate_primary_file(dataset)
-        rval = [
-            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
-            This composite dataset is composed of the following files:<p/><ul>"
-        ]
+        rval = [f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>"]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
             if composite_file.optional:
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 80bdae7b66e..d6f6811e74e 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -992,8 +992,7 @@ class Registry:
 
     def to_xml_file(self, path):
         if not self._registry_xml_string:
-            registry_string_template = Template(
-                """<?xml version="1.0"?>
+            registry_string_template = Template("""<?xml version="1.0"?>
             <datatypes>
               <registration converters_path="$converters_path" display_path="$display_path">
                 $datatype_elems
@@ -1002,8 +1001,7 @@ class Registry:
                 $sniffer_elems
               </sniffers>
             </datatypes>
-            """
-            )
+            """)
             converters_path = self.converters_path_attr or ""
             display_path = self.display_path_attr or ""
             datatype_elems = "".join(galaxy.util.xml_to_string(elem) for elem in self.datatype_elems)
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
index e32b035abd4..c1436345c46 100644
--- a/lib/galaxy/datatypes/tracks.py
+++ b/lib/galaxy/datatypes/tracks.py
@@ -35,10 +35,8 @@ class UCSCTrackHub(Html):
         This is called only at upload to write the html file
         cannot rename the datasets here - they come with the default unfortunately
         """
-        rval = [
-            f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
-            This composite dataset is composed of the following files:<p/><ul>"
-        ]
+        rval = [f"<html><head><title>Files for Composite Dataset ({self.file_ext})</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>"]
         for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             opt_text = ""
             if composite_file.optional:
diff --git a/lib/galaxy/datatypes/util/maf_utilities.py b/lib/galaxy/datatypes/util/maf_utilities.py
index eba48f71aa7..d7595bafcc0 100644
--- a/lib/galaxy/datatypes/util/maf_utilities.py
+++ b/lib/galaxy/datatypes/util/maf_utilities.py
@@ -2,6 +2,7 @@
 """
 Provides wrappers and utilities for working with MAF files and alignments.
 """
+
 # Dan Blankenberg
 
 import functools
diff --git a/lib/galaxy/job_metrics/instrumenters/cgroup.py b/lib/galaxy/job_metrics/instrumenters/cgroup.py
index 406dcf0da0b..4f1796c9da8 100644
--- a/lib/galaxy/job_metrics/instrumenters/cgroup.py
+++ b/lib/galaxy/job_metrics/instrumenters/cgroup.py
@@ -93,9 +93,7 @@ if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" -a ! -f "{cgroup_mount}/cgroup.
         echo "__$(basename $f)__" >> {metrics}; cat "$f" >> {metrics} 2>/dev/null;
     done;
 fi
-""".replace(
-    "\n", " "
-).strip()
+""".replace("\n", " ").strip()
 CGROUPSV2_TEMPLATE = r"""
 if [ -e "/proc/$$/cgroup" -a -f "{cgroup_mount}/cgroup.controllers" ]; then
     cgroup_path=$(cat "/proc/$$/cgroup" | awk -F':' '($1=="0") {{print $3}}');
@@ -103,9 +101,7 @@ if [ -e "/proc/$$/cgroup" -a -f "{cgroup_mount}/cgroup.controllers" ]; then
         echo "__$(basename $f)__" >> {metrics}; cat "$f" >> {metrics} 2>/dev/null;
     done;
 fi
-""".replace(
-    "\n", " "
-).strip()
+""".replace("\n", " ").strip()
 
 
 Metric = namedtuple("Metric", ("key", "subkey", "value"))
diff --git a/lib/galaxy/job_metrics/instrumenters/env.py b/lib/galaxy/job_metrics/instrumenters/env.py
index 04608833e83..e58b4b31d8b 100644
--- a/lib/galaxy/job_metrics/instrumenters/env.py
+++ b/lib/galaxy/job_metrics/instrumenters/env.py
@@ -66,7 +66,7 @@ class EnvPlugin(InstrumentPlugin):
                 message = message_template % job_id
                 log.debug(message)
                 break
-            (var, value) = m.groups()
+            var, value = m.groups()
             if not variables or var in variables:
                 properties[var] = value
             env_string = env_string[m.end() :]
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 7048765a0a8..df346633796 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -148,7 +148,7 @@ class BaseJobRunner:
         while self._should_stop is False:
             with self.app.model.session():  # Create a Session instance and ensure it's closed.
                 try:
-                    (method, arg) = self.work_queue.get(timeout=1)
+                    method, arg = self.work_queue.get(timeout=1)
                 except Empty:
                     continue
                 if method is STOP_SIGNAL:
diff --git a/lib/galaxy/jobs/runners/cli.py b/lib/galaxy/jobs/runners/cli.py
index fe72d084272..3bfe38719b3 100644
--- a/lib/galaxy/jobs/runners/cli.py
+++ b/lib/galaxy/jobs/runners/cli.py
@@ -236,7 +236,7 @@ class ShellJobRunner(AsynchronousJobRunner[AsynchronousJobState]):
             }
             reported_jobstate = job_interface.parse_failure_reason(cmd_out.stdout, external_job_id)
             if reported_jobstate in jobstate_map:
-                (ajs.fail_message, logmsg) = jobstate_map.get(reported_jobstate)
+                ajs.fail_message, logmsg = jobstate_map.get(reported_jobstate)
                 ajs.runner_state = reported_jobstate
                 log.info(logmsg)
 
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index abd21cd2f0d..065f389b508 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -355,7 +355,7 @@ class PBSJobRunner(AsynchronousJobRunner[AsynchronousJobState]):
         """
         new_watched = []
         # reduce pbs load by batching status queries
-        (failures, statuses) = self.check_all_jobs()
+        failures, statuses = self.check_all_jobs()
         for pbs_job_state in self.watched:
             job_id = pbs_job_state.job_id
             galaxy_job_id = pbs_job_state.job_wrapper.get_id_tag()
diff --git a/lib/galaxy/jobs/runners/util/cli/job/slurm.py b/lib/galaxy/jobs/runners/util/cli/job/slurm.py
index 78432c397b4..0f4fd1f8563 100644
--- a/lib/galaxy/jobs/runners/util/cli/job/slurm.py
+++ b/lib/galaxy/jobs/runners/util/cli/job/slurm.py
@@ -115,7 +115,7 @@ class Slurm(BaseJobExec):
 
                 splitjobdata = jobline.split("|")
                 if len(splitjobdata) >= 2:
-                    (s_jobid, s_jobstate) = splitjobdata
+                    s_jobid, s_jobstate = splitjobdata
                     if " " in s_jobstate:
                         s_jobstate, s_jobotherinfo = s_jobstate.split(" ", 1)
                     state = self.slurm_longjobstate_to_shortjobstate.get(s_jobstate, "UN")
@@ -158,7 +158,7 @@ class Slurm(BaseJobExec):
             splitjobdata = line.split("|")
             log.debug(f"State split line: {len(splitjobdata)}")
             if len(splitjobdata) >= 2:
-                (s_jobid, s_jobstate) = splitjobdata
+                s_jobid, s_jobstate = splitjobdata
                 if " " in s_jobstate:
                     s_jobstate, s_jobotherinfo = s_jobstate.split(" ", 1)
                     log.debug(f"Found space in jobstate, split into: {s_jobstate} - {s_jobotherinfo}")
diff --git a/lib/galaxy/jobs/runners/util/process_groups.py b/lib/galaxy/jobs/runners/util/process_groups.py
index 35a10392ce6..9a530785d51 100644
--- a/lib/galaxy/jobs/runners/util/process_groups.py
+++ b/lib/galaxy/jobs/runners/util/process_groups.py
@@ -10,7 +10,7 @@ log = logging.getLogger(__name__)
 def check_pg(pgid):
     """Check whether processes in process group pgid are still alive."""
     try:
-        (pid, exit_status) = os.waitpid(-pgid, os.WNOHANG)
+        pid, exit_status = os.waitpid(-pgid, os.WNOHANG)
     except OSError as e:
         if e.errno == errno.ECHILD:
             log.debug("check_pg(): No process found in process group %d", pgid)
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 26ab331775b..7740a1fdbef 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -916,7 +916,7 @@ class DatasetCollectionManager:
     def _get_collection_contents_qry(self, parent_id, limit=None, offset=None):
         """Build query to find first level of collection contents by containing collection parent_id"""
         DCE = model.DatasetCollectionElement
-        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)  # type:ignore[var-annotated]
+        qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)  # type: ignore[var-annotated]
         qry = qry.order_by(DCE.element_index)
         qry = qry.options(
             joinedload(model.DatasetCollectionElement.child_collection), joinedload(model.DatasetCollectionElement.hda)
diff --git a/lib/galaxy/managers/export_tracker.py b/lib/galaxy/managers/export_tracker.py
index 14dd67dfe41..e6b4f2fba5c 100644
--- a/lib/galaxy/managers/export_tracker.py
+++ b/lib/galaxy/managers/export_tracker.py
@@ -41,7 +41,7 @@ class StoreExportTracker:
             export_association: StoreExportAssociation = self.session.execute(stmt).scalars().one()
         except NoResultFound:
             raise ObjectNotFound("Cannot set export metadata. Reason: Export association not found")
-        export_association.export_metadata = export_metadata.model_dump_json()  # type:ignore[assignment]
+        export_association.export_metadata = export_metadata.model_dump_json()  # type: ignore[assignment]
         self.session.commit()
 
     def get_export_association(self, export_association_id: int) -> StoreExportAssociation:
@@ -72,4 +72,4 @@ class StoreExportTracker:
             stmt = stmt.offset(offset)
         if limit:
             stmt = stmt.limit(limit)
-        return self.session.execute(stmt).scalars()  # type:ignore[return-value]
+        return self.session.execute(stmt).scalars()  # type: ignore[return-value]
diff --git a/lib/galaxy/managers/genomes.py b/lib/galaxy/managers/genomes.py
index 1934bfa820f..847364e9df6 100644
--- a/lib/galaxy/managers/genomes.py
+++ b/lib/galaxy/managers/genomes.py
@@ -97,7 +97,7 @@ class GenomeFilterMixin:
             if is_postgres(self.app.config.database_connection):
                 column = text("convert_from(metadata, 'UTF8')::json ->> 'dbkey'")
             else:
-                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")  # type:ignore[assignment]
+                column = func.json_extract(model_class.table.c._metadata, "$.dbkey")  # type: ignore[assignment]
             lower_val = val.lower()  # Ignore case
             # dbkey can either be "hg38" or '["hg38"]', so we need to check both
             if op == "eq":
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index f4c8e8e1640..5e6e77f958d 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -171,7 +171,7 @@ class HistoryContentsManager(base.SortableManager):
             select(sql.column("state"), func.count()).select_from(contents_subquery).group_by(sql.column("state"))
         )
         counts = self.app.model.session.execute(statement).fetchall()
-        return dict(counts)  # type:ignore[arg-type]
+        return dict(counts)  # type: ignore[arg-type]
 
     def active_counts(self, history):
         """
diff --git a/lib/galaxy/managers/job_connections.py b/lib/galaxy/managers/job_connections.py
index f90f3c7c849..0fbe0468879 100644
--- a/lib/galaxy/managers/job_connections.py
+++ b/lib/galaxy/managers/job_connections.py
@@ -58,7 +58,7 @@ class JobConnectionsManager:
             for val in graph["outputs"] + graph["inputs"]:
                 item_class = get_class(val["src"])
                 item_hid = self.sa_session.execute(select(item_class.hid).where(item_class.id == val["id"])).scalar()
-                result.append(item_hid)  # type:ignore[arg-type]
+                result.append(item_hid)  # type: ignore[arg-type]
         return result
 
     def _get_union_results(self, *selects):
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index c0e70aa5a71..6e1f2a59a04 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -1283,7 +1283,7 @@ def _remap_galaxy_markdown_containers(func, markdown):
         match = re.search(GALAXY_FENCED_BLOCK, from_markdown)
         if match is not None:
             replace = match.group(1)
-            (replacement, whole_block) = func(replace)
+            replacement, whole_block = func(replace)
             if whole_block:
                 start_pos = match.start()
                 end_pos = match.end()
diff --git a/lib/galaxy/managers/notification.py b/lib/galaxy/managers/notification.py
index 35584274b4f..6891ae4f6a5 100644
--- a/lib/galaxy/managers/notification.py
+++ b/lib/galaxy/managers/notification.py
@@ -213,7 +213,7 @@ class NotificationManager:
         for user in users:
             try:
                 if self._is_user_subscribed_to_notification(user, notification):
-                    settings = self._get_user_category_settings(user, notification.category)  # type:ignore[arg-type]
+                    settings = self._get_user_category_settings(user, notification.category)  # type: ignore[arg-type]
                     self._send_via_channels(notification, user, settings.channels)
             except Exception as e:
                 log.error(f"Error sending notification to user {user.id}. Reason: {util.unicodify(e)}")
@@ -236,7 +236,7 @@ class NotificationManager:
         if self._is_urgent(notification):
             # Urgent notifications are always sent
             return True
-        category_settings = self._get_user_category_settings(user, notification.category)  # type:ignore[arg-type]
+        category_settings = self._get_user_category_settings(user, notification.category)  # type: ignore[arg-type]
         return self._is_subscribed_to_category(category_settings)
 
     def _send_via_channels(self, notification: Notification, user: User, channel_settings: NotificationChannelSettings):
@@ -560,7 +560,7 @@ class DefaultStrategy(NotificationRecipientResolverStrategy):
         unique_user_ids.update(user_ids_from_groups_and_roles)
 
         stmt = select(User).where(User.id.in_(unique_user_ids))
-        return self.sa_session.scalars(stmt).all()  # type:ignore[return-value]
+        return self.sa_session.scalars(stmt).all()  # type: ignore[return-value]
 
     def _get_all_user_ids_from_roles_query(self, role_ids: set[int]) -> Select:
         stmt = (
@@ -724,7 +724,7 @@ class MessageEmailNotificationTemplateBuilder(EmailNotificationTemplateBuilder):
     }
 
     def get_content(self, template_format: TemplateFormats) -> AnyNotificationContent:
-        content = MessageNotificationContent.model_construct(**self.notification.content)  # type:ignore[arg-type]
+        content = MessageNotificationContent.model_construct(**self.notification.content)  # type: ignore[arg-type]
         content.message = self.markdown_to[template_format](content.message)
         return content
 
@@ -736,7 +736,7 @@ class MessageEmailNotificationTemplateBuilder(EmailNotificationTemplateBuilder):
 class NewSharedItemEmailNotificationTemplateBuilder(EmailNotificationTemplateBuilder):
 
     def get_content(self, template_format: TemplateFormats) -> AnyNotificationContent:
-        content = NewSharedItemNotificationContent.model_construct(**self.notification.content)  # type:ignore[arg-type]
+        content = NewSharedItemNotificationContent.model_construct(**self.notification.content)  # type: ignore[arg-type]
         return content
 
     def get_subject(self) -> str:
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index f84ab15f30f..a9f6625b32a 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -96,7 +96,7 @@ class SharableModelManager(
         # ... effectively a good fit to have this here, but not semantically
         if self.user_manager.is_admin(user, trans=kwargs.get("trans", None)):
             return True
-        return item.user == user  # type:ignore[attr-defined]
+        return item.user == user  # type: ignore[attr-defined]
 
     def is_accessible(self, item, user: Optional[User], **kwargs: Any) -> bool:
         """
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index b7a6ff61221..79119941b8e 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -174,7 +174,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
         """Get all jobs that are not ready yet and belong to the given user."""
         stmt = select(Job).where(and_(Job.user_id == user.id, Job.state.in_(Job.non_ready_states)))
         jobs = self.session().scalars(stmt)
-        return jobs  # type:ignore[return-value]
+        return jobs  # type: ignore[return-value]
 
     def undelete(self, user, flush=True):
         """Remove the deleted flag for the given user."""
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 0582c2c9236..1a9b40e416b 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -202,7 +202,7 @@ class WorkflowsManager(sharable.SharableModelManager[model.StoredWorkflow], dele
 
         latest_workflow_load = joinedload(StoredWorkflow.latest_workflow)
         if not payload.skip_step_counts:
-            latest_workflow_load = latest_workflow_load.undefer(Workflow.step_count)  # type:ignore[arg-type]
+            latest_workflow_load = latest_workflow_load.undefer(Workflow.step_count)  # type: ignore[arg-type]
         latest_workflow_load = latest_workflow_load.lazyload(Workflow.steps)
 
         stmt = stmt.options(joinedload(StoredWorkflow.annotations))
@@ -1985,7 +1985,7 @@ class WorkflowContentsManager(UsesAnnotations):
         for step in steps:
             # Input connections
             if step.temp_input_connections:  # populated by __module_from_dict
-                for input_name, conn_list in step.temp_input_connections.items():  # type:ignore[unreachable]
+                for input_name, conn_list in step.temp_input_connections.items():  # type: ignore[unreachable]
                     if not conn_list:
                         continue
                     if not isinstance(conn_list, list):  # Older style singleton connection
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index c70972861e5..6b8921ce353 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2301,13 +2301,11 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     def set_final_state(self, final_state):
         self.set_state(final_state)
         # TODO: migrate to where-in subqueries?
-        statement = text(
-            """
+        statement = text("""
             UPDATE workflow_invocation_step
             SET update_time = :update_time
             WHERE job_id = :job_id;
-        """
-        )
+        """)
         sa_session = required_object_session(self)
         update_time = now()
         self.update_hdca_update_time_for_job(update_time=update_time, sa_session=sa_session)
@@ -2337,18 +2335,15 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
     def update_output_states(self, supports_skip_locked):
         # TODO: migrate to where-in subqueries?
         statements = [
-            text(
-                """
+            text("""
             UPDATE dataset
             SET
                 state = :state,
                 update_time = :update_time
             WHERE
                 dataset.job_id = :job_id
-        """
-            ),
-            text(
-                """
+        """),
+            text("""
             UPDATE history_dataset_association
             SET
                 info = :info,
@@ -2357,10 +2352,8 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
             WHERE
                 history_dataset_association.dataset_id = dataset.id
                 AND dataset.job_id = :job_id;
-        """
-            ),
-            text(
-                """
+        """),
+            text("""
             UPDATE library_dataset_dataset_association
             SET
                 info = :info,
@@ -2369,8 +2362,7 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
             WHERE
                 library_dataset_dataset_association.dataset_id = dataset.id
                 AND dataset.job_id = :job_id;
-        """
-            ),
+        """),
         ]
         sa_session = required_object_session(self)
         update_time = now()
@@ -6456,10 +6448,8 @@ class LibraryDataset(Base, Serializable):
     )
     expired_datasets: Mapped[list["LibraryDatasetDatasetAssociation"]] = relationship(
         foreign_keys=[id, library_dataset_dataset_association_id],
-        primaryjoin=(
-            "and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \
-             not_(LibraryDataset.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.id))"
-        ),
+        primaryjoin=("and_(LibraryDataset.id == LibraryDatasetDatasetAssociation.library_dataset_id, \
+             not_(LibraryDataset.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.id))"),
         viewonly=True,
         uselist=True,
     )
@@ -6710,8 +6700,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
         # sets the update_time for all continaing folders up the tree
         ldda = self
 
-        sql = text(
-            """
+        sql = text("""
                 WITH RECURSIVE parent_folders_of(folder_id) AS
                     (SELECT folder_id
                     FROM library_dataset
@@ -6727,8 +6716,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
                     WHERE id = :ldda_id)
                 WHERE exists (SELECT 1 FROM parent_folders_of
                     WHERE library_folder.id = parent_folders_of.folder_id)
-            """
-        )
+            """)
 
         with required_object_session(self).bind.connect() as conn, conn.begin():
             ret = conn.execute(sql, {"library_dataset_id": ldda.library_dataset_id, "ldda_id": ldda.id})
@@ -6779,7 +6767,7 @@ class LibraryInfoAssociation(Base, RepresentById):
         primaryjoin=(
             lambda: and_(
                 LibraryInfoAssociation.library_id == Library.id,
-                not_(LibraryInfoAssociation.deleted),  # type:ignore[arg-type]
+                not_(LibraryInfoAssociation.deleted),  # type: ignore[arg-type]
             )
         ),
     )
@@ -7826,7 +7814,7 @@ class HistoryDatasetCollectionAssociation(
     def to_dict(self, view="collection"):
         original_dict_value = super().to_dict(view=view)
         if view == "dbkeysandextensions":
-            (dbkeys, extensions, *_) = self.dataset_dbkeys_and_extensions_summary
+            dbkeys, extensions, *_ = self.dataset_dbkeys_and_extensions_summary
             dict_value = dict(
                 dbkey=dbkeys.pop() if len(dbkeys) == 1 else "?",
                 extension=extensions.pop() if len(extensions) == 1 else "auto",
@@ -8472,7 +8460,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd
             .where(StoredWorkflow.id == self.id)
         )
         rows = sa_session.execute(stmt).all()
-        rows_as_dict = dict(r for r in rows if r[0] is not None)  # type:ignore[arg-type, var-annotated]
+        rows_as_dict = dict(r for r in rows if r[0] is not None)  # type: ignore[arg-type, var-annotated]
         return InvocationsStateCounts(rows_as_dict)
 
     def to_dict(self, view="collection", value_mapper=None):
@@ -9902,7 +9890,7 @@ class WorkflowInvocation(Base, UsesCreateAndUpdateTime, Dictifiable, Serializabl
         if "workflow_step_index_path" in message_dict and message_dict["workflow_step_index_path"] is not None:
             message_dict["workflow_step_index_path"] = message_dict["workflow_step_index_path"]
         self.messages.append(
-            WorkflowInvocationMessage(  # type:ignore[abstract]
+            WorkflowInvocationMessage(  # type: ignore[abstract]
                 workflow_invocation_id=self.id,
                 **message_dict,
             )
@@ -10604,7 +10592,7 @@ class MetadataFile(Base, StorableObject, Serializable):
             object_store = da.dataset.object_store
             store_by = object_store.get_store_by(da.dataset)
             if store_by == "id" and self.id is None:
-                self.flush()  # type:ignore[unreachable]
+                self.flush()  # type: ignore[unreachable]
             identifier = getattr(self, store_by)
             alt_name = f"metadata_{identifier}.dat"
             if not object_store.exists(self, extra_dir="_metadata_files", extra_dir_at_root=True, alt_name=alt_name):
@@ -10788,11 +10776,11 @@ class PSAAssociation(Base, AssociationMixin, RepresentById):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment]  # needed for social-auth-core Mixin class attributes
-    handle: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment]
-    secret: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment]
-    issued: Mapped[Optional[int]]  # type:ignore[assignment]
-    lifetime: Mapped[Optional[int]]  # type:ignore[assignment]
-    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))  # type:ignore[assignment]
+    handle: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment]
+    secret: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment]
+    issued: Mapped[Optional[int]]  # type: ignore[assignment]
+    lifetime: Mapped[Optional[int]]  # type: ignore[assignment]
+    assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))  # type: ignore[assignment]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10849,8 +10837,8 @@ class PSACode(Base, CodeMixin, RepresentById):
     __table_args__ = (UniqueConstraint("code", "email"),)
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    email: Mapped[Optional[str]] = mapped_column(VARCHAR(200))  # type:ignore[assignment]
-    code: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment]
+    email: Mapped[Optional[str]] = mapped_column(VARCHAR(200))  # type: ignore[assignment]
+    code: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type: ignore[assignment]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10876,9 +10864,9 @@ class PSANonce(Base, NonceMixin, RepresentById):
     __tablename__ = "psa_nonce"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment]
-    timestamp: Mapped[Optional[int]]  # type:ignore[assignment]
-    salt: Mapped[Optional[str]] = mapped_column(VARCHAR(40))  # type:ignore[assignment]
+    server_url: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment]
+    timestamp: Mapped[Optional[int]]  # type: ignore[assignment]
+    salt: Mapped[Optional[str]] = mapped_column(VARCHAR(40))  # type: ignore[assignment]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10912,10 +10900,10 @@ class PSAPartial(Base, PartialMixin, RepresentById):
     __tablename__ = "psa_partial"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    token: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment]
-    data: Mapped[Optional[str]] = mapped_column(TEXT)  # type:ignore[assignment]
-    next_step: Mapped[Optional[int]]  # type:ignore[assignment]
-    backend: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment]
+    token: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type: ignore[assignment]
+    data: Mapped[Optional[str]] = mapped_column(TEXT)  # type: ignore[assignment]
+    next_step: Mapped[Optional[int]]  # type: ignore[assignment]
+    backend: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type: ignore[assignment]
 
     # This static property is set at: galaxy.authnz.psa_authnz.PSAAuthnz
     sa_session = None
@@ -10955,14 +10943,14 @@ class UserAuthnzToken(Base, UserMixin, RepresentById):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
-    uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type:ignore[assignment]
-    provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type:ignore[assignment]
-    extra_data: Mapped[Optional[dict[str, Any]]] = mapped_column(  # type:ignore[assignment, unused-ignore]
+    uid: Mapped[Optional[str]] = mapped_column(VARCHAR(255))  # type: ignore[assignment]
+    provider: Mapped[Optional[str]] = mapped_column(VARCHAR(32))  # type: ignore[assignment]
+    extra_data: Mapped[Optional[dict[str, Any]]] = mapped_column(  # type: ignore[assignment, unused-ignore]
         MutableJSONType
     )
     lifetime: Mapped[Optional[int]]
     assoc_type: Mapped[Optional[str]] = mapped_column(VARCHAR(64))
-    user: Mapped[Optional["User"]] = relationship(  # type:ignore[assignment, unused-ignore]
+    user: Mapped[Optional["User"]] = relationship(  # type: ignore[assignment, unused-ignore]
         back_populates="social_auth"
     )
 
@@ -12606,14 +12594,14 @@ mapper_registry.map_imperatively(
 # ----------------------------------------------------------------------------------------
 # The following statements must not precede the mapped models defined above.
 
-History.average_rating = column_property(  # type:ignore[assignment]
+History.average_rating = column_property(  # type: ignore[assignment]
     select(func.avg(HistoryRatingAssociation.rating))
     .where(HistoryRatingAssociation.history_id == History.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-History.users_shared_with_count = column_property(  # type:ignore[assignment]
+History.users_shared_with_count = column_property(  # type: ignore[assignment]
     select(func.count(HistoryUserShareAssociation.id))
     .where(History.id == HistoryUserShareAssociation.history_id)
     .scalar_subquery(),
@@ -12625,21 +12613,21 @@ Page.average_rating = column_property(
     deferred=True,
 )
 
-StoredWorkflow.average_rating = column_property(  # type:ignore[assignment]
+StoredWorkflow.average_rating = column_property(  # type: ignore[assignment]
     select(func.avg(StoredWorkflowRatingAssociation.rating))
     .where(StoredWorkflowRatingAssociation.stored_workflow_id == StoredWorkflow.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-Visualization.average_rating = column_property(  # type:ignore[assignment]
+Visualization.average_rating = column_property(  # type: ignore[assignment]
     select(func.avg(VisualizationRatingAssociation.rating))
     .where(VisualizationRatingAssociation.visualization_id == Visualization.id)
     .scalar_subquery(),
     deferred=True,
 )
 
-Workflow.step_count = column_property(  # type:ignore[assignment]
+Workflow.step_count = column_property(  # type: ignore[assignment]
     select(func.count(WorkflowStep.id)).where(Workflow.id == WorkflowStep.workflow_id).scalar_subquery(), deferred=True
 )
 
diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index 15fdf283a7b..c4615f24ca9 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -192,6 +192,6 @@ def ensure_object_added_to_session(object_to_add, *, object_in_session=None, ses
         session.add(object_to_add)
         return True
     if object_in_session and object_session(object_in_session):
-        object_session(object_in_session).add(object_to_add)  # type:ignore[union-attr]
+        object_session(object_in_session).add(object_to_add)  # type: ignore[union-attr]
         return True
     return False
diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py b/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py
index a0572676503..fd9a7fbb986 100644
--- a/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py
+++ b/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py
@@ -103,110 +103,92 @@ def downgrade():
 
 
 def _restore_old_mappings(connection):
-    restore_hda_dataset_ids = text(
-        """
+    restore_hda_dataset_ids = text("""
         UPDATE history_dataset_association
         SET dataset_id=mapping.old_dataset_id
         FROM hda_dataset_mapping_pre_uuid_condense AS mapping
         WHERE mapping.id = history_dataset_association.id
-        """
-    )
+        """)
     connection.execute(restore_hda_dataset_ids)
-    restore_ldda_dataset_ids = text(
-        """
+    restore_ldda_dataset_ids = text("""
         UPDATE library_dataset_dataset_association
         SET dataset_id=mapping.old_dataset_id
         FROM ldda_dataset_mapping_pre_uuid_condense as mapping
         WHERE mapping.id = library_dataset_dataset_association.id
-        """
-    )
+        """)
     connection.execute(restore_ldda_dataset_ids)
 
 
 def _restore_dataset_uuids(connection):
-    restore_ldda_dataset_ids = text(
-        f"""
+    restore_ldda_dataset_ids = text(f"""
         UPDATE {dataset_table_name}
         SET {uuid_column}=backup_datasets.{uuid_column}
         FROM duplicate_datasets_by_uuid as backup_datasets
         WHERE backup_datasets.id = {dataset_table_name}.id
-        """
-    )
+        """)
     connection.execute(restore_ldda_dataset_ids)
 
 
 def _setup_duplicate_counts(connection):
-    duplicate_counts_query = text(
-        f"""
+    duplicate_counts_query = text(f"""
         CREATE TEMP TABLE temp_duplicates_counts AS
         SELECT {uuid_column}, COUNT(*)
         FROM {dataset_table_name}
         GROUP BY {uuid_column}
         HAVING COUNT(*) > 1
-        """
-    )
+        """)
     connection.execute(duplicate_counts_query)
 
 
 def _setup_backup_datasets_for_duplicated_uuids(connection):
-    duplicate_datasets = text(
-        f"""
+    duplicate_datasets = text(f"""
         CREATE TABLE duplicate_datasets_by_uuid AS
         SELECT *
         FROM {dataset_table_name}
         WHERE {uuid_column} IN (select {uuid_column} from temp_duplicates_counts)
-        """
-    )
+        """)
     connection.execute(duplicate_datasets)
 
 
 def _setup_duplicated_dataset_views_by_purged_status(connection):
-    duplicate_purged_datasets_query = text(
-        """
+    duplicate_purged_datasets_query = text("""
         CREATE TEMP VIEW temp_duplicate_datasets_purged AS
         SELECT *
         FROM duplicate_datasets_by_uuid
         WHERE purged = true
-        """
-    )
+        """)
     connection.execute(duplicate_purged_datasets_query)
 
-    duplicate_active_datasets_query = text(
-        """
+    duplicate_active_datasets_query = text("""
         CREATE TEMP VIEW temp_duplicate_datasets_active AS
         SELECT *
         FROM duplicate_datasets_by_uuid
         WHERE purged = false
-        """
-    )
+        """)
     connection.execute(duplicate_active_datasets_query)
     _debug(connection, "purged duplicated", text("select count(*) from temp_duplicate_datasets_purged"))
     _debug(connection, "active duplicated", text("select count(*) from temp_duplicate_datasets_active"))
 
 
 def _find_latest_active_dataset_for_each_uuid(connection):
-    latest_active_duplicate_query = text(
-        f"""
+    latest_active_duplicate_query = text(f"""
         CREATE TEMP TABLE temp_latest_active_duplicate AS
         SELECT {uuid_column}, MIN(id) as latest_dataset_id
         FROM temp_duplicate_datasets_active
         GROUP BY {uuid_column}
-        """
-    )
+        """)
     connection.execute(latest_active_duplicate_query)
     debug_query = text("select * from temp_latest_active_duplicate")
     _debug(connection, "latest active table", debug_query)
 
 
 def _map_active_uuids_to_latest(connection):
-    active_mapping_query = text(
-        f"""
+    active_mapping_query = text(f"""
         CREATE TEMP TABLE temp_active_mapping AS
         SELECT d.id as from_dataset_id, l.latest_dataset_id as to_dataset_id, l.{uuid_column} as uuid
         FROM temp_duplicate_datasets_active as d
         LEFT JOIN temp_latest_active_duplicate l ON d.{uuid_column} = l.{uuid_column}
-        """
-    )
+        """)
     connection.execute(active_mapping_query)
     debug_query = text("select * from temp_active_mapping")
     _debug(connection, "temp active mapping", debug_query)
@@ -215,35 +197,30 @@ def _map_active_uuids_to_latest(connection):
 
 
 def _randomize_uuids_for_purged_datasets_with_duplicated_uuids(connection):
-    updated_purged_uuids = text(
-        f"""
+    updated_purged_uuids = text(f"""
         UPDATE {dataset_table_name}
         SET uuid={new_uuid()}
         WHERE {uuid_column} IN (SELECT {uuid_column} FROM temp_duplicate_datasets_purged) AND purged = true
-        """
-    )
+        """)
     connection.execute(updated_purged_uuids)
 
 
 def _randomize_uuids_for_older_active_datasets_with_duplicated_uuids(connection):
     # sanity check...
-    duplicate_datasets_with_uuid_of_latest_active_uuid = text(
-        f"""
+    duplicate_datasets_with_uuid_of_latest_active_uuid = text(f"""
         SELECT COUNT(*)
         FROM {dataset_table_name} as d
         INNER JOIN temp_active_mapping AS a ON d.uuid = a.uuid
         GROUP BY d.{uuid_column}
         HAVING COUNT(*) > 1
-        """
-    )
+        """)
     _debug(
         connection,
         "(before) duplicate_datasets_with_uuid_of_latest_active_uuid",
         duplicate_datasets_with_uuid_of_latest_active_uuid,
     )
 
-    update_older_datasets = text(
-        f"""
+    update_older_datasets = text(f"""
         UPDATE {dataset_table_name}
         SET uuid={new_uuid()}
         WHERE EXISTS
@@ -252,8 +229,7 @@ def _randomize_uuids_for_older_active_datasets_with_duplicated_uuids(connection)
                 FROM temp_active_mapping as m
                 where m.from_dataset_id = {dataset_table_name}.id and m.from_dataset_id != m.to_dataset_id
             )
-        """
-    )
+        """)
     connection.execute(update_older_datasets)
 
     _debug(
@@ -262,65 +238,53 @@ def _randomize_uuids_for_older_active_datasets_with_duplicated_uuids(connection)
         duplicate_datasets_with_uuid_of_latest_active_uuid,
     )
 
-    duplicate_active_count = text(
-        """
+    duplicate_active_count = text("""
         SELECT COUNT(*)
         FROM temp_active_mapping
-        """
-    )
+        """)
     _debug(connection, "(after) duplicate_active_count", duplicate_active_count)
-    datasets_with_originally_duplicated_uuids = text(
-        f"""
+    datasets_with_originally_duplicated_uuids = text(f"""
         SELECT COUNT(*)
         FROM {dataset_table_name} as d
         INNER JOIN temp_active_mapping AS a ON d.uuid = a.uuid
-        """
-    )
+        """)
     _debug(connection, "(after) datasets_with_originally_duplicated_uuids", datasets_with_originally_duplicated_uuids)
 
 
 def _update_dataset_associations_to_point_to_latest_active_datasets(connection):
     # for others select one dataset to represent the dataset in HDAs/LDDAs
-    update_hda_links = text(
-        """
+    update_hda_links = text("""
         UPDATE history_dataset_association
         SET dataset_id=t.to_dataset_id
         FROM temp_active_mapping t
         WHERE t.from_dataset_id = dataset_id
-        """
-    )
+        """)
     connection.execute(update_hda_links)
-    update_ldda_links = text(
-        """
+    update_ldda_links = text("""
         UPDATE library_dataset_dataset_association
         SET dataset_id=t.to_dataset_id
         FROM temp_active_mapping t
         WHERE t.from_dataset_id = dataset_id
-        """
-    )
+        """)
     connection.execute(update_ldda_links)
 
 
 def _preserve_old_dataset_association_mappings(connection):
-    old_hda_mappings = text(
-        f"""
+    old_hda_mappings = text(f"""
         CREATE TABLE hda_dataset_mapping_pre_uuid_condense AS
         SELECT DISTINCT h.id as id, d.id as old_dataset_id
          FROM history_dataset_association AS h
          INNER JOIN dataset AS d ON h.dataset_id = d.id
          INNER JOIN duplicate_datasets_by_uuid AS duplicates ON d.{uuid_column} = duplicates.{uuid_column}
-        """
-    )
+        """)
     connection.execute(old_hda_mappings)
-    old_ldda_mappings = text(
-        f"""
+    old_ldda_mappings = text(f"""
         CREATE TABLE ldda_dataset_mapping_pre_uuid_condense AS
          SELECT l.id as id, d.id as old_dataset_id
          FROM library_dataset_dataset_association aS l
          INNER JOIN dataset AS d ON l.dataset_id = d.id
          INNER JOIN duplicate_datasets_by_uuid AS duplicates ON d.{uuid_column} = duplicates.{uuid_column}
-        """
-    )
+        """)
     connection.execute(old_ldda_mappings)
 
 
diff --git a/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py b/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py
index 4b9054872cd..61feb7646f1 100644
--- a/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py
+++ b/lib/galaxy/model/migrations/data_fixes/user_table_fixer.py
@@ -72,14 +72,12 @@ class EmailDeduplicator:
             self._deduplicate_users(email, duplicates)
 
     def _get_users_with_same_email(self, email: str):
-        sql = text(
-            """
+        sql = text("""
             SELECT u.id, EXISTS(SELECT h.id FROM history h WHERE h.user_id = u.id)
             FROM galaxy_user u
             WHERE u.email = :email
             ORDER BY u.create_time
-            """
-        )
+            """)
         params = {"email": email}
         return self.connection.execute(sql, params).all()
 
diff --git a/lib/galaxy/model/migrations/exceptions.py b/lib/galaxy/model/migrations/exceptions.py
index 039bfe79d94..c1fbd2d700e 100644
--- a/lib/galaxy/model/migrations/exceptions.py
+++ b/lib/galaxy/model/migrations/exceptions.py
@@ -53,20 +53,16 @@ class RevisionNotFoundError(Exception):
 
 class DatabaseDoesNotExistError(Exception):
     def __init__(self, db_url: str) -> None:
-        super().__init__(
-            f"""The database at {db_url} does not exist. You must
+        super().__init__(f"""The database at {db_url} does not exist. You must
             create and initialize the database before running this script. You
             can do so by (a) running `create_db.sh`; or by (b) starting Galaxy,
             in which case Galaxy will create and initialize the database
-            automatically."""
-        )
+            automatically.""")
 
 
 class DatabaseNotInitializedError(Exception):
     def __init__(self, db_url: str) -> None:
-        super().__init__(
-            f"""The database at {db_url} is empty. You must
+        super().__init__(f"""The database at {db_url} is empty. You must
             initialize the database before running this script. You can do so by
             (a) running `create_db.sh`; or by (b) starting Galaxy, in which case
-            Galaxy will initialize the database automatically."""
-        )
+            Galaxy will initialize the database automatically.""")
diff --git a/lib/galaxy/model/scripts/delete_job_metrics.py b/lib/galaxy/model/scripts/delete_job_metrics.py
index eb50b9f24c4..005392a2062 100644
--- a/lib/galaxy/model/scripts/delete_job_metrics.py
+++ b/lib/galaxy/model/scripts/delete_job_metrics.py
@@ -42,11 +42,9 @@ def _get_parser():
 
 def run(engine, max_update_time):
     """Delete galaxy_session records which were updated prior to `max_update_time`."""
-    confirm = input(
-        f"""
+    confirm = input(f"""
 WARNING: Executing this script will permanently delete all text and numeric job metrics up to {max_update_time.strftime("%B %d, %Y")}.
-Are your sure you want to proceed? Type "yes" to confirm: """
-    )
+Are your sure you want to proceed? Type "yes" to confirm: """)
     if confirm.lower() == "yes":
         _delete_metrics(engine, max_update_time, "job_metric_text")
         _delete_metrics(engine, max_update_time, "job_metric_numeric")
diff --git a/lib/galaxy/model/scripts/history_table_pruner.py b/lib/galaxy/model/scripts/history_table_pruner.py
index ebd60ba063f..396e2865d1a 100644
--- a/lib/galaxy/model/scripts/history_table_pruner.py
+++ b/lib/galaxy/model/scripts/history_table_pruner.py
@@ -119,13 +119,11 @@ class HistoryTablePruner:
     def _mark_histories_as_deleted_and_purged(self, low, high):
         """Mark target histories as deleted and purged to prevent their further usage."""
         log.info(" Marking histories as deleted and purged")
-        stmt = text(
-            """
+        stmt = text("""
             UPDATE history
             SET deleted = TRUE, purged = TRUE
             WHERE user_id IS NULL AND hid_counter = 1 AND create_time < :create_time AND id >= :low AND id < :high
-        """
-        )
+        """)
         params = self._get_stmt_params(low, high)
         with self.engine.begin() as conn:
             return conn.execute(stmt, params)
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 2ce7863a16d..7f0bfc2095e 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -625,15 +625,13 @@ class GalaxyRBACAgent(RBACAgent):
         if dataset.library_associations:
             return False
         else:
-            query = text(
-                """
+            query = text("""
 SELECT COUNT(*)
 FROM history
 INNER JOIN
     history_dataset_association on history_dataset_association.history_id = history.id
 WHERE history.user_id != :user_id and history_dataset_association.dataset_id = :dataset_id
-"""
-            ).bindparams(dataset_id=dataset.id, user_id=user.id if user else None)
+""").bindparams(dataset_id=dataset.id, user_id=user.id if user else None)
             return self.sa_session.scalars(query).first() == 0
 
     def get_item_actions(self, action, item):
diff --git a/lib/galaxy/model/unittest_utils/model_testing_utils.py b/lib/galaxy/model/unittest_utils/model_testing_utils.py
index a1af8dd23ba..73374290704 100644
--- a/lib/galaxy/model/unittest_utils/model_testing_utils.py
+++ b/lib/galaxy/model/unittest_utils/model_testing_utils.py
@@ -147,7 +147,7 @@ def drop_database(db_url, database):
         _drop_database(db_url, database)
     else:
         url = make_url(db_url)
-        os.remove(url.database)  # type:ignore[arg-type]
+        os.remove(url.database)  # type: ignore[arg-type]
 
 
 def dbcleanup_wrapper(session, obj, where_clause=None):
diff --git a/lib/galaxy/objectstore/rucio.py b/lib/galaxy/objectstore/rucio.py
index f68a33c40a3..56cb6c16a48 100644
--- a/lib/galaxy/objectstore/rucio.py
+++ b/lib/galaxy/objectstore/rucio.py
@@ -161,16 +161,14 @@ class RucioBroker:
             self.rucio_config_path = os.path.join(temp_directory, "rucio.cfg")
             key_for_pass = "password"
             with open(self.rucio_config_path, "w") as f:
-                f.write(
-                    f"""[client]
+                f.write(f"""[client]
 rucio_host = {self.config['host']}
 auth_host = {self.config['auth_host']}
 account = {self.config['account']}
 auth_type = {self.config['auth_type']}
 username = {self.config['username']}
 {key_for_pass} = {self.config[key_for_pass]}
-"""
-                )
+""")
         # We may have crossed a forkpool boundary. No harm setting the env var again.
         # Fixes rucio integration tests
         os.environ["RUCIO_CONFIG"] = self.rucio_config_path
diff --git a/lib/galaxy/quota/__init__.py b/lib/galaxy/quota/__init__.py
index fa223d5c590..083ac524d94 100644
--- a/lib/galaxy/quota/__init__.py
+++ b/lib/galaxy/quota/__init__.py
@@ -121,8 +121,7 @@ class DatabaseQuotaAgent(QuotaAgent):
         """
         if not user:
             return self._default_unregistered_quota(quota_source_label)
-        query = text(
-            """
+        query = text("""
 SELECT (
         COALESCE(MAX(CASE WHEN union_quota.operation = '='
                           THEN union_quota.bytes
@@ -167,10 +166,7 @@ FROM (
         AND group_quota.quota_source_label {label_cond}
         AND guser.id = :user_id
 ) as union_quota
-""".format(
-                label_cond="IS NULL" if quota_source_label is None else " = :label"
-            )
-        )
+""".format(label_cond="IS NULL" if quota_source_label is None else " = :label"))
         engine = self.sa_session.get_bind()
         with engine.connect() as conn:
             res = conn.execute(query, {"is_true": True, "user_id": user.id, "label": quota_source_label}).fetchone()
@@ -275,16 +271,14 @@ ON CONFLICT
 
     def _default_quota(self, default_type, quota_source_label):
         label_condition = "IS NULL" if quota_source_label is None else "= :label"
-        query = text(
-            f"""
+        query = text(f"""
 SELECT bytes
 FROM quota as default_quota
 LEFT JOIN default_quota_association on default_quota.id = default_quota_association.quota_id
 WHERE default_quota_association.type = :default_type
     AND default_quota.deleted != :is_true
     AND default_quota.quota_source_label {label_condition}
-"""
-        )
+""")
         engine = self.sa_session.get_bind()
         with engine.connect() as conn:
             res = conn.execute(
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index 67cbfc6e07c..0e53c48051f 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -113,7 +113,7 @@ class InstalledRepositoryManager:
                 tpm=tpm,
                 repository=repository,
                 changeset_revision=repository.changeset_revision,
-                metadata_dict=repository.metadata_,  # type:ignore[arg-type]
+                metadata_dict=repository.metadata_,  # type: ignore[arg-type]
             )
             repository_tools_tups = irmm.get_repository_tools_tups()
             # Reload tools into the appropriate tool panel section.
@@ -135,7 +135,7 @@ class InstalledRepositoryManager:
                 dmh = data_manager.DataManagerHandler(self.app)
                 dmh.install_data_managers(
                     self.app.config.shed_data_manager_config_file,
-                    repository.metadata_,  # type:ignore[arg-type]
+                    repository.metadata_,  # type: ignore[arg-type]
                     repository.get_shed_config_dict(self.app),
                     data_manager_relative_install_dir,
                     repository,
diff --git a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
index f25bd46de48..11a185a8808 100644
--- a/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
@@ -128,7 +128,7 @@ class InstalledRepositoryMetadataManager(GalaxyMetadataGenerator):
             original_metadata_dict = self.repository.metadata_
             self.generate_metadata_for_changeset_revision()
             if self.metadata_dict != original_metadata_dict:
-                self.repository.metadata_ = self.metadata_dict  # type:ignore[assignment]
+                self.repository.metadata_ = self.metadata_dict  # type: ignore[assignment]
                 self.update_in_shed_tool_config()
 
                 session = self.app.install_model.context
diff --git a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
index f579c6ad205..c4a749f1236 100644
--- a/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
@@ -113,7 +113,7 @@ class UpdateRepositoryManager:
         if tool_shed_status_dict:
             repository.tool_shed_status = tool_shed_status_dict
         else:
-            repository.tool_shed_status = None  # type:ignore[assignment]
+            repository.tool_shed_status = None  # type: ignore[assignment]
         session = self.app.install_model.context
         session.add(repository)
         session.commit()
diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py
index 6422639bc3f..0ad9a8e6abb 100644
--- a/lib/galaxy/tool_shed/metadata/metadata_generator.py
+++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py
@@ -870,7 +870,7 @@ class GalaxyMetadataGenerator(BaseMetadataGenerator):
     """A MetadataGenerator building on Galaxy's app and repository constructs."""
 
     app: InstallationTarget
-    repository: Optional[ToolShedRepository]  # type:ignore[assignment]
+    repository: Optional[ToolShedRepository]  # type: ignore[assignment]
 
     def __init__(
         self,
diff --git a/lib/galaxy/tool_shed/util/repository_util.py b/lib/galaxy/tool_shed/util/repository_util.py
index d12a7fc890c..6da054d11cb 100644
--- a/lib/galaxy/tool_shed/util/repository_util.py
+++ b/lib/galaxy/tool_shed/util/repository_util.py
@@ -64,7 +64,7 @@ def check_for_updates(
             message += "Unable to retrieve status from the tool shed for the following repositories:\n"
             message += ", ".join(repository_names_not_updated)
     else:
-        repository = install_model_context.get(ToolShedRepository, repository_id)  # type:ignore[assignment]
+        repository = install_model_context.get(ToolShedRepository, repository_id)  # type: ignore[assignment]
         assert repository
         ok, updated = _check_or_update_tool_shed_status_for_installed_repository(
             tool_shed_registry, install_model_context, repository
diff --git a/lib/galaxy/tool_util/deps/mulled/get_tests.py b/lib/galaxy/tool_util/deps/mulled/get_tests.py
index 7ff662856d1..367d691b22b 100644
--- a/lib/galaxy/tool_util/deps/mulled/get_tests.py
+++ b/lib/galaxy/tool_util/deps/mulled/get_tests.py
@@ -5,6 +5,7 @@ searches for tests for packages in the bioconda-recipes repo and on Anaconda, lo
 
 A shallow search (default for singularity and conda generation scripts) just checks once on Anaconda for the specified version.
 """
+
 import json
 import logging
 from glob import glob
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
index c5f1ccc6a88..c3064f570a4 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_build_tool.py
@@ -8,6 +8,7 @@ Build mulled images for requirements defined in a tool:
     mulled-build-tool build path/to/tool_file.xml
 
 """
+
 from typing import (
     List,
     TYPE_CHECKING,
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
index 1cd87d5a3d0..f847c4914f5 100644
--- a/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_hash.py
@@ -7,6 +7,7 @@ Produce a mulled hash with:
 
     mulled-hash samtools=1.3.1,bedtools=2.22
 """
+
 from typing_extensions import Literal
 
 from ._cli import arg_parser
diff --git a/lib/galaxy/tool_util/toolbox/filters/__init__.py b/lib/galaxy/tool_util/toolbox/filters/__init__.py
index aec7574b9e6..d2e1175043d 100644
--- a/lib/galaxy/tool_util/toolbox/filters/__init__.py
+++ b/lib/galaxy/tool_util/toolbox/filters/__init__.py
@@ -66,7 +66,7 @@ class FilterFactory:
         """
         if ":" in filter_name:
             # Should be a submodule of filters (e.g. examples:restrict_development_tools)
-            (module_name, function_name) = filter_name.rsplit(":", 1)
+            module_name, function_name = filter_name.rsplit(":", 1)
             function = self._import_filter(module_name, function_name)
         else:
             # No module found, just load a function from this file or
diff --git a/lib/galaxy/tool_util/toolbox/integrated_panel.py b/lib/galaxy/tool_util/toolbox/integrated_panel.py
index 4ceb8a5ae24..d68ce96e5f2 100644
--- a/lib/galaxy/tool_util/toolbox/integrated_panel.py
+++ b/lib/galaxy/tool_util/toolbox/integrated_panel.py
@@ -69,16 +69,14 @@ class ManagesIntegratedToolPanelMixin:
             filename = os.path.join(tracking_directory, name)
         else:
             filename = destination
-        template = string.Template(
-            """<?xml version="1.0"?>
+        template = string.Template("""<?xml version="1.0"?>
 <toolbox>
     <!--
     $INTEGRATED_TOOL_PANEL_DESCRIPTION
     -->
 $INTEGRATED_TOOL_PANEL
 </toolbox>
-"""
-        )
+""")
         integrated_tool_panel = []
         for _, item_type, item in self._integrated_tool_panel.panel_items_iter():
             if item:
diff --git a/lib/galaxy/tool_util/toolbox/watcher.py b/lib/galaxy/tool_util/toolbox/watcher.py
index 05db57fd304..270a4d47fdc 100644
--- a/lib/galaxy/tool_util/toolbox/watcher.py
+++ b/lib/galaxy/tool_util/toolbox/watcher.py
@@ -5,7 +5,7 @@ import threading
 try:
     from watchdog.events import FileSystemEventHandler
 except ImportError:
-    FileSystemEventHandler = object  # type:ignore[assignment, misc, unused-ignore]
+    FileSystemEventHandler = object  # type: ignore[assignment, misc, unused-ignore]
 
 from galaxy.util.hash_util import md5_hash_file
 from galaxy.util.watcher import (
diff --git a/lib/galaxy/tool_util/unittest_utils/sample_data.py b/lib/galaxy/tool_util/unittest_utils/sample_data.py
index e9b19283401..6fe816a15e9 100644
--- a/lib/galaxy/tool_util/unittest_utils/sample_data.py
+++ b/lib/galaxy/tool_util/unittest_utils/sample_data.py
@@ -7,16 +7,14 @@ SIMPLE_TOOL_WITH_MACRO = """<tool id="tool_with_macro" name="macro_annotation" v
     </macros>
 </tool>"""
 
-SIMPLE_MACRO = Template(
-    """
+SIMPLE_MACRO = Template("""
 <macros>
     <token name="@WRAPPER_VERSION@">$tool_version</token>
     <macro name="inputs">
         <inputs/>
     </macro>
 </macros>
-"""
-)
+""")
 
 VALID_XML_VALIDATORS = [
     """<validator type="empty_dataset" />""",
diff --git a/lib/galaxy/tool_util_models/parameter_validators.py b/lib/galaxy/tool_util_models/parameter_validators.py
index 7a685461f43..20eebaad333 100644
--- a/lib/galaxy/tool_util_models/parameter_validators.py
+++ b/lib/galaxy/tool_util_models/parameter_validators.py
@@ -475,8 +475,8 @@ AnySafeValidatorModel = Annotated[
     Field(discriminator="type"),
 ]
 
-DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
-DiscriminatedAnySafeValidatorModel = TypeAdapter(AnySafeValidatorModel)  # type:ignore[var-annotated]
+DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type: ignore[var-annotated]
+DiscriminatedAnySafeValidatorModel = TypeAdapter(AnySafeValidatorModel)  # type: ignore[var-annotated]
 
 
 def raise_error_if_validation_fails(
diff --git a/lib/galaxy/tool_util_models/parameters.py b/lib/galaxy/tool_util_models/parameters.py
index 135f04af196..692d78e7960 100644
--- a/lib/galaxy/tool_util_models/parameters.py
+++ b/lib/galaxy/tool_util_models/parameters.py
@@ -816,7 +816,7 @@ AdaptedDataCollectionRequest = Annotated[
     ],
     Field(discriminator="adapter_type"),
 ]
-AdaptedDataCollectionRequestTypeAdapter = TypeAdapter(AdaptedDataCollectionRequest)  # type:ignore[var-annotated]
+AdaptedDataCollectionRequestTypeAdapter = TypeAdapter(AdaptedDataCollectionRequest)  # type: ignore[var-annotated]
 
 
 class DatasetCollectionElementReference(StrictModel):
@@ -856,7 +856,7 @@ AdaptedDataCollectionRequestInternal = Annotated[
 ]
 AdaptedDataCollectionRequestInternalTypeAdapter = TypeAdapter(
     AdaptedDataCollectionRequestInternal
-)  # type:ignore[var-annotated]
+)  # type: ignore[var-annotated]
 
 
 class DataCollectionParameterModel(BaseGalaxyToolParameterModelDefinition):
diff --git a/lib/galaxy/tool_util_models/tool_source.py b/lib/galaxy/tool_util_models/tool_source.py
index b4c2fbeea61..f03109c721b 100644
--- a/lib/galaxy/tool_util_models/tool_source.py
+++ b/lib/galaxy/tool_util_models/tool_source.py
@@ -82,15 +82,13 @@ class JavascriptRequirement(ToolSourceBaseModel):
                 Field(
                     title="expression_lib",
                     description="Provide Javascript/ECMAScript 5.1 code here that will be available for expressions inside the `shell_command` field.",
-                    examples=[
-                        r"""function pickValue() {
+                    examples=[r"""function pickValue() {
     if (inputs.conditional_parameter.test_parameter == "a") {
         return inputs.conditional_parameter.integer_parameter
     } else {
         return inputs.conditional_parameter.boolean_parameter
     }
-}"""
-                    ],
+}"""],
                 ),
             ]
         ]
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 6a28b0760b1..33ff3a020c4 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -503,7 +503,7 @@ class DefaultToolAction(ToolAction):
                 incoming[f"{name}|__identifier__"] = identifier
 
         # Collect chromInfo dataset and add as parameters to incoming
-        (chrom_info, db_dataset) = execution_cache.get_chrom_info(tool.id, input_dbkey)
+        chrom_info, db_dataset = execution_cache.get_chrom_info(tool.id, input_dbkey)
 
         if db_dataset:
             inp_data.update({"chromInfo": db_dataset})
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index 388ca7d47a1..556167c74c8 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -108,7 +108,7 @@ def handle_library_params(
         template = session.get(FormDefinition, template_id)
         if template and template.fields:
             for field in template.fields:
-                field_name = field["name"]  # type:ignore[index]
+                field_name = field["name"]  # type: ignore[index]
                 if params.get(field_name, False):
                     field_value = util.restore_text(params.get(field_name, ""))
                     template_field_contents[field_name] = field_value
diff --git a/lib/galaxy/tools/expressions/evaluation.py b/lib/galaxy/tools/expressions/evaluation.py
index f6f4786dd3b..58acd0a51db 100644
--- a/lib/galaxy/tools/expressions/evaluation.py
+++ b/lib/galaxy/tools/expressions/evaluation.py
@@ -66,7 +66,7 @@ def evaluate(config, input):
     )
     input_str = f"{json.dumps(new_input)}\n\n"
     input_bytes = input_str.encode("utf-8")
-    (stdoutdata, stderrdata) = sp.communicate(input_bytes)
+    stdoutdata, stderrdata = sp.communicate(input_bytes)
     if sp.returncode != 0:
         message = f"Expression engine returned non-zero exit code on evaluation of\n{json.dumps(new_input, indent=4)}{stdoutdata}{stderrdata}"
         raise Exception(message)
diff --git a/lib/galaxy/tools/imp_exp/export_history.py b/lib/galaxy/tools/imp_exp/export_history.py
index c16c4768db5..c2ad1f38697 100644
--- a/lib/galaxy/tools/imp_exp/export_history.py
+++ b/lib/galaxy/tools/imp_exp/export_history.py
@@ -39,7 +39,7 @@ def main(argv=None):
         "--galaxy-version", dest="galaxy_version", help="Galaxy version that initiated the command.", default=None
     )
     parser.add_option("--file-sources", type=str, help="file sources json")
-    (options, args) = parser.parse_args(argv)
+    options, args = parser.parse_args(argv)
 
     gzip = bool(options.gzip)
     assert len(args) >= 2
diff --git a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
index d9aab095fba..a87c6497e4c 100644
--- a/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
+++ b/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
@@ -90,5 +90,5 @@ if __name__ == "__main__":
         help="Source and destination dir values are base64 encoded.",
     )
     parser.add_option("--file-sources", type=str, help="file sources json")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     main(options, args)
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d0a0a2c8a52..e75c813bdf2 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2257,7 +2257,7 @@ class DataToolParameter(BaseDataToolParameter):
                     )
                 match = dataset_matcher.hda_match(value_to_check)
                 if match and match.implicit_conversion:
-                    value_to_check.implicit_conversion = True  # type:ignore[attr-defined]
+                    value_to_check.implicit_conversion = True  # type: ignore[attr-defined]
             elif isinstance(value_to_check, HistoryDatasetCollectionAssociation):
                 if value_to_check.deleted:
                     raise ParameterValueError("the previously selected dataset collection has been deleted.", self.name)
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index 9b276694b36..7f87a08fcff 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -391,7 +391,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
             if isinstance(dataset_instance, HasTags):
                 self.groups = {
                     tag.user_value.lower()
-                    for tag in dataset_instance.tags  # type:ignore[unused-ignore, attr-defined]
+                    for tag in dataset_instance.tags  # type: ignore[unused-ignore, attr-defined]
                     if tag.user_tname == "group"
                 }
             else:
diff --git a/lib/galaxy/util/config_templates.py b/lib/galaxy/util/config_templates.py
index b0b35e2df8a..6ff34c03471 100644
--- a/lib/galaxy/util/config_templates.py
+++ b/lib/galaxy/util/config_templates.py
@@ -47,9 +47,9 @@ try:
     )
     from jinja2.nativetypes import NativeEnvironment
 except ImportError:
-    NativeEnvironment = None  # type:ignore[assignment, misc, unused-ignore]
-    StrictUndefined = None  # type:ignore[assignment, misc, unused-ignore]
-    UndefinedError = None  # type:ignore[assignment, misc, unused-ignore]
+    NativeEnvironment = None  # type: ignore[assignment, misc, unused-ignore]
+    StrictUndefined = None  # type: ignore[assignment, misc, unused-ignore]
+    UndefinedError = None  # type: ignore[assignment, misc, unused-ignore]
 
 from galaxy.exceptions import (
     ObjectNotFound,
diff --git a/lib/galaxy/util/watcher.py b/lib/galaxy/util/watcher.py
index d57188280c7..141fd8136e0 100644
--- a/lib/galaxy/util/watcher.py
+++ b/lib/galaxy/util/watcher.py
@@ -13,9 +13,9 @@ try:
 
     can_watch = True
 except ImportError:
-    Observer = None  # type:ignore[assignment, unused-ignore]
-    FileSystemEventHandler = object  # type:ignore[assignment,misc, unused-ignore]
-    PollingObserver = None  # type:ignore[assignment, misc, unused-ignore]
+    Observer = None  # type: ignore[assignment, unused-ignore]
+    FileSystemEventHandler = object  # type: ignore[assignment,misc, unused-ignore]
+    PollingObserver = None  # type: ignore[assignment, misc, unused-ignore]
     can_watch = False
 
 from galaxy.util.hash_util import md5_hash_file
diff --git a/lib/galaxy/web/framework/middleware/error.py b/lib/galaxy/web/framework/middleware/error.py
index df5ad74efe0..86e1738efe7 100644
--- a/lib/galaxy/web/framework/middleware/error.py
+++ b/lib/galaxy/web/framework/middleware/error.py
@@ -9,6 +9,7 @@ Error handler middleware
 When an exception is thrown from the wrapper application, this logs
 the exception and displays an error page.
 """
+
 import logging
 import sys
 import traceback
@@ -421,12 +422,9 @@ def handle_exception(
         extra_data = ""
         reported = True
     else:
-        msg = (
-            error_message
-            or """
+        msg = error_message or """
         An error occurred.
         """
-        )
         extra = "<p><b>The error has been logged to our team.</b>"
         if "sentry_event_id" in environ:
             extra += " If you want to contact us about this error, please reference the following<br><br>"
diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py
index cd988621dfa..1d41ccd1b67 100644
--- a/lib/galaxy/web/framework/middleware/translogger.py
+++ b/lib/galaxy/web/framework/middleware/translogger.py
@@ -3,6 +3,7 @@
 """
 Middleware for logging requests, using Apache combined log format
 """
+
 import logging
 import time
 from urllib.parse import quote
diff --git a/lib/galaxy/web/proxy/__init__.py b/lib/galaxy/web/proxy/__init__.py
index e11d80d5949..eedcfb720c6 100644
--- a/lib/galaxy/web/proxy/__init__.py
+++ b/lib/galaxy/web/proxy/__init__.py
@@ -275,14 +275,12 @@ class SqliteProxyIpc:
                 c = conn.cursor()
                 try:
                     # Create table
-                    c.execute(
-                        """CREATE TABLE gxproxy2
+                    c.execute("""CREATE TABLE gxproxy2
                                  (key text PRIMARY KEY,
                                   host text,
                                   port integer,
                                   container_ids text,
-                                  container_interface text)"""
-                    )
+                                  container_interface text)""")
                 except Exception:
                     pass
                 delete = """DELETE FROM gxproxy2 WHERE key=?"""
diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index fcc32ac9650..2e236757f51 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -657,8 +657,7 @@ async def try_get_request_body_as_json(request: Request) -> Optional[Any]:
     return None
 
 
-search_description_template = Template(
-    """A mix of free text and GitHub-style tags used to filter the index operation.
+search_description_template = Template("""A mix of free text and GitHub-style tags used to filter the index operation.
 
 ## Query Structure
 
@@ -683,8 +682,7 @@ ${tags}
 Free text search terms will be searched against the following attributes of the
 ${model_name}s: ${freetext}.
 
-"""
-)
+""")
 
 
 class IndexQueryTag(NamedTuple):
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index aee0c277f45..96547c0d28c 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -338,7 +338,7 @@ class FastAPIJobs:
         for job_input_assoc in job.input_datasets:
             input_dataset_instance = job_input_assoc.dataset
             if input_dataset_instance is None:
-                continue  # type:ignore[unreachable]  # TODO if job_input_assoc.dataset is indeed never None, remove the above check
+                continue  # type: ignore[unreachable]  # TODO if job_input_assoc.dataset is indeed never None, remove the above check
             if input_dataset_instance.get_total_size() == 0:
                 has_empty_inputs = True
             input_instance_id = input_dataset_instance.id
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index e0211e4de78..9208653ae79 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1202,12 +1202,10 @@ LegacyJobStateQueryParam = Annotated[
     bool,
     Query(
         title="Replace with job state",
-        description=(
-            """Populate the invocation step state with the job state instead of the invocation step state.
+        description=("""Populate the invocation step state with the job state instead of the invocation step state.
         This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections.
         Partially scheduled steps may provide incomplete information and the listed steps outputs
-        are not the mapped over step outputs but the individual job outputs."""
-        ),
+        are not the mapped over step outputs but the individual job outputs."""),
     ),
 ]
 
diff --git a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
index f02c51977cc..6f2be4ed2b3 100644
--- a/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/services/tool_shed_repositories.py
@@ -74,7 +74,7 @@ class ToolShedRepositoriesService:
         stmt = select(ToolShedRepository)
         for key, value in kwd.items():
             if value is not None:
-                column = ToolShedRepository.__table__.c[key]  # type:ignore[attr-defined]
+                column = ToolShedRepository.__table__.c[key]  # type: ignore[attr-defined]
                 stmt = stmt.filter(column == value)
         stmt = stmt.order_by(ToolShedRepository.name).order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
         session = self._install_model_context
diff --git a/lib/galaxy_test/api/test_datasets.py b/lib/galaxy_test/api/test_datasets.py
index ab2f65a2202..a97cfe5885b 100644
--- a/lib/galaxy_test/api/test_datasets.py
+++ b/lib/galaxy_test/api/test_datasets.py
@@ -331,13 +331,11 @@ class TestDatasetsApi(ApiTestCase):
         assert input_hda["id"] == query_hda["id"]
 
     def test_display(self, history_id):
-        contents = textwrap.dedent(
-            """\
+        contents = textwrap.dedent("""\
         1   2   3   4
         A   B   C   D
         10  20  30  40
-        """
-        )
+        """)
         hda1 = self.dataset_populator.new_dataset(history_id, content=contents, wait=True)
         display_response = self._get(f"histories/{history_id}/contents/{hda1['id']}/display", {"raw": "True"})
         self._assert_status_code_is(display_response, 200)
@@ -376,13 +374,11 @@ class TestDatasetsApi(ApiTestCase):
         )
 
     def test_get_content_as_text(self, history_id):
-        contents = textwrap.dedent(
-            """\
+        contents = textwrap.dedent("""\
         1   2   3   4
         A   B   C   D
         10  20  30  40
-        """
-        )
+        """)
         hda1 = self.dataset_populator.new_dataset(history_id, content=contents, wait=True)
         get_content_as_text_response = self._get(f"datasets/{hda1['id']}/get_content_as_text")
         self._assert_status_code_is(get_content_as_text_response, 200)
@@ -414,13 +410,11 @@ class TestDatasetsApi(ApiTestCase):
             self._assert_status_code_is(get_content_as_text_response, 403)
 
     def test_dataprovider_chunk(self, history_id):
-        contents = textwrap.dedent(
-            """\
+        contents = textwrap.dedent("""\
         1   2   3   4
         A   B   C   D
         10  20  30  40
-        """
-        )
+        """)
         # test first chunk
         hda1 = self.dataset_populator.new_dataset(history_id, content=contents, wait=True)
         kwds = {
@@ -488,13 +482,11 @@ class TestDatasetsApi(ApiTestCase):
         return self.dataset_populator.display_chunk(dataset_id, offset, ck_size)
 
     def test_tabular_chunking_through_display_endpoint(self, history_id):
-        contents = textwrap.dedent(
-            """\
+        contents = textwrap.dedent("""\
         1   2   3   4
         A   B   C   D
         10  20  30  40
-        """
-        )
+        """)
         # test first chunk
         hda1 = self.dataset_populator.new_dataset(history_id, content=contents, wait=True, file_type="tabular")
         dataset_id = hda1["id"]
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index b7fe5a2854f..ff2fcdb2a04 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -169,8 +169,7 @@ steps:
     @pytest.mark.require_new_history
     @skip_without_tool("multi_data_optional")
     def test_index_workflow_filter_implicit_jobs(self, history_id):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_datasets: collection
@@ -179,8 +178,7 @@ steps:
     tool_id: multi_data_optional
     in:
       input1: input_datasets
-"""
-        )
+""")
         hdca_id = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
         self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         inputs = {
diff --git a/lib/galaxy_test/api/test_landing.py b/lib/galaxy_test/api/test_landing.py
index 24f73af9c01..a9e4c12dd42 100644
--- a/lib/galaxy_test/api/test_landing.py
+++ b/lib/galaxy_test/api/test_landing.py
@@ -475,8 +475,7 @@ class TestLandingApi(ApiTestCase):
         """Test that executing a workflow from landing request preserves sample sheet metadata in output."""
         with self.dataset_populator.test_history() as history_id:
             # Create a simple workflow that maps cat1 over a collection input
-            workflow_id = self.workflow_populator.upload_yaml_workflow(
-                """
+            workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_collection:
@@ -487,8 +486,7 @@ steps:
     tool_id: cat1
     in:
       input1: input_collection
-"""
-            )
+""")
 
             # Create request state with sample sheet collection
             input_b64_1 = b64encode(b"sample1 data").decode("utf-8")
@@ -599,8 +597,7 @@ steps:
                 "sample2": [2, "treatment"],
             }
 
-            workflow_id = self.workflow_populator.upload_yaml_workflow(
-                """
+            workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_collection:
@@ -611,8 +608,7 @@ steps:
     tool_id: cat1
     in:
       input1: input_collection
-"""
-            )
+""")
 
             # Create paired elements (forward/reverse for each sample)
             forward_b64_1 = b64encode(b"sample1 forward data").decode("utf-8")
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index 974d7f61e16..68221a21847 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -834,8 +834,7 @@ class TestWorkflowsApi(BaseWorkflowsApiTestCase, ChangeDatatypeTests):
             assert initial_instance_download["name"] == original_name
 
     def test_workflow_run_input_extension_restriction_applied(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   tabular_input:
@@ -847,8 +846,7 @@ steps:
     tool_id: cat1
     in:
       input1: tabular_input
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             # Upload a txt file that should NOT be available for the tabular input
             self.dataset_populator.new_dataset(history_id, content="hello world", file_type="txt", wait=True)
@@ -951,8 +949,7 @@ steps:
         assert workflow_dict["license"] == "AAL"
 
     def test_update_name_for_workflow_with_subworkflows(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 label: old name
 inputs:
@@ -978,8 +975,7 @@ steps:
     tool_id: cat1
     in:
       input1: subworkflow/output
-"""
-        )
+""")
         self.workflow_populator.download_workflow(workflow_id)
         new_name = "my cool new name"
         data = {"name": new_name}
@@ -1007,8 +1003,7 @@ steps:
 
     @skip_without_tool("select_from_dataset_in_conditional")
     def test_workflow_run_form_with_broken_dataset(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   dataset: data
@@ -1024,8 +1019,7 @@ steps:
         inner_cond:
           inner_cond: single
           select_single: abc
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             self.dataset_populator.new_dataset(history_id, content="a", file_type="tabular", wait=True)
             workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
@@ -1033,8 +1027,7 @@ steps:
             assert workflow["steps"][1]["inputs"][0]["value"] == {"__class__": "ConnectedValue"}
 
     def test_refactor(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -1043,8 +1036,7 @@ steps:
     tool_id: cat
     in:
       input1: test_input
-"""
-        )
+""")
         actions = [
             {"action_type": "update_step_label", "step": {"order_index": 0}, "label": "new_label"},
         ]
@@ -1073,8 +1065,7 @@ steps:
         assert workflow_dict["steps"]["0"]["label"] == "new_label"
 
     def test_refactor_tool_state_upgrade(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs: {}
 steps:
@@ -1085,8 +1076,7 @@ steps:
       inttest: 1
       cond:
         bool_to_select: false
-"""
-        )
+""")
         actions = [{"action_type": "upgrade_all_steps"}]
         refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=True)
         refactor_response.raise_for_status()
@@ -1187,8 +1177,7 @@ steps:
             self._assert_user_has_workflow_with_name("imported: test_import_published_deprecated")
 
     def test_import_export_dynamic(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   - type: input
@@ -1216,8 +1205,7 @@ steps:
           $link: embed1/output1
 test_data:
   input1: "hello world"
-"""
-        )
+""")
         downloaded_workflow = self._download_workflow(workflow_id)
         # The _upload_yaml_workflow entry point uses an admin key, but if we try to
         # do the raw re-import as a regular user we expect a 403 error.
@@ -1263,8 +1251,7 @@ test_data:
             assert subworkflow_content_id != imported_subworkflow_content_id
 
     def test_subworkflow_inputs_optional_editor(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   nested_workflow:
@@ -1276,8 +1263,7 @@ steps:
       outputs:
         - outputSource: inner_input/output
       steps: []
-"""
-        )
+""")
         workflow_contents = self._download_workflow(workflow_id, style="editor")
         assert workflow_contents["steps"]["0"]["inputs"][0]["optional"]
 
@@ -1573,13 +1559,11 @@ steps:
 
     @skip_without_tool("output_filter_exception_1")
     def test_export_editor_filtered_outputs_exception_handling(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   - tool_id: output_filter_exception_1
-"""
-        )
+""")
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
         outputs = downloaded_workflow["steps"]["0"]["outputs"]
         assert len(outputs) == 2
@@ -1598,8 +1582,7 @@ steps:
 
     @skip_without_tool("collection_type_source")
     def test_export_editor_subworkflow_collection_type_source(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -1621,8 +1604,7 @@ steps:
             input_collect: inner_input
     in:
       inner_input: outer_input
-"""
-        )
+""")
         downloaded_workflow = self._download_workflow(workflow_id, style="editor")
         steps = downloaded_workflow["steps"]
         assert len(steps) == 2
@@ -1868,8 +1850,7 @@ steps:
             assert message["reason"] == "dataset_failed"
 
     def _run_multi_data_workflow(self, history_id, invalid_hash=False):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input:
@@ -1880,8 +1861,7 @@ steps:
     tool_id: multi_data_optional
     in:
       input1: input
-    """
-        )
+    """)
         input_b64_1 = base64.b64encode(b"1 2 3").decode("utf-8")
         deferred = False
         hashes_1 = [
@@ -1916,8 +1896,7 @@ steps:
     @skip_without_tool("collection_paired_default")
     def test_run_workflow_with_url_paired_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input:
@@ -1928,8 +1907,7 @@ steps:
     tool_id: collection_paired_default
     in:
       f1: input
-    """
-            )
+    """)
             forward_b64_1 = base64.b64encode(b"1 2 3").decode("utf-8")
             reverse_b64_2 = base64.b64encode(b"4 5 6").decode("utf-8")
             deferred = False
@@ -2002,8 +1980,7 @@ steps:
     @skip_without_tool("implicit_conversion_format_input")
     def test_run_workflow_from_url_with_implicit_conversion_on_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_fastq_gz: collection
@@ -2015,8 +1992,7 @@ steps:
     tool_id: implicit_conversion_format_input
     in:
       input1: input_fastq_gz
-    """
-            )
+    """)
             base64_url = self.dataset_populator.base64_url_for_test_file("1.fasta.gz")
             deferred = False
             inputs = {
@@ -2050,8 +2026,7 @@ steps:
     @skip_without_tool("implicit_conversion_format_input")
     def test_run_workflow_from_urls_with_implicit_conversion_on_collection(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_fastq_gz: File
@@ -2063,8 +2038,7 @@ steps:
     tool_id: implicit_conversion_format_input
     in:
       input1: input_fastq_gz
-    """
-            )
+    """)
             base64_url = self.dataset_populator.base64_url_for_test_file("1.fasta.gz")
             deferred = False
             inputs = {
@@ -2143,8 +2117,7 @@ steps:
     @skip_without_tool("job_properties")
     @skip_without_tool("identifier_multiple_in_conditional")
     def test_workflow_resume_from_failed_step(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   job_props:
@@ -2167,8 +2140,7 @@ steps:
     in:
       input1: identifier/output1
       queries_0|input2: identifier/output1
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             invocation_response = self.workflow_populator.invoke_workflow(workflow_id, history_id=history_id)
             invocation_id = invocation_response.json()["id"]
@@ -2200,8 +2172,7 @@ steps:
     @skip_without_tool("job_properties")
     @skip_without_tool("collection_creates_list")
     def test_workflow_resume_from_failed_step_with_hdca_input(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   job_props:
@@ -2217,8 +2188,7 @@ steps:
     tool_id: identifier_collection
     in:
       input1: list_in_list_out/list_output
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             invocation_id = self.__invoke_workflow(workflow_id, history_id=history_id)
             self.workflow_populator.wait_for_invocation_and_jobs(
@@ -2392,8 +2362,7 @@ test_data:
     @skip_without_tool("multi_data_optional")
     def test_workflow_list_list_multi_data_map_over(self):
         # Test that a list:list is reduced to list with a multiple="true" data input
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_datasets: collection
@@ -2402,8 +2371,7 @@ steps:
     tool_id: multi_data_optional
     in:
       input1: input_datasets
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             hdca_id = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
@@ -2450,8 +2418,7 @@ steps:
         # A more advanced output collection workflow, testing regression of
         # https://github.com/galaxyproject/galaxy/issues/776
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input_1: data
@@ -2467,8 +2434,7 @@ steps:
     in:
       queries_0|input: test_input_1
       queries2_0|input2: split_up/split_output
-"""
-            )
+""")
             hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
             hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t20.0\nsamp2\t40.0\n")
             hda3 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t60.0\n")
@@ -2490,8 +2456,7 @@ steps:
     def test_workflow_run_dynamic_output_collections_3(self):
         # Test a workflow that create a list:list:list followed by a mapping step.
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   text_input1: data
@@ -2514,8 +2479,7 @@ steps:
     tool_id: cat
     in:
       input1: split_up_2/split_output
-"""
-            )
+""")
             hda1 = self.dataset_populator.new_dataset(history_id, content="samp1\t10.0\nsamp2\t20.0\n")
             hda2 = self.dataset_populator.new_dataset(history_id, content="samp1\t30.0\nsamp2\t40.0\n")
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
@@ -5604,8 +5568,7 @@ test_data:
     def _deleted_inputs_workflow(self, purge):
         # We run a workflow on a collection with a deleted element.
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   input1:
@@ -5620,8 +5583,7 @@ steps:
     tool_id: cat
     in:
       input1: first_cat/out_file1
-"""
-            )
+""")
             DELETED = 0
             PAUSED_1 = 1
             PAUSED_2 = 2
@@ -5741,8 +5703,7 @@ input1:
 
     def test_run_subworkflow_with_optional_data_unspecified(self):
         with self.dataset_populator.test_history() as history_id:
-            subworkflow = yaml.safe_load(
-                """
+            subworkflow = yaml.safe_load("""
 class: GalaxyWorkflow
 inputs:
   required: data
@@ -5754,8 +5715,7 @@ test_data:
   required:
     value: 1.bed
     type: File
-"""
-            )
+""")
             subworkflow["steps"]["nested_workflow"]["run"] = yaml.safe_load(WORKFLOW_OPTIONAL_INPUT_DELAYED_SCHEDULING)
             self._run_workflow(
                 subworkflow,
@@ -6237,8 +6197,7 @@ input_collection:
             assert "null" in filter_content, f"Expected 'null' in filter output, got: {filter_content}"
 
     def test_conditional_flat_crossproduct_subworkflow(self):
-        parent = yaml.safe_load(
-            """
+        parent = yaml.safe_load("""
 class: GalaxyWorkflow
 inputs:
   collection_a: collection
@@ -6299,8 +6258,7 @@ test_data:
         content: fallbackC
       - identifier: fallbackD
         content: fallbackD
-"""
-        )
+""")
         parent["steps"]["subworkflow_step"]["run"] = yaml.safe_load(WORKFLOW_FLAT_CROSS_PRODUCT)
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow(
@@ -7809,8 +7767,7 @@ steps:
 
     @skip_without_tool("dbkey_filter_input")
     def test_value_restriction_with_data_meta_filter(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   select_text:
@@ -7821,8 +7778,7 @@ steps:
     tool_id: dbkey_filter_input
     in:
       index: select_text
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
         options = run_workflow["steps"][0]["inputs"][0]["options"]
@@ -7830,8 +7786,7 @@ steps:
 
     @skip_without_tool("filter_param_value")
     def test_value_restriction_with_filter_param_value(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   select_text:
@@ -7844,8 +7799,7 @@ steps:
       select1: "hg19_value"
     in:
       select3: select_text
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
         options = run_workflow["steps"][0]["inputs"][0]["options"]
@@ -7853,8 +7807,7 @@ steps:
         assert options[0] == ["hg19", "hg19_value", False]
 
     def test_value_restriction_with_select_and_text_param(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   select_text:
@@ -7869,8 +7822,7 @@ steps:
     tool_id: param_text_option
     in:
       text_param: select_text
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
         options = run_workflow["steps"][0]["inputs"][0]["options"]
@@ -7878,8 +7830,7 @@ steps:
         assert options[0] == ["Ex1", "--ex1", False]
 
     def test_value_restriction_with_select_from_subworkflow_input(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   Outer input parameter:
@@ -7903,8 +7854,7 @@ steps:
       in:
         select_ex:
           source: inner input parameter
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
         options = run_workflow["steps"][0]["inputs"][0]["options"]
@@ -8047,8 +7997,7 @@ steps:
     @skip_without_tool("validation_repeat")
     def test_parameter_substitution_validation_value_errors_0(self):
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   validation:
@@ -8056,8 +8005,7 @@ steps:
     state:
       r2:
         - text: "abd"
-"""
-            )
+""")
             workflow_request = dict(
                 history=f"hist_id={history_id}", parameters=dumps(dict(validation_repeat={"r2_0|text": ""}))
             )
@@ -8071,8 +8019,7 @@ steps:
         # Tests what the legacy run form submits
         with self.dataset_populator.test_history() as history_id:
             hdca = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()["outputs"][0]
-            workflow_id = self._upload_yaml_workflow(
-                """
+            workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   "0":
@@ -8081,8 +8028,7 @@ steps:
       cond:
         input1:
           __class__: RuntimeValue
-"""
-            )
+""")
             workflow_request = {
                 "history": f"hist_id={history_id}",
                 "parameters": dumps({"0": {"cond|input1": {"values": [{"id": hdca["id"], "src": "hdca"}]}}}),
@@ -8592,8 +8538,7 @@ steps: []
         assert invocation_steps[1]["state"] == "ok"
 
     def test_data_input_recovery_on_delayed_input(self):
-        self.workflow_populator.run_workflow(
-            """
+        self.workflow_populator.run_workflow("""
 class: GalaxyWorkflow
 inputs: {}
 outputs:
@@ -8628,8 +8573,7 @@ steps:
           in:
             input1: input_dataset
             when:
-              source: run_step"""
-        )
+              source: run_step""")
 
     def test_subworkflow_output_not_found_fails(self):
         # This test might start failing if we ever validate connections before attempting to schedule
@@ -9106,8 +9050,7 @@ class TestAdminWorkflowsApi(BaseWorkflowsApiTestCase):
     require_admin_user = True
 
     def test_import_export_dynamic_tools(self, history_id):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   - type: input
@@ -9135,8 +9078,7 @@ steps:
           $link: embed1/output1
 test_data:
   input1: "hello world"
-"""
-        )
+""")
         downloaded_workflow = self._download_workflow(workflow_id)
         response = self.workflow_populator.create_workflow_response(downloaded_workflow)
         workflow_id = response.json()["id"]
diff --git a/lib/galaxy_test/api/test_workflows_from_yaml.py b/lib/galaxy_test/api/test_workflows_from_yaml.py
index 8aaf98c964e..6f7cbdcfa32 100644
--- a/lib/galaxy_test/api/test_workflows_from_yaml.py
+++ b/lib/galaxy_test/api/test_workflows_from_yaml.py
@@ -208,8 +208,7 @@ $graph:
         assert content == "hello world\nhello world\nhello world\nhello world\n"
 
     def test_pause(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   test_input:
@@ -227,13 +226,11 @@ steps:
     tool_id: cat1
     in:
       input1: the_pause
-"""
-        )
+""")
         self.workflow_populator.dump_workflow(workflow_id)
 
     def test_implicit_connections(self):
-        workflow_id = self._upload_yaml_workflow(
-            """
+        workflow_id = self._upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -257,8 +254,7 @@ steps:
     state:
       input1:
         $link: test_input
-"""
-        )
+""")
         self.workflow_populator.dump_workflow(workflow_id)
 
     def test_conditional_ints(self, history_id):
diff --git a/lib/galaxy_test/driver/uses_shed.py b/lib/galaxy_test/driver/uses_shed.py
index 0b1165785f6..55b4fb1333d 100644
--- a/lib/galaxy_test/driver/uses_shed.py
+++ b/lib/galaxy_test/driver/uses_shed.py
@@ -22,11 +22,9 @@ CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 TOOL_SHEDS_CONF = os.path.join(SCRIPT_DIRECTORY, "tool_sheds_conf.xml")
 
-SHED_TOOL_CONF = string.Template(
-    """<?xml version="1.0"?>
+SHED_TOOL_CONF = string.Template("""<?xml version="1.0"?>
 <toolbox tool_path="$shed_tools_path">
-</toolbox>"""
-)
+</toolbox>""")
 
 SHED_DATA_MANAGER_CONF = """<?xml version="1.0"?>
 <data_managers>
diff --git a/lib/galaxy_test/selenium/test_custom_tools.py b/lib/galaxy_test/selenium/test_custom_tools.py
index a0ef8cc84da..4aed15638a2 100644
--- a/lib/galaxy_test/selenium/test_custom_tools.py
+++ b/lib/galaxy_test/selenium/test_custom_tools.py
@@ -88,16 +88,13 @@ inputs:
 type: data
 
 """
-        tool_yaml_three = (
-            """
+        tool_yaml_three = """
 outputs:
 - name: output1
   type: data
 format_source: datasets
 from_work_dir: output.txt
 """
-            ""
-        )
         # Try finding Monaco editor and replace skeleton content
         self.sleep_for(self.wait_types.UX_RENDER)  # Allow editor to initialize
         # Use the stable .monaco-editor container, not .view-line which gets re-rendered
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index 2bcfbe60ebb..fc9cdfa68d6 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -329,8 +329,7 @@ class TestWorkflowEditor(SeleniumTestCase, RunsWorkflows):
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_data_column_input_editing(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 steps:
   column_param_list:
@@ -338,8 +337,7 @@ steps:
     state:
       col: ["1","2","3"]
       col_names: ["a", "b", "c"]
-      """
-        )
+      """)
         editor = self.components.workflow_editor
         node = editor.node._(label="column_param_list")
         node.title.wait_for_and_click()
@@ -387,8 +385,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_non_data_connections(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs:
   input_int: integer
@@ -401,8 +398,7 @@ steps:
   cat1:
     # regression test, ensures connecting works in the presence of data input terminals
     tool_id: cat1
-"""
-        )
+""")
         self.screenshot("workflow_editor_parameter_connection_simple")
         self.assert_connected("input_int#output", "tool_exec#inttest")
 
@@ -473,16 +469,14 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_connecting_display_in_upload_false_connections(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 steps:
   step1:
     tool_id: test_sam_to_bam_conversions
   step2:
     tool_id: test_sam_to_bam_conversions
-        """
-        )
+        """)
 
         self.workflow_editor_connect("step1#qname_input_sorted_bam_output", "step2#input5")
         self.assert_connected("step1#qname_input_sorted_bam_output", "step2#input5")
@@ -809,8 +803,7 @@ steps:
         embedded_workflow = yaml.safe_load(WORKFLOW_WITH_OLD_TOOL_VERSION)
         # Create invalid tool state
         embedded_workflow["steps"]["mul_versions"]["state"]["inttest"] = "Invalid"
-        outer_workflow = yaml.safe_load(
-            """
+        outer_workflow = yaml.safe_load("""
 class: GalaxyWorkflow
 inputs:
   outer_input: data
@@ -819,8 +812,7 @@ steps:
     run: {}
     in:
       input1: outer_input
-        """
-        )
+        """)
         outer_workflow["steps"]["nested_workflow"]["run"] = embedded_workflow
         workflow_populator.upload_yaml_workflow(json.dumps(outer_workflow), exact_tools=True)
         self.workflow_index_open()
@@ -843,8 +835,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_change_datatype(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs: []
 steps:
@@ -854,8 +845,7 @@ steps:
     label: checksum
     in:
       input: create_2/out_file1
-"""
-        )
+""")
         editor = self.components.workflow_editor
         self.assert_connected("create_2#out_file1", "checksum#input")
         node = editor.node._(label="create_2")
@@ -881,8 +871,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_change_datatype_post_job_action_lost_regression(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs: []
 steps:
@@ -895,8 +884,7 @@ steps:
     label: metadata_bam
     in:
       input_bam: create_2/out_file1
-"""
-        )
+""")
         self.assert_connected("create_2#out_file1", "metadata_bam#input_bam")
         editor = self.components.workflow_editor
         node = editor.node._(label="create_2")
@@ -906,8 +894,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_change_datatype_in_subworkflow(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs: []
 steps:
@@ -926,8 +913,7 @@ steps:
             outputSource: create_2/out_file1
   metadata_bam:
     tool_id: metadata_bam
-"""
-        )
+""")
         editor = self.components.workflow_editor
         node = editor.node._(label="nested_workflow")
         node.wait_for_and_click()
@@ -941,8 +927,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_edit_subworkflow(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs: []
 steps:
@@ -953,8 +938,7 @@ steps:
         steps:
           - tool_id: create_2
             label: create_2
-"""
-        )
+""")
         editor = self.components.workflow_editor
         node = editor.node._(label="nested_workflow")
         node.wait_for_and_click()
@@ -1014,8 +998,7 @@ steps:
         workflow_populator = self.workflow_populator
         child_workflow_name = self._get_random_name()
         workflow_populator.upload_yaml_workflow(WORKFLOW_OPTIONAL_TRUE_INPUT_COLLECTION, name=child_workflow_name)
-        parent_workflow_id = workflow_populator.upload_yaml_workflow(
-            """class: GalaxyWorkflow
+        parent_workflow_id = workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
 inputs:
   input_collection:
     type: collection
@@ -1026,8 +1009,7 @@ steps:
     label: multiple_versions
     state:
       foo: bar
-        """
-        )
+        """)
         self.workflow_index_open()
         self.components.workflows.edit_button.wait_for_and_click()
         editor = self.components.workflow_editor
@@ -1170,8 +1152,7 @@ steps:
     @selenium_test
     def test_missing_tools(self):
         workflow_populator = self.workflow_populator
-        workflow_populator.upload_yaml_workflow(
-            """
+        workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   - id: input1
@@ -1180,8 +1161,7 @@ steps:
     label: first_cat
     state:
       foo: bar
-"""
-        )
+""")
         self.workflow_index_open()
         self.components.workflows.edit_button.wait_for_and_click()
         self.assert_modal_has_text("Tool is not installed")
@@ -1245,14 +1225,12 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_insert_input_handling(self):
-        self.open_in_workflow_editor(
-            """class: GalaxyWorkflow
+        self.open_in_workflow_editor("""class: GalaxyWorkflow
 inputs: []
 steps:
   build_list:
     tool_id: __BUILD_LIST__
-        """
-        )
+        """)
         editor = self.components.workflow_editor
         node = editor.node._(label="build_list")
         node.wait_for_and_click()
@@ -1338,8 +1316,7 @@ steps:
     @selenium_only("Not yet migrated to support Playwright backend")
     @selenium_test
     def test_map_over_output_indicator(self):
-        self.open_in_workflow_editor(
-            """
+        self.open_in_workflow_editor("""
 class: GalaxyWorkflow
 inputs:
   list:
@@ -1351,8 +1328,7 @@ inputs:
 steps:
   filter:
     tool_id: __FILTER_FROM_FILE__
-"""
-        )
+""")
         self.assert_node_output_is("filter#output_filtered", "any")
         self.workflow_editor_connect("list#output", "filter#input")
         self.assert_node_output_is("filter#output_filtered", "list")
diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py
index 31334e166ad..863689ce1c7 100644
--- a/lib/galaxy_test/selenium/test_workflow_run.py
+++ b/lib/galaxy_test/selenium/test_workflow_run.py
@@ -399,8 +399,7 @@ SRR5681005\tinput\t\t
     @selenium_test
     @managed_history
     def test_runtime_parameters_simple_optional(self):
-        self.workflow_run_open_workflow(
-            """
+        self.workflow_run_open_workflow("""
 class: GalaxyWorkflow
 inputs: {}
 steps:
@@ -408,8 +407,7 @@ steps:
     tool_id: expression_null_handling_integer
     runtime_inputs:
       - int_input
-"""
-        )
+""")
         self.tool_parameter_div("int_input")
         self._set_num_lines_to_3("int_input")
         self.screenshot("workflow_run_optional_runtime_parameters_modified")
@@ -473,8 +471,7 @@ steps:
     def test_step_parameter_inputs(self):
         self.perform_upload(self.get_filename("1.txt"))
         self.wait_for_history()
-        self.workflow_run_open_workflow(
-            """
+        self.workflow_run_open_workflow("""
 class: GalaxyWorkflow
 inputs:
   input_int: integer
@@ -486,8 +483,7 @@ steps:
     in:
       inttest: input_int
       files_0|file: input_data
-"""
-        )
+""")
         self.workflow_run_ensure_expanded()
         workflow_run = self.components.workflow_run
         input_div_element = workflow_run.input_div(label="input_int").wait_for_visible()
@@ -569,8 +565,7 @@ steps:
     @selenium_test
     @managed_history
     def test_execution_with_text_default_value_connected_to_restricted_select(self):
-        self.workflow_run_open_workflow(
-            """
+        self.workflow_run_open_workflow("""
 class: GalaxyWorkflow
 inputs:
   text_param:
@@ -584,8 +579,7 @@ steps:
     in:
       select_ex:
         source: text_param
-"""
-        )
+""")
         element = self.components.workflow_run.input_select_field(label="text_param").wait_for_present()
         assert element.text == "Ex2"
         self.workflow_run_submit()
@@ -634,8 +628,7 @@ steps:
     @selenium_test
     @managed_history
     def test_workflow_run_button_disabled_when_required_input_missing(self):
-        self.workflow_run_open_workflow(
-            """
+        self.workflow_run_open_workflow("""
 class: GalaxyWorkflow
 inputs:
   text_param:
@@ -646,8 +639,7 @@ inputs:
   collection_param:
     type: data_collection
 steps: {}
-"""
-        )
+""")
         workflow_run = self.components.workflow_run
         # None of the required parameters are present
         workflow_run.run_workflow_disabled.wait_for_present()
diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py
index 5c26eb70f10..b475d56a41c 100644
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -46,7 +46,7 @@ class ToolShedMetadataGenerator(BaseMetadataGenerator):
     """A MetadataGenerator building on ToolShed's app and repository constructs."""
 
     app: ToolShedApp
-    repository: Optional[Repository]  # type:ignore[assignment]
+    repository: Optional[Repository]  # type: ignore[assignment]
 
     # why is mypy making me re-annotate these things from the base class, it didn't
     # when they were in the same file
diff --git a/lib/tool_shed/test/base/playwrightbrowser.py b/lib/tool_shed/test/base/playwrightbrowser.py
index 62c55917eee..e4726cf7b92 100644
--- a/lib/tool_shed/test/base/playwrightbrowser.py
+++ b/lib/tool_shed/test/base/playwrightbrowser.py
@@ -131,7 +131,7 @@ class PlaywrightShedBrowser(ShedBrowser):
         input_s = form.locator(f"select[name='{control_name}']")
         if input_i.count():
             if control_name in ["redirect"]:
-                input_i.input_value = value  # type:ignore[assignment, unused-ignore]
+                input_i.input_value = value  # type: ignore[assignment, unused-ignore]
             else:
                 if isinstance(value, bool):
                     if value and not input_i.is_checked():
@@ -141,9 +141,9 @@ class PlaywrightShedBrowser(ShedBrowser):
                 else:
                     input_i.fill(value)
         if input_t.count():
-            input_t.fill(value)  # type:ignore[arg-type, unused-ignore]
+            input_t.fill(value)  # type: ignore[arg-type, unused-ignore]
         if input_s.count():
-            input_s.select_option(value)  # type:ignore[arg-type, unused-ignore]
+            input_s.select_option(value)  # type: ignore[arg-type, unused-ignore]
 
     def edit_repository_categories(self, categories_to_add: list[str], categories_to_remove: list[str]) -> None:
         multi_select = "form[name='categories'] select[name='category_id']"
diff --git a/lib/tool_shed/test/base/twillbrowser.py b/lib/tool_shed/test/base/twillbrowser.py
index 2630c7b6145..6b294914423 100644
--- a/lib/tool_shed/test/base/twillbrowser.py
+++ b/lib/tool_shed/test/base/twillbrowser.py
@@ -1,7 +1,7 @@
 import tempfile
 
 import twill.commands as tc
-from twill.browser import FormElement  # type:ignore[attr-defined, unused-ignore]
+from twill.browser import FormElement  # type: ignore[attr-defined, unused-ignore]
 
 from galaxy.util import smart_str
 from .browser import (
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index bf6bfd3bc5f..6cd16a055bb 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -1295,7 +1295,7 @@ class ShedTwillTestCase(ShedApiTestCase):
             # assert original_information[input_elem_name]
             for input_elem_name in ["repo_name", "description", "long_description"]:
                 self._browser.fill_form_value(
-                    "edit_repository", input_elem_name, original_information[input_elem_name]  # type:ignore[arg-type]
+                    "edit_repository", input_elem_name, original_information[input_elem_name]  # type: ignore[arg-type]
                 )
                 strings_displayed.append(self.escape_html(original_information[input_elem_name]))
             self._browser.submit_form_with_name("edit_repository", "edit_repository_button")
@@ -2046,7 +2046,7 @@ class ShedTwillTestCase(ShedApiTestCase):
         assert "tools" in installed_repository.metadata_, f"No valid tools were defined in {installed_repository.name}."
         tools = installed_repository.metadata_["tools"]
         found_it = False
-        for tool in tools:  # type:ignore[attr-defined]
+        for tool in tools:  # type: ignore[attr-defined]
             if "id" not in tool:
                 continue
             if tool["id"] == tool_id:
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index d1629622c2b..d739ac568d1 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -283,7 +283,7 @@ def handle_email_alerts(
                     email_alerts.append(user.email)
         else:
             subject = f"Galaxy tool shed update alert for repository named {str(repository.name)}"
-            email_alerts = json.loads(repository.email_alerts)  # type:ignore[arg-type]
+            email_alerts = json.loads(repository.email_alerts)  # type: ignore[arg-type]
         for email in email_alerts:
             to = email.strip()
             # Send it
diff --git a/scripts/api/copy_hda_to_library_folder.py b/scripts/api/copy_hda_to_library_folder.py
index e997c330e6f..b491aa9928a 100755
--- a/scripts/api/copy_hda_to_library_folder.py
+++ b/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:
diff --git a/scripts/api/create.py b/scripts/api/create.py
index 378d3cb52fa..209f688ca62 100644
--- a/scripts/api/create.py
+++ b/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
diff --git a/scripts/api/data_manager_example_execute.py b/scripts/api/data_manager_example_execute.py
index 3bac2833da9..df55c4ee933 100644
--- a/scripts/api/data_manager_example_execute.py
+++ b/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.")
diff --git a/scripts/api/delete.py b/scripts/api/delete.py
index 5780f3f723d..ec1f9efc478 100644
--- a/scripts/api/delete.py
+++ b/scripts/api/delete.py
@@ -4,6 +4,7 @@ Generic DELETE/delete script
 
 usage: delete.py key url
 """
+
 import sys
 
 from common import delete
diff --git a/scripts/api/library_upload_dir.py b/scripts/api/library_upload_dir.py
index a85a1b550a7..0b8af9a9898 100644
--- a/scripts/api/library_upload_dir.py
+++ b/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
diff --git a/scripts/api/reset_metadata_on_installed_repositories.py b/scripts/api/reset_metadata_on_installed_repositories.py
index 69cdd09d8cb..6dbe9641ba9 100644
--- a/scripts/api/reset_metadata_on_installed_repositories.py
+++ b/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
diff --git a/scripts/api/update.py b/scripts/api/update.py
index cd21e139298..a7333350c04 100644
--- a/scripts/api/update.py
+++ b/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
diff --git a/scripts/cwl_conformance_to_test_cases.py b/scripts/cwl_conformance_to_test_cases.py
index 1a440c00ab5..4ee3f2ff15e 100644
--- a/scripts/cwl_conformance_to_test_cases.py
+++ b/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": [
diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py
index a08116b94a4..015d449d1cb 100755
--- a/scripts/external_chown_script.py
+++ b/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)))
diff --git a/scripts/galaxy_main.py b/scripts/galaxy_main.py
index 855e1f81253..e1aedda216d 100755
--- a/scripts/galaxy_main.py
+++ b/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
diff --git a/scripts/grt/export.py b/scripts/grt/export.py
index 795b1717882..311eda2c1cb 100644
--- a/scripts/grt/export.py
+++ b/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
diff --git a/scripts/grt/upload.py b/scripts/grt/upload.py
index 5f227b99cec..50d86754132 100644
--- a/scripts/grt/upload.py
+++ b/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
diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py
index cf891e081ac..10c82eab553 100644
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/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(",")]
diff --git a/scripts/release-diff.py b/scripts/release-diff.py
index 10e69a620af..1c44e69a7af 100644
--- a/scripts/release-diff.py
+++ b/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)
 
diff --git a/scripts/secret_decoder_ring.py b/scripts/secret_decoder_ring.py
index 5bb09a330b1..a0aff6ea60e 100644
--- a/scripts/secret_decoder_ring.py
+++ b/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
diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py
index 993122c7713..706b4a69e8a 100644
--- a/scripts/tool_shed/deprecate_repositories_without_metadata.py
+++ b/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:
diff --git a/scripts/tools/re_escape_output.py b/scripts/tools/re_escape_output.py
index 0ec3ee1e1ed..3240602452b 100644
--- a/scripts/tools/re_escape_output.py
+++ b/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")
diff --git a/test/integration/objectstore/_base.py b/test/integration/objectstore/_base.py
index df94dbb00a5..76a77058501 100644
--- a/test/integration/objectstore/_base.py
+++ b/test/integration/objectstore/_base.py
@@ -22,8 +22,7 @@ OBJECT_STORE_RUCIO_USERNAME = os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_RU
 OBJECT_STORE_RUCIO_RSE_NAME = "TEST"
 OBJECT_STORE_RUCIO_ACCESS = os.environ.get("GALAXY_INTEGRATION_OBJECT_STORE_RUCIO_ACCESS", "rucio")
 
-OBJECT_STORE_CONFIG = string.Template(
-    """
+OBJECT_STORE_CONFIG = string.Template("""
 <object_store type="hierarchical" id="primary">
     <backends>
         <object_store id="swifty" type="generic_s3" weight="1" order="0">
@@ -36,10 +35,8 @@ OBJECT_STORE_CONFIG = string.Template(
         </object_store>
     </backends>
 </object_store>
-"""
-)
-RUCIO_OBJECT_STORE_CONFIG = string.Template(
-    """
+""")
+RUCIO_OBJECT_STORE_CONFIG = string.Template("""
     type: rucio
     upload_rse_name: ${rucio_rse}
     upload_scheme: file
@@ -59,10 +56,8 @@ RUCIO_OBJECT_STORE_CONFIG = string.Template(
       path: ${temp_directory}/object_store_cache
       size: 1000
       cache_updated_data: ${cache_updated_data}
-"""
-)
-AZURE_OBJECT_STORE_CONFIG = string.Template(
-    """
+""")
+AZURE_OBJECT_STORE_CONFIG = string.Template("""
 type: distributed
 backends:
 - type: azure_blob
@@ -99,14 +94,12 @@ backends:
     path: "${temp_directory}/database/job_working_directory_azure_2"
   - type: temp
     path: "${temp_directory}/database/tmp_azure_2"
-"""
-)
+""")
 
 # Onedata setup for the test is done according to this documentation:
 # https://onedata.org/#/home/documentation/topic/stable/demo-mode
 ONEDATA_DEMO_SPACE_NAME = "demo-space"
-ONEDATA_OBJECT_STORE_CONFIG = string.Template(
-    """
+ONEDATA_OBJECT_STORE_CONFIG = string.Template("""
 <object_store type="onedata">
     <auth access_token="${access_token}" />
     <connection onezone_domain="${onezone_domain}" disable_tls_certificate_validation="True"/>
@@ -115,8 +108,7 @@ ONEDATA_OBJECT_STORE_CONFIG = string.Template(
     <extra_dir type="job_work" path="${temp_directory}/job_working_directory_onedata"/>
     <extra_dir type="temp" path="${temp_directory}/tmp_onedata"/>
 </object_store>
-"""
-)
+""")
 
 
 def wait_rucio_ready(container_name):
diff --git a/test/integration/objectstore/test_changing_objectstore.py b/test/integration/objectstore/test_changing_objectstore.py
index a0f63f63d7c..62e8d80b6ce 100644
--- a/test/integration/objectstore/test_changing_objectstore.py
+++ b/test/integration/objectstore/test_changing_objectstore.py
@@ -4,8 +4,7 @@ import string
 
 from ._base import BaseObjectStoreIntegrationTestCase
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="default" allow_selection="true" type="disk" weight="1" device="tmp_disk" name="Default Store 1">
@@ -27,8 +26,7 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
diff --git a/test/integration/objectstore/test_jobs.py b/test/integration/objectstore/test_jobs.py
index 3d1bab41e37..845893ff046 100644
--- a/test/integration/objectstore/test_jobs.py
+++ b/test/integration/objectstore/test_jobs.py
@@ -13,8 +13,7 @@ from ._base import (
 )
 from .test_selection_with_resource_parameters import DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE
 
-HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>
         <object_store type="distributed" id="primary" order="0">
@@ -38,8 +37,7 @@ HIERARCHICAL_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </object_store>
     </backends>
 </object_store>
-"""
-)
+""")
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
diff --git a/test/integration/objectstore/test_mixed_store_by.py b/test/integration/objectstore/test_mixed_store_by.py
index ccabc6afc2d..f100376f197 100644
--- a/test/integration/objectstore/test_mixed_store_by.py
+++ b/test/integration/objectstore/test_mixed_store_by.py
@@ -10,8 +10,7 @@ from ._base import (
     files_count,
 )
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="files1" type="disk" weight="1" store_by="uuid">
@@ -26,8 +25,7 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
diff --git a/test/integration/objectstore/test_objectstore_datatype_upload.py b/test/integration/objectstore/test_objectstore_datatype_upload.py
index a383e43edaa..96abef84c51 100644
--- a/test/integration/objectstore/test_objectstore_datatype_upload.py
+++ b/test/integration/objectstore/test_objectstore_datatype_upload.py
@@ -38,8 +38,7 @@ IRODS_OBJECT_STORE_ZONE = os.environ.get("GALAXY_INTEGRATION_IRODS_OBJECT_STORE_
 # Run test for only the first 10 test files
 TEST_CASES = dict(list(TEST_CASES.items())[0:10])
 SINGLE_TEST_CASE = dict(list(TEST_CASES.items())[0:1])
-DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template(
-    """
+DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template("""
 <object_store type="distributed">
     <backends>
         <backend id="files1" type="disk" weight="1">
@@ -54,10 +53,8 @@ DISTRIBUTED_OBJECT_STORE_CONFIG = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
-DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template(
-    """
+""")
+DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template("""
 <object_store type="distributed">
     <backends>
         <backend id="files1" type="disk" weight="1">
@@ -76,10 +73,8 @@ DISTRIBUTED_IRODS_OBJECT_STORE_CONFIG = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
-IRODS_OBJECT_STORE_CONFIG = string.Template(
-    """<object_store type="irods">
+""")
+IRODS_OBJECT_STORE_CONFIG = string.Template("""<object_store type="irods">
     <auth username="${username}" password="${password}"/>
     <resource name="${resource}"/>
     <zone name="${zone}"/>
@@ -88,8 +83,7 @@ IRODS_OBJECT_STORE_CONFIG = string.Template(
     <extra_dir type="job_work" path="${temp_directory}/job_working_directory_irods"/>
     <extra_dir type="temp" path="${temp_directory}/tmp_irods"/>
 </object_store>
-"""
-)
+""")
 
 
 def check_container_active(container_name):
diff --git a/test/integration/objectstore/test_private_handling.py b/test/integration/objectstore/test_private_handling.py
index 66ec63f0671..37d5e088696 100644
--- a/test/integration/objectstore/test_private_handling.py
+++ b/test/integration/objectstore/test_private_handling.py
@@ -5,15 +5,13 @@ import string
 from galaxy_test.base import api_asserts
 from ._base import BaseObjectStoreIntegrationTestCase
 
-PRIVATE_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+PRIVATE_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="disk" id="primary" private="true">
     <files_dir path="${temp_directory}/files1"/>
     <extra_dir type="temp" path="${temp_directory}/tmp1"/>
     <extra_dir type="job_work" path="${temp_directory}/job_working_directory1"/>
 </object_store>
-"""
-)
+""")
 
 TEST_INPUT_FILES_CONTENT = "1 2 3"
 
diff --git a/test/integration/objectstore/test_selection_with_resource_parameters.py b/test/integration/objectstore/test_selection_with_resource_parameters.py
index 19550075b31..4bbbf957bf4 100644
--- a/test/integration/objectstore/test_selection_with_resource_parameters.py
+++ b/test/integration/objectstore/test_selection_with_resource_parameters.py
@@ -19,8 +19,7 @@ SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_conf.xml")
 JOB_RESOURCE_PARAMETERS_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_resource_parameters_conf.xml")
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="default" type="disk" weight="1" name="Default Store">
@@ -48,8 +47,7 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 
 class TestObjectStoreSelectionWithResourceParameterIntegration(BaseObjectStoreIntegrationTestCase):
diff --git a/test/integration/objectstore/test_selection_with_user_preferred_object_store.py b/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
index 9d64ada0eff..145a1c63412 100644
--- a/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
+++ b/test/integration/objectstore/test_selection_with_user_preferred_object_store.py
@@ -20,8 +20,7 @@ from ._base import BaseObjectStoreIntegrationTestCase
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 
-DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="default" allow_selection="true" type="disk" weight="1" name="Default Store">
@@ -49,8 +48,7 @@ DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 
 TEST_WORKFLOW = """
diff --git a/test/integration/test_cli_runners.py b/test/integration/test_cli_runners.py
index 4cdd5177c24..6e9548f8b6c 100644
--- a/test/integration/test_cli_runners.py
+++ b/test/integration/test_cli_runners.py
@@ -68,8 +68,7 @@ def stop_ssh_docker(container_name, remote_connection):
 
 
 def cli_job_config(remote_connection, shell_plugin="ParamikoShell", job_plugin="Slurm"):
-    job_conf_template = string.Template(
-        """<job_conf>
+    job_conf_template = string.Template("""<job_conf>
     <plugins>
         <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="1"/>
     </plugins>
@@ -87,8 +86,7 @@ def cli_job_config(remote_connection, shell_plugin="ParamikoShell", job_plugin="
         </destination>
     </destinations>
 </job_conf>
-"""
-    )
+""")
     job_conf_str = job_conf_template.substitute(
         shell_plugin=shell_plugin, job_plugin=job_plugin, **remote_connection._asdict()
     )
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 15fbe486eac..913821bcba5 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -251,15 +251,13 @@ class TestMappingContainerResolver(IntegrationTestCase):
         disable_dependency_resolution(config)
         container_resolvers_config_path = os.path.join(cls.jobs_directory, "container_resolvers.yml")
         with open(container_resolvers_config_path, "w") as f:
-            f.write(
-                """
+            f.write("""
 - type: mapping
   mappings:
     - container_type: docker
       tool_id: mulled_example_broken_no_requirements
       identifier: 'quay.io/biocontainers/bwa:0.7.15--0'
-"""
-            )
+""")
         config["container_resolvers_config_file"] = container_resolvers_config_path
 
     @classmethod
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
index 43507c45545..0b9dbbe119f 100644
--- a/test/integration/test_kubernetes_runner.py
+++ b/test/integration/test_kubernetes_runner.py
@@ -46,8 +46,7 @@ class KubeSetupConfigTuple(Config):
 
 
 def persistent_volume(path: str, persistent_volume_name: str) -> KubeSetupConfigTuple:
-    volume_yaml = string.Template(
-        """
+    volume_yaml = string.Template("""
 kind: PersistentVolume
 apiVersion: v1
 metadata:
@@ -71,16 +70,14 @@ spec:
           operator: NotIn
           values:
             - 'i-do-not-exist'
-    """
-    ).substitute(path=path, persistent_volume_name=persistent_volume_name)
+    """).substitute(path=path, persistent_volume_name=persistent_volume_name)
     with tempfile.NamedTemporaryFile(suffix="_persistent_volume.yml", mode="w", delete=False) as volume:
         volume.write(volume_yaml)
     return KubeSetupConfigTuple(path=volume.name)
 
 
 def persistent_volume_claim(persistent_volume_name: str, persistent_volum_claim_name: str) -> KubeSetupConfigTuple:
-    peristent_volume_claim_yaml = string.Template(
-        """
+    peristent_volume_claim_yaml = string.Template("""
 kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
@@ -93,18 +90,14 @@ spec:
     requests:
       storage: 2Gi
   storageClassName: manual
-"""
-    ).substitute(
-        persistent_volume_name=persistent_volume_name, persistent_volume_claim_name=persistent_volum_claim_name
-    )
+""").substitute(persistent_volume_name=persistent_volume_name, persistent_volume_claim_name=persistent_volum_claim_name)
     with tempfile.NamedTemporaryFile(suffix="_persistent_volume_claim.yml", mode="w", delete=False) as volume_claim:
         volume_claim.write(peristent_volume_claim_yaml)
     return KubeSetupConfigTuple(path=volume_claim.name)
 
 
 def job_config(jobs_directory: str) -> Config:
-    job_conf_template = string.Template(
-        """<job_conf>
+    job_conf_template = string.Template("""<job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
         <plugin id="k8s" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
@@ -144,8 +137,7 @@ def job_config(jobs_directory: str) -> Config:
         <tool id="create_2" destination="k8s_destination_walltime_short"/>
     </tools>
 </job_conf>
-"""
-    )
+""")
     job_conf_str = job_conf_template.substitute(
         jobs_directory=jobs_directory,
         tool_directory=TOOL_DIR,
diff --git a/test/integration/test_page_revision_json_encoding.py b/test/integration/test_page_revision_json_encoding.py
index 596291e9062..9a3f13ef7c0 100644
--- a/test/integration/test_page_revision_json_encoding.py
+++ b/test/integration/test_page_revision_json_encoding.py
@@ -51,9 +51,7 @@ class TestPageJsonEncodingIntegration(integration_util.IntegrationTestCase):
             title="MY PAGE",
             content="""```galaxy
 history_dataset_display(history_dataset_id={})
-```""".format(
-                dataset["id"]
-            ),
+```""".format(dataset["id"]),
             content_format="markdown",
         )
         page_response = self._post("pages", request, json=True)
@@ -61,12 +59,9 @@ history_dataset_display(history_dataset_id={})
         sa_session = self._app.model.session
         page_revision = sa_session.scalars(select(model.PageRevision).filter_by(content_format="markdown")).all()[0]
         assert page_revision.content is not None
-        assert (
-            """```galaxy
+        assert """```galaxy
 history_dataset_display(history_dataset_id=1)
-```"""
-            in page_revision.content
-        ), page_revision.content
+```""" in page_revision.content, page_revision.content
         assert (
             f"""::: history_dataset_display history_dataset_id={dataset_id}""" not in page_revision.content
         ), page_revision.content
@@ -74,15 +69,9 @@ history_dataset_display(history_dataset_id=1)
         show_page_response = self._get("pages/{}".format(page_response.json()["id"]))
         api_asserts.assert_status_code_is_ok(show_page_response)
         content = show_page_response.json()["content"]
-        assert (
-            """```galaxy
+        assert """```galaxy
 history_dataset_display(history_dataset_id=1)
-```"""
-            not in content
-        ), content
-        assert (
-            f"""```galaxy
+```""" not in content, content
+        assert f"""```galaxy
 history_dataset_display(history_dataset_id={dataset_id})
-```"""
-            in content
-        ), content
+```""" in content, content
diff --git a/test/integration/test_recalculate_user_disk_usage.py b/test/integration/test_recalculate_user_disk_usage.py
index c23d12c7775..806fc8992da 100644
--- a/test/integration/test_recalculate_user_disk_usage.py
+++ b/test/integration/test_recalculate_user_disk_usage.py
@@ -6,8 +6,7 @@ from galaxy_test.driver.integration_util import IntegrationTestCase
 from .objectstore._base import BaseObjectStoreIntegrationTestCase
 from .objectstore.test_selection_with_resource_parameters import DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE
 
-SIMPLE_DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """<?xml version="1.0"?>
+SIMPLE_DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="distributed" id="primary" order="0">
     <backends>
         <backend id="default" type="disk" weight="1" name="Default Store">
@@ -23,8 +22,7 @@ SIMPLE_DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 
 class RecalculateDiskUsage:
diff --git a/test/integration/test_user_defined_tool_job_conf.py b/test/integration/test_user_defined_tool_job_conf.py
index 3794eeb0aab..19c5423c786 100644
--- a/test/integration/test_user_defined_tool_job_conf.py
+++ b/test/integration/test_user_defined_tool_job_conf.py
@@ -15,8 +15,7 @@ from galaxy_test.driver import integration_util
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
 EMBEDDED_PULSAR_TPV_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_tpv_job_conf.yml")
-TOOL_WITH_RESOURCE_SPECIFICATION = yaml.safe_load(
-    """class: GalaxyUserTool
+TOOL_WITH_RESOURCE_SPECIFICATION = yaml.safe_load("""class: GalaxyUserTool
 id: resource_requirement
 version: "0.1"
 name: resource_requirement
@@ -32,8 +31,7 @@ outputs:
     type: data
     format: txt
     from_work_dir: galaxy_cores.txt
-"""
-)
+""")
 
 
 class TestUserDefinedToolRecommendedJobSetup(integration_util.IntegrationTestCase, TestsTools):
diff --git a/test/integration/test_workflow_handler_configuration.py b/test/integration/test_workflow_handler_configuration.py
index ed8df0937e0..11e3db488d7 100644
--- a/test/integration/test_workflow_handler_configuration.py
+++ b/test/integration/test_workflow_handler_configuration.py
@@ -17,8 +17,7 @@ from galaxy_test.driver import integration_util
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 WORKFLOW_HANDLER_CONFIGURATION_JOB_CONF = os.path.join(SCRIPT_DIRECTORY, "workflow_handler_configuration_job_conf.xml")
 
-WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template(
-    """
+WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template("""
 <job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
@@ -42,11 +41,9 @@ WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template(
         </destination>
     </destinations>
 </job_conf>
-"""
-)
+""")
 
-POOL_JOB_CONFIG_TEMPLATE = string.Template(
-    """<job_conf>
+POOL_JOB_CONFIG_TEMPLATE = string.Template("""<job_conf>
     <plugins>
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
     </plugins>
@@ -57,11 +54,9 @@ POOL_JOB_CONFIG_TEMPLATE = string.Template(
         </destination>
     </destinations>
 </job_conf>
-"""
-)
+""")
 
-WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template(
-    """
+WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template("""
 <workflow_schedulers default="core">
   <core id="core" />
   <handlers default="workflow_handlers" $assign_with>
@@ -69,8 +64,7 @@ WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template(
     <handler id="work2" tags="workflow_handlers" />
   </handlers>
 </workflow_schedulers>
-"""
-)
+""")
 JOB_HANDLER_PATTERN = re.compile(r"handler\d")
 WORKFLOW_SCHEDULER_HANDLER_PATTERN = re.compile(r"work\d")
 
diff --git a/test/integration/test_workflow_invocation.py b/test/integration/test_workflow_invocation.py
index 3ef39b06779..b73fbcf9a94 100644
--- a/test/integration/test_workflow_invocation.py
+++ b/test/integration/test_workflow_invocation.py
@@ -140,8 +140,7 @@ test_data:
     def test_run_workflow_with_missing_tool(self):
         self.install_repository("iuc", "compose_text_param", "feb3acba1e0a")  # 0.1.0
         with self.dataset_populator.test_history() as history_id:
-            workflow_id = self.workflow_populator.upload_yaml_workflow(
-                """
+            workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   nonexistent:
@@ -152,8 +151,7 @@ steps:
     tool_id: compose_text_param
     tool_version: "0.0.1"
     label: compose_text_param
-"""
-            )
+""")
             # should fail and return both tool ids since version 0.0.1 of compose_text_param does not exist
             invocation_response = self.workflow_populator.invoke_workflow(
                 workflow_id, history_id=history_id, request={"require_exact_tool_versions": True}
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index 7d5a4da15ee..89e39edcda5 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -294,8 +294,7 @@ class TestWorkflowRefactoringIntegration(integration_util.IntegrationTestCase, U
         # test parameters used in PJA without being used in tool state.
         # These will work fine with the simplified workflow UI, but should probably
         # be formalized and assigned a unique label and informative annotation.
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -307,8 +306,7 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-"""
-        )
+""")
         actions: ActionsJson = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param"},
         ]
@@ -317,8 +315,7 @@ steps:
 
     def test_refactoring_legacy_parameters_without_tool_state_dry_run(self):
         # same as above but dry run...
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -330,8 +327,7 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-"""
-        )
+""")
         actions: ActionsJson = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param"},
         ]
@@ -343,8 +339,7 @@ steps:
 
     def test_refactoring_legacy_parameters_without_tool_state_relabel(self):
         # same thing as above, but apply relabeling and ensure PJA gets updated.
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   test_input: data
@@ -356,8 +351,7 @@ steps:
     outputs:
       out_file1:
         rename: "${pja_only_param} name"
-"""
-        )
+""")
         actions: ActionsJson = [
             {"action_type": "extract_untyped_parameter", "name": "pja_only_param", "label": "new_label"},
         ]
@@ -511,8 +505,7 @@ steps:
         assert message.input_name == "num_lines"
 
     def test_tool_version_upgrade_no_state_change(self):
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   the_step:
@@ -520,8 +513,7 @@ steps:
     tool_version: '0.1'
     state:
       inttest: 0
-"""
-        )
+""")
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
         actions: ActionsJson = [
             {"action_type": "upgrade_tool", "step": {"label": "the_step"}},
@@ -535,8 +527,7 @@ steps:
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.2"
 
     def test_tool_version_upgrade_keeps_when_expression(self):
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 inputs:
   the_bool:
@@ -550,8 +541,7 @@ steps:
     state:
       inttest: 0
     when: $(inputs.when)
-"""
-        )
+""")
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
         actions: ActionsJson = [
             {"action_type": "upgrade_tool", "step": {"label": "the_step"}},
@@ -564,8 +554,7 @@ steps:
         assert step.when_expression
 
     def test_tool_version_upgrade_state_added(self):
-        self.workflow_populator.upload_yaml_workflow(
-            """
+        self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   the_step:
@@ -573,8 +562,7 @@ steps:
     tool_version: '0.1'
     state:
       inttest: 0
-"""
-        )
+""")
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
         actions: ActionsJson = [
             {"action_type": "upgrade_tool", "step": {"label": "the_step"}, "tool_version": "0.2"},
diff --git a/test/integration/test_workflow_scheduling_options.py b/test/integration/test_workflow_scheduling_options.py
index c1757067cc7..b769dba1dcf 100644
--- a/test/integration/test_workflow_scheduling_options.py
+++ b/test/integration/test_workflow_scheduling_options.py
@@ -62,8 +62,7 @@ class TestMaximumWorkflowJobsPerSchedulingIteration(integration_util.Integration
         config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
 
     def test_collection_explicit_and_implicit(self):
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""
 class: GalaxyWorkflow
 steps:
   - type: input_collection
@@ -79,8 +78,7 @@ steps:
     state:
       input1:
         $link: 2/out1
-"""
-        )
+""")
         with self.dataset_populator.test_history() as history_id:
             fetch_response = self.dataset_collection_populator.create_list_in_history(
                 history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]
diff --git a/test/integration/test_workflow_tasks.py b/test/integration/test_workflow_tasks.py
index 7014845fff0..5231cae6965 100644
--- a/test/integration/test_workflow_tasks.py
+++ b/test/integration/test_workflow_tasks.py
@@ -183,8 +183,7 @@ input_data:
             self.dataset_collection_populator.create_list_in_history(history_id=history_id, wait=True).json()
             new_history = self.dataset_populator.copy_history(history_id=history_id).json()
             copied_collection = self.dataset_populator.get_history_collection_details(new_history["id"])
-            workflow_id = self.workflow_populator.upload_yaml_workflow(
-                """class: GalaxyWorkflow
+            workflow_id = self.workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
 inputs:
   input:
     type: collection
@@ -198,8 +197,7 @@ steps:
 outputs:
   extracted_dataset:
     outputSource: extract_dataset/output
-"""
-            )
+""")
             inputs = {"input": {"src": "hdca", "id": copied_collection["id"]}}
             workflow_request = {"history": f"hist_id={new_history['id']}", "inputs_by": "name", "inputs": inputs}
             invocation = self.workflow_populator.invoke_workflow_raw(
diff --git a/test/integration_selenium/test_objectstore_expiration.py b/test/integration_selenium/test_objectstore_expiration.py
index 2b2f9e15651..a5b91ff911b 100644
--- a/test/integration_selenium/test_objectstore_expiration.py
+++ b/test/integration_selenium/test_objectstore_expiration.py
@@ -17,8 +17,7 @@ if TYPE_CHECKING:
         SeleniumSessionDatasetPopulator,
     )
 
-OBJECT_STORES_CONFIG = string.Template(
-    """
+OBJECT_STORES_CONFIG = string.Template("""
 type: distributed
 backends:
   - id: default
@@ -58,8 +57,7 @@ backends:
     - type: job_work
       path: "${temp_directory}/job_working_directory2"
     object_expires_after_days: ${mid_term_expiration_days}
-"""
-)
+""")
 
 AvailableObjectStoreIDs = Literal["default", "short_term", "mid_term"]
 
diff --git a/test/integration_selenium/test_objectstore_selection.py b/test/integration_selenium/test_objectstore_selection.py
index aa7f28b0118..678420226d8 100644
--- a/test/integration_selenium/test_objectstore_selection.py
+++ b/test/integration_selenium/test_objectstore_selection.py
@@ -12,8 +12,7 @@ if TYPE_CHECKING:
     from galaxy_test.selenium.framework import SeleniumSessionDatasetPopulator
 
 
-MSI_EXAMPLE_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
-    """
+MSI_EXAMPLE_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""
 <object_store type="distributed">
     <backends>
         <backend id="high_performance" allow_selection="true" type="disk" weight="1" name="High Performance Storage">
@@ -78,8 +77,7 @@ More information about MSI Storage can be found [here](https://www.msi.umn.edu/c
         </backend>
     </backends>
 </object_store>
-"""
-)
+""")
 
 
 class TestObjectStoreSelectionSeleniumIntegration(SeleniumIntegrationTestCase, ConfiguresObjectStores):
diff --git a/test/integration_selenium/test_workflow_repository_tool_update.py b/test/integration_selenium/test_workflow_repository_tool_update.py
index b81f6935beb..2f92ec56873 100644
--- a/test/integration_selenium/test_workflow_repository_tool_update.py
+++ b/test/integration_selenium/test_workflow_repository_tool_update.py
@@ -55,15 +55,13 @@ steps:
     def test_tool_shed_unmatched_version_upgrade(self):
         self.install_repository("iuc", "compose_text_param", "e188c9826e0f")  # 0.1.1
         self.login()
-        workflow_id = self.workflow_populator.upload_yaml_workflow(
-            """class: GalaxyWorkflow
+        workflow_id = self.workflow_populator.upload_yaml_workflow("""class: GalaxyWorkflow
 inputs: []
 steps:
   - tool_id: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.0.0
     tool_version: 0.0.0
     label: compose_text_param
-        """
-        )
+        """)
         self.workflow_index_open()
         self.components.workflows.edit_button.wait_for_and_click()
         self.assert_modal_has_text("Using version '0.1.1' instead of version '0.0.0'")
diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py
index 20c1f73a8bd..836ff979d47 100644
--- a/test/manual/workflows_scaling.py
+++ b/test/manual/workflows_scaling.py
@@ -5,6 +5,7 @@
 $ .venv/bin/python scripts/summarize_timings.py --file /tmp/<work_dir>/handler1.log --pattern 'Workflow step'
 $ .venv/bin/python scripts/summarize_timings.py --file /tmp/<work_dir>/handler1.log --pattern 'Created step'
 """
+
 import functools
 import json
 import os
diff --git a/test/unit/app/managers/test_CollectionManager.py b/test/unit/app/managers/test_CollectionManager.py
index e22ce580e0a..2a3273d238c 100644
--- a/test/unit/app/managers/test_CollectionManager.py
+++ b/test/unit/app/managers/test_CollectionManager.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """ """
+
 from galaxy import model
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.datasets import DatasetManager
diff --git a/test/unit/app/managers/test_markdown_export.py b/test/unit/app/managers/test_markdown_export.py
index 5ab1f0c66bf..4f512a831ec 100644
--- a/test/unit/app/managers/test_markdown_export.py
+++ b/test/unit/app/managers/test_markdown_export.py
@@ -434,12 +434,9 @@ I ran a cool analysis with two inputs of types ${galaxy history_dataset_type(his
 """
         self.app.hda_manager.get_accessible.side_effect = [hda, hda2]
         _, export_markdown, _ = self._ready_export(example)
-        assert (
-            export_markdown
-            == """
+        assert export_markdown == """
 I ran a cool analysis with two inputs of types fasta and fastqsanger.
 """
-        )
 
     def test_export_replaces_embedded_history_dataset_name(self):
         hda = self._new_hda()
@@ -452,22 +449,17 @@ I ran a cool analysis with two inputs of types ${galaxy history_dataset_name(his
 """
         self.app.hda_manager.get_accessible.side_effect = [hda, hda2]
         _, export_markdown, _ = self._ready_export(example)
-        assert (
-            export_markdown
-            == """
+        assert export_markdown == """
 I ran a cool analysis with two inputs of types foo bar and cow dog.
 """
-        )
 
     def test_export_replaces_embedded_generate_time(self):
         example = """
 I ran a cool analysis at ${galaxy generate_time()}.
 """
         _, export_markdown, _ = self._ready_export(example)
-        assert export_markdown.startswith(
-            """
-I ran a cool analysis at 2"""
-        )
+        assert export_markdown.startswith("""
+I ran a cool analysis at 2""")
 
     def test_export_replaces_embedded_invocation_time(self):
         invocation = self._new_invocation()
@@ -476,22 +468,17 @@ I ran a cool analysis at 2"""
 I ran a cool analysis at ${galaxy invocation_time(invocation_id=1)}.
 """
         _, export_markdown, _ = self._ready_export(example)
-        assert export_markdown.startswith(
-            """
-I ran a cool analysis at 2"""
-        )
+        assert export_markdown.startswith("""
+I ran a cool analysis at 2""")
 
     def test_export_replaces_embedded_galaxy_version(self):
         example = """
 I ran a cool analysis with Galaxy ${galaxy generate_galaxy_version()}.
 """
         _, export_markdown, _ = self._ready_export(example)
-        assert (
-            export_markdown
-            == """
+        assert export_markdown == """
 I ran a cool analysis with Galaxy 19.09.
 """
-        )
 
     def test_export_replaces_embedded_access_link(self):
         self.trans.app.config.instance_access_url = "http://mycoolgalaxy.org"
@@ -499,12 +486,9 @@ I ran a cool analysis with Galaxy 19.09.
 I ran a cool analysis at ${galaxy instance_access_link()}.
 """
         _, export_markdown, _ = self._ready_export(example)
-        assert (
-            export_markdown
-            == """
+        assert export_markdown == """
 I ran a cool analysis at [http://mycoolgalaxy.org](http://mycoolgalaxy.org).
 """
-        )
 
     def _ready_export(self, example: str):
         return ready_galaxy_markdown_for_export(self.trans, example)
diff --git a/test/unit/app/managers/test_markdown_to_html.py b/test/unit/app/managers/test_markdown_to_html.py
index 59cbc58f93e..43116c9baf2 100644
--- a/test/unit/app/managers/test_markdown_to_html.py
+++ b/test/unit/app/managers/test_markdown_to_html.py
@@ -9,8 +9,7 @@ from galaxy.managers.markdown_util import to_html
 
 
 def test_basics():
-    as_html = to_html(
-        """
+    as_html = to_html("""
 # My header!
 
 My cool document. **Bold** text.
@@ -18,52 +17,43 @@ My cool document. **Bold** text.
 ## My sub header
 
 Less important content.
-"""
-    )
+""")
     assert "<h1>My header!</h1>" in as_html
     assert "<strong>Bold</strong>" in as_html
 
 
 def test_indent_code_blocks():
-    as_html = to_html(
-        """
+    as_html = to_html("""
 A Code Block Follows:
 
     This is code right?
     Here is another line.
-"""
-    )
+""")
     assert "<pre><code>This is code right?\nHere is another line." in as_html
 
 
 def test_tables():
-    as_html = to_html(
-        """
+    as_html = to_html("""
 |animal|sound|
 |------|-----|
 |dog   |bark |
 |cat   |meow |
-"""
-    )
+""")
     assert "<table>" in as_html, as_html
 
 
 def test_tags_escaped():
-    as_html = to_html(
-        """
+    as_html = to_html("""
 Bad block approaches <br>
 
 <script>window.location.href = "bad_place";</script>
-"""
-    )
+""")
     assert "<script>" not in as_html, as_html
 
 
 def test_embed_img_tags():
-    as_html = to_html(
-        """
+    as_html = to_html("""
 ![Red dot](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAUAAAAFCAYAAACNbyblAAAAHElEQVQI12P4//8/w38GIAXDIBKE0DHxgljNBAAO9TXL0Y4OHwAAAABJRU5ErkJggg==)
-"""
-    )
+""")
     assert "img" in as_html, as_html
     assert "iVBORw0KGgoAAAANSUhEUgAAAAUAAA" in as_html, as_html
diff --git a/test/unit/app/test_markdown_validate.py b/test/unit/app/test_markdown_validate.py
index f8d1b738473..1eb253affca 100644
--- a/test/unit/app/test_markdown_validate.py
+++ b/test/unit/app/test_markdown_validate.py
@@ -19,13 +19,10 @@ def assert_markdown_invalid(markdown, at_line: Optional[int] = None):
 
 
 def test_markdown_validation():
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 hello world
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 hello ``world``
 
 Here is some more text.
@@ -34,19 +31,15 @@ Here is some more text.
 import <stdio>
 printf('hello')
 ```
-"""
-    )
+""")
     # assert valid container is fine.
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 ```
-"""
-    )
+""")
     # assert multiple valid container is fine.
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 ```
@@ -57,16 +50,13 @@ Markdown between directives.
 job_metrics(job_id=THISFAKEID)
 ```
 
-"""
-    )
+""")
 
     # assert valid container is fine at end of document.
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 job_metrics(job_id=THISFAKEID)
-```"""
-    )
+```""")
     # assert valid containers require container close
     assert_markdown_invalid(
         """
@@ -76,114 +66,86 @@ job_metrics(job_id=THISFAKEID)
         at_line=1,
     )
     # assert valid containers require container close, even at end...
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
-job_metrics(job_id=THISFAKEID)"""
-    )
+job_metrics(job_id=THISFAKEID)""")
     # assert only one command allowed
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(job_id=THISFAKEID)
 job_metrics(job_id=THISFAKEID2)
 ```
-"""
-    )
+""")
     # assert command paren is closed
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(job_id=THISFAKEID
 ```
-"""
-    )
+""")
     # assert command arg is named.
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(THISFAKEID)
 ```
-"""
-    )
+""")
     # assert quotes are fine
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 job_metrics(step="Moo Cow")
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 ```galaxy
 job_metrics(step='Moo Cow')
 ```
-"""
-    )
+""")
     # assert spaces require quotes
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(output=Moo Cow)
 ```
-"""
-    )
+""")
     # assert unmatched quotes invalid
-    assert_markdown_invalid(
-        """
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(output="Moo Cow)
 ```
-"""
-    )
-    assert_markdown_invalid(
-        """
+""")
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(output=Moo Cow")
 ```
-"""
-    )
-    assert_markdown_invalid(
-        """
+""")
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(output='Moo Cow)
 ```
-"""
-    )
-    assert_markdown_invalid(
-        """
+""")
+    assert_markdown_invalid("""
 ```galaxy
 job_metrics(output=Moo Cow')
 ```
-"""
-    )
+""")
 
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 workflow_display()
 ```
-"""
-    )
+""")
 
     # Test image with a composite path (param needs to be closed, can't be misnamed i.e. pathx)
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 
 ```galaxy
 history_dataset_as_image(output="cow", path="foo/bar.png")
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 
 ```galaxy
 history_dataset_as_image(output=cow, path="foo/bar.png")
 ```
-"""
-    )
+""")
     assert_markdown_invalid(
         """
 
@@ -204,13 +166,11 @@ history_dataset_as_image(output="cow", pathx="foo/bar.png")
     )
 
     # Test validation of three arguments
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 history_dataset_link(output=moo, path="cow.png", label="my label")
 ```
-"""
-    )
+""")
     assert_markdown_invalid(
         """
 ```galaxy
@@ -237,34 +197,26 @@ history_dataset_link(output=moo, path="cow.png", labelx="my label")
     )
 
     # Test validation of arguments with different whitespaces
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 history_dataset_link(output= moo, path= "cow.png", label= "my label")
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 ```galaxy
 history_dataset_link(output = moo, path = "cow.png", label = "my label")
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 ```galaxy
 history_dataset_link(output = moo, path ="cow.png", label= "my label" )
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 ```galaxy
 history_dataset_link(  output = moo, path ="cow.png", label= "my label" )
 ```
-"""
-    )
+""")
     assert_markdown_invalid(
         """
 ```galaxy
@@ -290,41 +242,31 @@ history_dataset_link(  output = moo, path ="cow.png", labelx= "my label" )
         at_line=2,
     )
 
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 ```galaxy
 visualization(id=1)
 ```
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 ```galaxy
 visualization(foo|bar=hello)
 ```
-"""
-    )
+""")
 
 
 def test_markdown_validation_embed():
-    assert_markdown_valid(
-        """
+    assert_markdown_valid("""
 | moo | cow |
 | 1 | 2 |
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 | moo | cow |
 | 1 | ${galaxy generate_galaxy_version()} |
-"""
-    )
-    assert_markdown_valid(
-        """
+""")
+    assert_markdown_valid("""
 | moo | cow |
 | 1 | ${galaxy history_dataset_name(input=foobar)} |
-"""
-    )
+""")
     assert_markdown_invalid(
         """
 | moo | cow |
diff --git a/test/unit/app/tools/test_actions.py b/test/unit/app/tools/test_actions.py
index 242a5665214..de6efdca29d 100644
--- a/test/unit/app/tools/test_actions.py
+++ b/test/unit/app/tools/test_actions.py
@@ -204,12 +204,10 @@ def test_determine_output_format():
     # Test change_format but no match
     __assert_output_format_is("fastq", change_format_output, param_context={"options_type": {"output_type": "sanger"}})
 
-    change_on_metadata_xml_template = string.Template(
-        """<data><change_format>
+    change_on_metadata_xml_template = string.Template("""<data><change_format>
         <when input_dataset="${input}" attribute="random_field" value="1" format="fastqsolexa" />
         <when input_dataset="${input}" attribute="random_field" value="2" format="fastqillumina" />
-    </change_format></data>"""
-    )
+    </change_format></data>""")
 
     change_on_metadata_illumina = change_on_metadata_xml_template.safe_substitute({"input": "i2"})
     change_on_metadata_output = quick_output("fastq", change_format_xml=change_on_metadata_illumina)
diff --git a/test/unit/app/tools/test_collect_primary_datasets.py b/test/unit/app/tools/test_collect_primary_datasets.py
index d5529667b2c..b65572f912a 100644
--- a/test/unit/app/tools/test_collect_primary_datasets.py
+++ b/test/unit/app/tools/test_collect_primary_datasets.py
@@ -62,12 +62,10 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         assert created_hda_1.dbkey == "?"
 
     def test_collect_multiple_recurse(self):
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="__name__" directory="subdir1" recurse="true" ext="txt" />
             <discover_datasets pattern="__name__" directory="subdir2" recurse="true" ext="txt" />
-        </output>"""
-        )
+        </output>""")
         path1 = self._setup_extra_file(filename="test1", subdir="subdir1")
         path2 = self._setup_extra_file(filename="test2", subdir="subdir2/nested1/")
         path3 = self._setup_extra_file(filename="test3", subdir="subdir2")
@@ -128,11 +126,9 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         assert_created_with_path(self.app.object_store, created_hda_3.dataset, path3)
 
     def test_collect_collection_default_format(self):
-        self._replace_output_collectors(
-            """<dataset_collection name="parent" format="abcdef">
+        self._replace_output_collectors("""<dataset_collection name="parent" format="abcdef">
             <discover_datasets pattern="__name__" directory="subdir_for_name_discovery" sort_by="reverse_filename" />
-        </dataset_collection>"""
-        )
+        </dataset_collection>""")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test2")
 
@@ -142,11 +138,9 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
             assert dataset.ext == "abcdef"
 
     def test_collect_sorted_reverse(self):
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="__name__" directory="subdir_for_name_discovery" sort_by="reverse_filename" ext="txt" />
-        </output>"""
-        )
+        </output>""")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test2")
 
@@ -157,11 +151,9 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         assert list(datasets[DEFAULT_TOOL_OUTPUT].keys()) == ["test2", "test1"]
 
     def test_collect_sorted_name(self):
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="[abc](?P&lt;name&gt;.*)" directory="subdir_for_name_discovery" sort_by="name" ext="txt" />
-        </output>"""
-        )
+        </output>""")
         # Setup filenames in reverse order and ensure name is used as key.
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="ctest1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="btest2")
@@ -174,11 +166,9 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         assert list(datasets[DEFAULT_TOOL_OUTPUT].keys()) == ["test1", "test2", "test3"]
 
     def test_collect_sorted_numeric(self):
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="[abc](?P&lt;name&gt;.*)" directory="subdir_for_name_discovery" sort_by="numeric_name" ext="txt" />
-        </output>"""
-        )
+        </output>""")
         # Setup filenames in reverse order and ensure name is used as key.
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="c1")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="b10")
@@ -330,12 +320,10 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         in grouping patterns and named patterns such as __designation__,
         __name__, __designation_and_ext__, and __name_and_ext__.
         """
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="__name_and_ext__" directory="subdir_for_name_discovery" />
             <discover_datasets pattern="__designation_and_ext__" directory="subdir_for_designation_discovery" />
-        </output>"""
-        )
+        </output>""")
         self._setup_extra_file(subdir="subdir_for_name_discovery", filename="example1.txt")
         self._setup_extra_file(subdir="subdir_for_designation_discovery", filename="example2.txt")
         primary_outputs = self._collect()[DEFAULT_TOOL_OUTPUT]
@@ -347,11 +335,9 @@ class TestCollectPrimaryDatasets(TestCase, tools_support.UsesTools):
         assert designation_output.name == "{} ({})".format(self.hda.name, "example2")
 
     def test_cannot_read_files_outside_job_directory(self):
-        self._replace_output_collectors(
-            """<output>
+        self._replace_output_collectors("""<output>
             <discover_datasets pattern="__name_and_ext__" directory="../../secrets" />
-        </output>"""
-        )
+        </output>""")
         exception_thrown = False
         try:
             self._collect()
diff --git a/test/unit/app/tools/test_dynamic_options.py b/test/unit/app/tools/test_dynamic_options.py
index 3de57c332e5..1d06b9cc235 100644
--- a/test/unit/app/tools/test_dynamic_options.py
+++ b/test/unit/app/tools/test_dynamic_options.py
@@ -14,8 +14,7 @@ def get_from_url_option():
     )
 
     return DynamicOptions(
-        XML(
-            """
+        XML("""
 <options from_url="https://usegalaxy.org/api/genomes/dm6" request_method="POST">
     <request_headers type="json">
         {"x-api-key": "${__user__.extra_preferences.resource_api_key if $__user__ else "anon"}"}
@@ -31,8 +30,7 @@ def get_from_url_option():
         }
     }]]></postprocess_expression>
 </options>
-"""
-        ),
+"""),
         tool_param,
     )
 
diff --git a/test/unit/app/tools/test_evaluation.py b/test/unit/app/tools/test_evaluation.py
index a562d7cd675..1f83cb5e79e 100644
--- a/test/unit/app/tools/test_evaluation.py
+++ b/test/unit/app/tools/test_evaluation.py
@@ -167,12 +167,10 @@ class TestToolEvaluator(TestCase, UsesApp):
 
     def __test_arbitrary_path_rewriting(self):
         self.job.parameters = [JobParameter(name="index_path", value='"/old/path/human"')]
-        xml = XML(
-            """<param name="index_path" type="select">
+        xml = XML("""<param name="index_path" type="select">
             <option value="/old/path/human">Human</option>
             <option value="/old/path/mouse">Mouse</option>
-        </param>"""
-        )
+        </param>""")
         parameter = SelectToolParameter(cast("Tool", self.tool), xml)
 
         def get_field_by_name_for_value(name, value, trans, other_values):
diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
index e826ff5068b..a102fa81331 100644
--- a/test/unit/app/tools/test_parameter_parsing.py
+++ b/test/unit/app/tools/test_parameter_parsing.py
@@ -71,93 +71,75 @@ class TestParameterParsing(BaseParameterTestCase):
     """
 
     def test_parse_help_and_label(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault" label="x" help="y" />
-        """
-        )
+        """)
         assert param.label == "x"
         assert param.help == "y"
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault">
                 <label>x2</label>
                 <help>y2</help>
             </param>
-        """
-        )
+        """)
         assert param.label == "x2"
         assert param.help == "y2"
 
     def test_parse_sanitizers(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault">
               <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=","/> </valid>
               </sanitizer>
             </param>
-        """
-        )
+        """)
         sanitizer = param.sanitizer
         assert sanitizer is not None
         assert sanitizer.sanitize_param("a") == ""
         assert sanitizer.sanitize_param(",") == ","
 
     def test_parse_optional(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault">
                 <validator type="empty_field" />
             </param>
-        """
-        )
+        """)
         assert param.optional is False
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault" optional="true" />
-        """
-        )
+        """)
         assert param.optional is True
 
     def test_parse_validators(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault">
                 <validator type="unspecified_build" message="no genome?" />
             </param>
-        """
-        )
+        """)
         assert param.validators[0].message == "no genome?"
 
     def test_text_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="texti" value="mydefault" />
-        """
-        )
+        """)
         assert param.value == "mydefault"
         assert param.type == "text"
         assert not param.area
 
     def test_text_area_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="text" name="textarea" area="true" />
-        """
-        )
+        """)
         assert param.value is None
         assert param.type == "text"
         assert param.area
 
     def test_integer_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="integer" name="intp" min="8" max="9" value="9" />
-        """
-        )
+        """)
         assert param.name == "intp"
         assert param.value == "9"
         assert param.type == "integer"
@@ -166,11 +148,9 @@ class TestParameterParsing(BaseParameterTestCase):
             param.validate(10)
 
     def test_float_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="float" name="floatp" min="7.8" max="9.5" value="9" />
-        """
-        )
+        """)
         assert param.name == "floatp"
         assert param.value == "9"
         assert param.type == "float"
@@ -179,78 +159,62 @@ class TestParameterParsing(BaseParameterTestCase):
             param.validate(10.0)
 
     def test_boolean_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="boolean" name="boolp" />
-        """
-        )
+        """)
         assert param.name == "boolp"
         assert param.truevalue == "true"
         assert param.falsevalue == "false"
         assert param.type == "boolean"
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="boolean" name="boolp" truevalue="t" falsevalue="f" />
-        """
-        )
+        """)
         assert param.truevalue == "t"
         assert param.falsevalue == "f"
 
     def test_file_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="file" name="filep" />
-        """
-        )
+        """)
         assert param.name == "filep"
         assert param.type == "file"
 
     def test_ftpfile_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param type="ftpfile" name="ftpfilep" />
-        """
-        )
+        """)
         assert param.name == "ftpfilep"
         assert param.type == "ftpfile"
 
     def test_hidden(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="hiddenp" type="hidden" value="a hidden value" />
-        """
-        )
+        """)
         assert param.name == "hiddenp"
         assert param.type == "hidden"
         assert param.value == "a hidden value"
 
     def test_base_url(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="urlp" type="baseurl" value="http://twitter.com/" />
-        """
-        )
+        """)
         assert param.name == "urlp"
         assert param.type == "baseurl"
         assert param.value == "http://twitter.com/"
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="urlp" type="baseurl" />
-        """
-        )
+        """)
         assert param.value == ""
 
     def test_select_static(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="selectp" type="select" multiple="true">
                 <option value="a">A</option>
                 <option value="b" selected="true">B</option>
             </param>
-        """
-        )
+        """)
         assert param.display is None
         assert param.multiple is True
         assert param.name == "selectp"
@@ -271,12 +235,10 @@ class TestParameterParsing(BaseParameterTestCase):
         assert options[1][2]
 
     def test_select_dynamic(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="selectp" type="select" dynamic_options="cow" display="checkboxes" separator="moo">
             </param>
-        """
-        )
+        """)
         assert param.multiple is False
         assert param.options is None
         assert param.dynamic_options == "cow"
@@ -288,14 +250,12 @@ class TestParameterParsing(BaseParameterTestCase):
         assert param.separator == "moo"
 
     def test_select_options_from(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="selectp" type="select">
                 <options from_data_table="cow">
                 </options>
             </param>
-        """
-        )
+        """)
         assert param.dynamic_options is None
         assert param.is_dynamic
 
@@ -304,110 +264,89 @@ class TestParameterParsing(BaseParameterTestCase):
         assert param.options.missing_tool_data_table_name == "cow"
 
     def test_genome_build(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="genomep" type="genomebuild">
             </param>
-        """
-        )
+        """)
         assert param.type == "genomebuild"
         assert param.name == "genomep"
         assert param.static_options
 
     def test_column_params(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="col1" type="data_column" data_ref="input1">
             </param>
-        """
-        )
+        """)
         assert param.data_ref == "input1"
         assert param.usecolnames is False
         assert param.optional is False
         assert param.numerical is False
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="col1" type="data_column" data_ref="input1" use_header_names="true" numerical="true" force_select="false">
             </param>
-        """
-        )
+        """)
         assert param.data_ref == "input1"
         assert param.usecolnames is True
         assert param.optional is True
         assert param.numerical is True
 
     def test_data_param_no_validation(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data">
             </param>
-        """
-        )
+        """)
         assert len(param.validators) == 1
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data" no_validation="true">
             </param>
-        """
-        )
+        """)
         assert len(param.validators) == 0
 
     def test_data_param_dynamic_options(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data" />
-        """
-        )
+        """)
         assert param.options is None
         assert param.options_filter_attribute is None
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data">
                 <options from_data_table="cow">
                 </options>
             </param>
-        """
-        )
+        """)
         assert param.options is not None
         assert param.options_filter_attribute is None
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data">
                 <options from_data_table="cow" options_filter_attribute="cow">
                 </options>
             </param>
-        """
-        )
+        """)
         assert param.options is not None
         assert param.options_filter_attribute == "cow"
 
     def test_conversions(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data" />
-        """
-        )
+        """)
         assert param.conversions == []
 
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="input" type="data">
                 <conversion name="foo" type="txt" />
                 <conversion name="foo2" type="bam" />
             </param>
-        """
-        )
+        """)
         assert param.conversions[0][0] == "foo"
         assert param.conversions[0][1] == "txt"
         assert param.conversions[1][0] == "foo2"
         assert param.conversions[1][1] == "bam"
 
     def test_drilldown(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
               <options>
                <option name="Heading 1" value="heading1">
@@ -421,8 +360,7 @@ class TestParameterParsing(BaseParameterTestCase):
                <option name="Option 5" value="option5"/>
               </options>
             </param>
-        """
-        )
+        """)
         assert param.type == "drill_down"
         assert param.name == "some_name"
         assert param.options
@@ -443,20 +381,16 @@ class TestParameterParsing(BaseParameterTestCase):
         assert len(option5["options"]) == 0
 
     def test_tool_collection(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="datac" type="data_collection" collection_type="list,list:paired" format="txt">
             </param>
-        """
-        )
+        """)
         assert param.type == "data_collection"
         assert param.collection_types == ["list", "list:paired"]
 
     def test_data_allow_uri_if_protocol(self):
-        param = self._parameter_for(
-            xml="""
+        param = self._parameter_for(xml="""
             <param name="deferred" type="data" allow_uri_if_protocol="https,s3">
             </param>
-        """
-        )
+        """)
         assert param.allow_uri_if_protocol == ["https", "s3"]
diff --git a/test/unit/app/tools/test_parameter_validation.py b/test/unit/app/tools/test_parameter_validation.py
index d2022c4cba4..712b184498b 100644
--- a/test/unit/app/tools/test_parameter_validation.py
+++ b/test/unit/app/tools/test_parameter_validation.py
@@ -17,57 +17,47 @@ def get_test_data_path(name: str):
 
 class TestParameterValidation(BaseParameterTestCase):
     def test_simple_ExpressionValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="">
     <validator type="expression" message="Not gonna happen">value.lower() == "foo"</validator>
-</param>"""
-        )
+</param>""")
         p.validate("Foo")
         p.validate("foo")
         with self.assertRaisesRegex(ValueError, "Not gonna happen"):
             p.validate("Fop")
 
     def test_negated_ExpressionValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="10">
     <validator type="expression" message="Not gonna happen" negate="true">value.lower() == "foo"</validator>
 </param>
-"""
-        )
+""")
         with self.assertRaisesRegex(ValueError, "Not gonna happen"):
             p.validate("Foo")
         p.validate("Fop")
 
     def test_boolean_ExpressionValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="">
     <validator type="expression" message="Not gonna happen">value</validator>
-</param>"""
-        )
+</param>""")
         p.validate("Foo")
         with self.assertRaisesRegex(ValueError, "Not gonna happen"):
             p.validate("")
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="integer" value="">
     <validator type="expression" message="Not gonna happen">value</validator>
-</param>"""
-        )
+</param>""")
         p.validate(3)
         with self.assertRaisesRegex(ValueError, "Not gonna happen"):
             p.validate(0)
 
     def test_ExpressionValidator_message(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="">
     <validator type="expression">value.lower() == "foo"</validator>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(
             ValueError, r"Value 'Fop' does not evaluate to True for 'value.lower\(\) == \"foo\"'"
         ):
@@ -78,55 +68,45 @@ class TestParameterValidation(BaseParameterTestCase):
             p.validate(1)
 
     def test_NoOptionsValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="index" type="select" label="Select reference genome">
     <validator type="no_options" message="No options available for selection"/>
-</param>"""
-        )
+</param>""")
         p.validate("foo")
         with self.assertRaisesRegex(ValueError, "Parameter 'index': No options available for selection"):
             p.validate(None)
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="index" type="select" label="Select reference genome">
     <options from_data_table="bowtie2_indexes"/>
     <validator type="no_options" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "Parameter 'index': Options available for selection"):
             p.validate("foo")
         p.validate(None)
 
     def test_EmptyTextfieldValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="">
     <validator type="empty_field"/>
-</param>"""
-        )
+</param>""")
         p.validate("foo")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field requires a value"):
             p.validate("")
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="">
     <validator type="empty_field" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field must not set a value"):
             p.validate("foo")
         p.validate("")
 
     def test_RegexValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="10">
     <validator type="regex">[Ff]oo</validator>
-</param>"""
-        )
+</param>""")
         p.validate("Foo")
         p.validate("foo")
         with self.assertRaisesRegex(
@@ -141,12 +121,10 @@ class TestParameterValidation(BaseParameterTestCase):
         ):
             p.validate(["Foo", "Fop"])
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="10">
     <validator type="regex" negate="true">[Ff]oo</validator>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(
             ValueError, r"Parameter 'blah': Value 'Foo' does match regular expression '\[Ff\]oo'"
         ):
@@ -163,12 +141,10 @@ class TestParameterValidation(BaseParameterTestCase):
         p.validate(["Fop", "fop"])
 
     def test_LengthValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="foobar">
     <validator type="length" min="2" max="8"/>
-</param>"""
-        )
+</param>""")
         p.validate("foo")
         p.validate("bar")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
@@ -176,34 +152,28 @@ class TestParameterValidation(BaseParameterTestCase):
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
             p.validate("foobarbaz")
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" value="foobar">
     <validator type="length" min="2" max="8" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("foo")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("bar")
         p.validate("f")
         p.validate("foobarbaz")
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="text" optional="false">
     <validator type="length" min="2" max="8"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "No value provided"):
             p.validate(None)
 
     def test_InRangeValidator(self):
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="integer" value="10">
     <validator type="in_range" message="Doh!! %s not in range" min="10" exclude_min="true" max="20"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 10 not in range"):
             p.validate(10)
         p.validate(15)
@@ -211,12 +181,10 @@ class TestParameterValidation(BaseParameterTestCase):
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 21 not in range"):
             p.validate(21)
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
  <param name="blah" type="integer" value="10">
     <validator type="in_range" min="10" exclude_min="true" max="20" negate="true"/>
-</param>"""
-        )
+</param>""")
         p.validate(10)
         with self.assertRaisesRegex(
             ValueError,
@@ -244,24 +212,20 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         notok_hda.state = Dataset.states.EMPTY
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data" no_validation="true">
     <validator type="dataset_ok_validator"/>
-</param>"""
-        )
+</param>""")
         p.validate(ok_hda)
         with self.assertRaisesRegex(
             ValueError,
             "Parameter 'blah': The selected dataset is still being generated, select another dataset or wait until it is completed",
         ):
             p.validate(notok_hda)
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data" no_validation="true">
     <validator type="dataset_ok_validator" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(ValueError, "Parameter 'blah': The selected dataset must not be in state OK"):
             p.validate(ok_hda)
         p.validate(notok_hda)
@@ -280,24 +244,20 @@ class TestParameterValidation(BaseParameterTestCase):
             HistoryDatasetAssociation(id=2, extension="interval", dataset=full_dataset, sa_session=sa_session)
         )
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data">
     <validator type="empty_dataset"/>
-</param>"""
-        )
+</param>""")
         p.validate(full_hda)
         with self.assertRaisesRegex(
             ValueError, "Parameter 'blah': The selected dataset is empty, this tool expects non-empty files."
         ):
             p.validate(empty_hda)
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data">
     <validator type="empty_dataset" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(
             ValueError, "Parameter 'blah': The selected dataset is non-empty, this tool expects empty files."
         ):
@@ -320,12 +280,10 @@ class TestParameterValidation(BaseParameterTestCase):
         has_no_extra_hda.dataset.file_size = 10
         has_no_extra_hda.dataset.total_size = 10
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data">
     <validator type="empty_extra_files_path"/>
-</param>"""
-        )
+</param>""")
         p.validate(has_extra_hda)
         with self.assertRaisesRegex(
             ValueError,
@@ -333,12 +291,10 @@ class TestParameterValidation(BaseParameterTestCase):
         ):
             p.validate(has_no_extra_hda)
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data">
     <validator type="empty_extra_files_path" negate="true"/>
-</param>"""
-        )
+</param>""")
 
         with self.assertRaisesRegex(
             ValueError,
@@ -428,12 +384,10 @@ class TestParameterValidation(BaseParameterTestCase):
         )
         has_no_dbkey_hda.state = Dataset.states.OK
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data" no_validation="true">
     <validator type="unspecified_build"/>
-</param>"""
-        )
+</param>""")
         p.validate(has_dbkey_hda)
         with self.assertRaisesRegex(
             ValueError,
@@ -441,12 +395,10 @@ class TestParameterValidation(BaseParameterTestCase):
         ):
             p.validate(has_no_dbkey_hda)
 
-        p = self._parameter_for(
-            xml="""
+        p = self._parameter_for(xml="""
 <param name="blah" type="data" no_validation="true">
     <validator type="unspecified_build" negate="true"/>
-</param>"""
-        )
+</param>""")
         with self.assertRaisesRegex(
             ValueError,
             "Parameter 'blah': Specified genome build, click the pencil icon in the history item to remove the genome build",
@@ -456,12 +408,10 @@ class TestParameterValidation(BaseParameterTestCase):
 
     def test_RegexValidator_global_flag_inline(self):
         # tests that global inline flags continue to work past python 3.10
-        p = self._parameter_for(
-            xml=r"""
+        p = self._parameter_for(xml=r"""
 <param name="blah" type="text" value="">
     <validator type="regex">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
-</param>"""
-        )
+</param>""")
         p.validate("select id from job where id = 1;")
         with self.assertRaises(ValueError):
             p.validate("not sql")
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index 7fc20e8fa06..e11b9538d6d 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -41,13 +41,11 @@ def with_mock_tool(func):
 def selectwrapper(tool, value, multiple=False, optional=False):
     optional = 'optional="true"' if optional else ""
     multiple = 'multiple="true"' if multiple else ""
-    xml = XML(
-        f"""<param name="blah" type="select" {multiple} {optional}>
+    xml = XML(f"""<param name="blah" type="select" {multiple} {optional}>
         <option value="x">I am X</option>
         <option value="y" selected="true">I am Y</option>
         <option value="z">I am Z</option>
-    </param>"""
-    )
+    </param>""")
     parameter = SelectToolParameter(tool, xml)
     return SelectToolParameterWrapper(parameter, value)
 
@@ -265,8 +263,7 @@ def test_dataset_false_extra_files_path():
 
 
 def _drilldown_parameter(tool):
-    xml = XML(
-        """<param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
+    xml = XML("""<param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
         <options>
             <option name="Heading 1" value="heading1">
                 <option name="Option 1" value="option1"/>
@@ -278,23 +275,20 @@ def _drilldown_parameter(tool):
             </option>
            <option name="Option 5" value="option5"/>
       </options>
-    </param>"""
-    )
+    </param>""")
     parameter = DrillDownSelectToolParameter(tool, xml)
     return parameter
 
 
 def _setup_blast_tool(tool, multiple=False):
     tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
-    xml = XML(
-        f"""<param name="database" type="select" label="Nucleotide BLAST database" multiple="{multiple}">
+    xml = XML(f"""<param name="database" type="select" label="Nucleotide BLAST database" multiple="{multiple}">
         <options from_file="blastdb.loc">
             <column name="value" index="0"/>
             <column name="name" index="1"/>
             <column name="path" index="2"/>
         </options>
-    </param>"""
-    )
+    </param>""")
     parameter = SelectToolParameter(tool, xml)
     return parameter
 
diff --git a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
index 6a1c9e5ca25..7d133c84aa8 100644
--- a/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
+++ b/test/unit/app/visualizations/plugins/test_VisualizationsRegistry.py
@@ -134,8 +134,7 @@ class TestVisualizationsRegistry(VisualizationsBase_TestCase):
 
     def test_script_entry(self):
         """"""
-        script_entry_config = clean_multiline_string(
-            """\
+        script_entry_config = clean_multiline_string("""\
         <?xml version="1.0" encoding="UTF-8"?>
         <visualization name="js-test">
             <data_sources>
@@ -145,8 +144,7 @@ class TestVisualizationsRegistry(VisualizationsBase_TestCase):
             </data_sources>
             <entry_point container="mycontainer" src="mysrc" css="mycss"></entry_point>
         </visualization>
-        """
-        )
+        """)
 
         mock_app_dir = galaxy_mock.MockDir(
             {
diff --git a/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py b/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
index 0bfb6c41d77..0bb45aca8b6 100644
--- a/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
+++ b/test/unit/data/datatypes/dataproviders/test_base_dataproviders.py
@@ -138,13 +138,11 @@ class Test_BaseDataProvider(BaseTestCase):
 
     def test_stringio(self):
         """should work with StringIO"""
-        contents = clean_multiline_string(
-            """
+        contents = clean_multiline_string("""
             One
             Two
             Three
-        """
-        )
+        """)
         source = StringIO(contents)
         provider = self.provider_class(source)
         data = list(provider)
@@ -154,7 +152,7 @@ class Test_BaseDataProvider(BaseTestCase):
 
     def test_file(self):
         """should work with files"""
-        (contents, provider, data) = self.contents_provider_and_data()
+        contents, provider, data = self.contents_provider_and_data()
         assert data == self.parses_default_content_as()
         # provider should call close on file
         assert hasattr(provider.source, "read")
@@ -171,7 +169,7 @@ class Test_FilteredDataProvider(Test_BaseDataProvider):
 
     def test_counters(self):
         """should count: lines read, lines that passed the filter, lines returned"""
-        (contents, provider, data) = self.contents_provider_and_data()
+        contents, provider, data = self.contents_provider_and_data()
         self.assertCounters(provider, 3, 3, 3)
 
     def test_filter_fn(self):
@@ -184,7 +182,7 @@ class Test_FilteredDataProvider(Test_BaseDataProvider):
                 return None
             return string
 
-        (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
+        contents, provider, data = self.contents_provider_and_data(filter_fn=filter_ts)
         self.assertCounters(provider, 3, 1, 1)
 
 
@@ -193,56 +191,56 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
 
     def test_offset_1(self):
         """when offset is 1, should skip first"""
-        (contents, provider, data) = self.contents_provider_and_data(offset=1)
+        contents, provider, data = self.contents_provider_and_data(offset=1)
         assert data == self.parses_default_content_as()[1:]
         self.assertCounters(provider, 3, 3, 2)
 
     def test_offset_all(self):
         """when offset >= num lines, should return empty list"""
-        (contents, provider, data) = self.contents_provider_and_data(offset=4)
+        contents, provider, data = self.contents_provider_and_data(offset=4)
         assert data == []
         self.assertCounters(provider, 3, 3, 0)
 
     def test_offset_none(self):
         """when offset is 0, should return all"""
-        (contents, provider, data) = self.contents_provider_and_data(offset=0)
+        contents, provider, data = self.contents_provider_and_data(offset=0)
         assert data == self.parses_default_content_as()
         self.assertCounters(provider, 3, 3, 3)
 
     def test_offset_negative(self):
         """when offset is negative, should return all"""
-        (contents, provider, data) = self.contents_provider_and_data(offset=-1)
+        contents, provider, data = self.contents_provider_and_data(offset=-1)
         assert data == self.parses_default_content_as()
         self.assertCounters(provider, 3, 3, 3)
 
     def test_limit_1(self):
         """when limit is one, should return first"""
-        (contents, provider, data) = self.contents_provider_and_data(limit=1)
+        contents, provider, data = self.contents_provider_and_data(limit=1)
         assert data == self.parses_default_content_as()[:1]
         self.assertCounters(provider, 1, 1, 1)
 
     def test_limit_all(self):
         """when limit >= num lines, should return all"""
-        (contents, provider, data) = self.contents_provider_and_data(limit=4)
+        contents, provider, data = self.contents_provider_and_data(limit=4)
         assert data == self.parses_default_content_as()
         self.assertCounters(provider, 3, 3, 3)
 
     def test_limit_zero(self):
         """when limit >= num lines, should return empty list"""
-        (contents, provider, data) = self.contents_provider_and_data(limit=0)
+        contents, provider, data = self.contents_provider_and_data(limit=0)
         assert data == []
         self.assertCounters(provider, 0, 0, 0)
 
     def test_limit_none(self):
         """when limit is None, should return all"""
-        (contents, provider, data) = self.contents_provider_and_data(limit=None)
+        contents, provider, data = self.contents_provider_and_data(limit=None)
         assert data == self.parses_default_content_as()
         self.assertCounters(provider, 3, 3, 3)
 
     # TODO: somehow re-use tmpfile here
     def test_limit_with_offset(self):
         def limit_offset_combo(limit, offset, data_should_be, read, valid, returned):
-            (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset)
+            contents, provider, data = self.contents_provider_and_data(limit=limit, offset=offset)
             assert data == data_should_be
             # self.assertCounters(provider, read, valid, returned)
 
@@ -269,7 +267,7 @@ class Test_LimitedOffsetDataProvider(Test_FilteredDataProvider):
                     return None
                 return string
 
-            (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset, filter_fn=only_ts)
+            contents, provider, data = self.contents_provider_and_data(limit=limit, offset=offset, filter_fn=only_ts)
             assert data == data_should_be
             # self.assertCounters(provider, read, valid, returned)
 
diff --git a/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py b/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
index 6d04fd534a2..e03477f3954 100644
--- a/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
+++ b/test/unit/data/datatypes/dataproviders/test_line_dataproviders.py
@@ -32,7 +32,7 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
 
     def test_counters(self):
         """should count: lines read, lines that passed the filter, lines returned"""
-        (contents, provider, data) = self.contents_provider_and_data()
+        contents, provider, data = self.contents_provider_and_data()
         self.assertCounters(provider, 7, 3, 3)
 
     def test_filter_fn(self):
@@ -45,12 +45,12 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
                 return None
             return string
 
-        (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
+        contents, provider, data = self.contents_provider_and_data(filter_fn=filter_ts)
         self.assertCounters(provider, 7, 1, 1)
 
     def test_limit_with_offset(self):
         def limit_offset_combo(limit, offset, data_should_be, read, valid, returned):
-            (contents, provider, data) = self.contents_provider_and_data(limit=limit, offset=offset)
+            contents, provider, data = self.contents_provider_and_data(limit=limit, offset=offset)
             assert data == data_should_be
             # self.assertCounters(provider, read, valid, returned)
 
@@ -73,19 +73,19 @@ class Test_FilteredLineDataProvider(test_base_dataproviders.Test_FilteredDataPro
 
     def test_provide_blank(self):
         """should return blank lines if ``provide_blank`` is true."""
-        (contents, provider, data) = self.contents_provider_and_data(provide_blank=True)
+        contents, provider, data = self.contents_provider_and_data(provide_blank=True)
         assert data == ["One", "", "Two", "Three"]
         self.assertCounters(provider, 7, 4, 4)
 
     def test_strip_lines(self):
         """should return unstripped lines if ``strip_lines`` is false."""
-        (contents, provider, data) = self.contents_provider_and_data(strip_lines=False)
+        contents, provider, data = self.contents_provider_and_data(strip_lines=False)
         assert data == ["One\n", "\n", "    Two\n", "Three\n"]
         self.assertCounters(provider, 7, 4, 4)
 
     def test_comment_char(self):
         """should return unstripped lines if ``strip_lines`` is false."""
-        (contents, provider, data) = self.contents_provider_and_data(comment_char="T")
+        contents, provider, data = self.contents_provider_and_data(comment_char="T")
         assert data == [
             "# this should be stripped out",
             "One",
@@ -109,36 +109,36 @@ class Test_RegexLineDataProvider(Test_FilteredLineDataProvider):
 
     def test_regex(self):
         """should return lines matching regex (AFTER strip, comments, blanks)."""
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O"])
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^O"])
         assert data == ["One"]
         self.assertCounters(provider, 7, 1, 1)
 
     def test_regex_list(self):
         """should return regex matches using more than one regex by ORing them."""
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O", r"T"])
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^O", r"T"])
         assert data == ["One", "Two", "Three"]
         self.assertCounters(provider, 7, 3, 3)
 
     def test_inverse(self):
         """should return inverse matches when ``invert`` is true."""
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^O"], invert=True)
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^O"], invert=True)
         assert data == ["Two", "Three"]
         self.assertCounters(provider, 7, 2, 2)
 
     def test_regex_no_match(self):
         """should return empty if no regex matches."""
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^Z"])
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^Z"])
         assert data == []
         self.assertCounters(provider, 7, 0, 0)
 
     def test_regex_w_limit_offset(self):
         """regex should play well with limit and offset"""
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^T"], limit=1)
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^T"], limit=1)
         assert data == ["Two"]
         # TODO: once again, valid data, returned data is off
         self.assertCounters(provider, 6, 1, 1)
 
-        (contents, provider, data) = self.contents_provider_and_data(regex_list=[r"^T"], limit=1, offset=1)
+        contents, provider, data = self.contents_provider_and_data(regex_list=[r"^T"], limit=1, offset=1)
         assert data == ["Three"]
         self.assertCounters(provider, 7, 2, 1)
 
@@ -169,7 +169,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
 
     def test_file(self):
         """should work with files"""
-        (contents, provider, data) = self.contents_provider_and_data()
+        contents, provider, data = self.contents_provider_and_data()
         assert data == self.parses_default_content_as()
         assert isinstance(provider.source, line.FilteredLineDataProvider)
         assert hasattr(provider.source.source, "read")
@@ -178,7 +178,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
 
     def test_counters(self):
         """should count: lines read, lines that passed the filter, lines returned"""
-        (contents, provider, data) = self.contents_provider_and_data()
+        contents, provider, data = self.contents_provider_and_data()
         self.assertCounters(provider, 6, 6, 6)
 
     def test_filter_fn(self):
@@ -191,7 +191,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
                 return None
             return string
 
-        (contents, provider, data) = self.contents_provider_and_data(filter_fn=filter_ts)
+        contents, provider, data = self.contents_provider_and_data(filter_fn=filter_ts)
         # no block fns here, so will parse as lines
         assert data == [["One"], ["ABCD"], ["ABCD"], ["EFGH"]]
         self.assertCounters(provider, 4, 4, 4)
@@ -204,7 +204,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
             return strip_diff == 0
 
         # in order to use indentation as a delimiter, we need to strip the newlines only
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented
         )
         assert data == [["One", "    ABCD"], ["Two", "    ABCD", "    EFGH"], ["Three"]]
@@ -227,7 +227,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
                 return None
             return block
 
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented, block_filter_fn=no_tw
         )
         assert data == [["One", "    ABCD"], ["Three"]]
@@ -248,7 +248,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
                 return None
             return {"header": block[0].strip(), "data": [b.strip() for b in block[1:] if b.strip()]}
 
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             strip_lines=False, strip_newlines=True, new_block_delim_fn=is_not_indented, block_filter_fn=empty_block
         )
         assert data == [{"header": "One", "data": ["ABCD"]}, {"header": "Two", "data": ["ABCD", "EFGH"]}]
@@ -266,7 +266,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
                 return None
             return block
 
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             strip_lines=False,
             strip_newlines=True,
             new_block_delim_fn=is_not_indented,
@@ -275,7 +275,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
         )
         assert data == [["One", "    ABCD"]]
         self.assertCounters(provider, 1, 1, 1)
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             strip_lines=False,
             strip_newlines=True,
             new_block_delim_fn=is_not_indented,
@@ -304,7 +304,7 @@ class Test_BlockDataProvider(test_base_dataproviders.Test_FilteredDataProvider):
         def id_seq(block):
             return {"id": block[0][1:], "seq": ("".join(block[1:]))}
 
-        (contents, provider, data) = self.contents_provider_and_data(
+        contents, provider, data = self.contents_provider_and_data(
             contents=file_contents, new_block_delim_fn=fasta_header, block_filter_fn=id_seq
         )
         assert data == [{"id": "One", "seq": "ABCD"}, {"id": "Two", "seq": "ABCDEFGH"}]
diff --git a/test/unit/data/datatypes/test_qiime2.py b/test/unit/data/datatypes/test_qiime2.py
index 9bfddc4e003..aa8948f5bed 100644
--- a/test/unit/data/datatypes/test_qiime2.py
+++ b/test/unit/data/datatypes/test_qiime2.py
@@ -45,13 +45,10 @@ def test_qza_set_peek():
         qza.set_meta(dataset)
         qza.set_peek(dataset)
 
-        assert (
-            dataset.peek
-            == """Type: SingleInt1
+        assert dataset.peek == """Type: SingleInt1
 UUID: ba8c55e1-a2bc-47ea-beb2-b37b0b3b4032
 Format: SingleIntDirectoryFormat
 Version: 2022.2.1"""
-        )
 
 
 # Tests for QIIME2Visualization:
@@ -86,12 +83,9 @@ def test_qzv_set_peek():
         qzv.set_meta(dataset)
         qzv.set_peek(dataset)
 
-        assert (
-            dataset.peek
-            == """Type: Visualization
+        assert dataset.peek == """Type: Visualization
 UUID: 368ba1e7-3a7c-4dbc-98da-79f41aeece63
 Version: 2022.2.1"""
-        )
 
 
 # Tets for QIIME2Metadata:
diff --git a/test/unit/data/model/db/conftest.py b/test/unit/data/model/db/conftest.py
index e7d5c6ad0b3..182b667daf4 100644
--- a/test/unit/data/model/db/conftest.py
+++ b/test/unit/data/model/db/conftest.py
@@ -52,7 +52,7 @@ def init_database(engine: "Engine") -> None:
 
 @pytest.fixture(autouse=True, scope="module")
 def init_object_store() -> None:
-    m.Dataset.object_store = MockObjectStore()  # type:ignore[assignment]
+    m.Dataset.object_store = MockObjectStore()  # type: ignore[assignment]
 
 
 @pytest.fixture(autouse=True, scope="module")
diff --git a/test/unit/data/model/test_engine_factory.py b/test/unit/data/model/test_engine_factory.py
index 361fc1f608d..3fac690805c 100644
--- a/test/unit/data/model/test_engine_factory.py
+++ b/test/unit/data/model/test_engine_factory.py
@@ -15,7 +15,7 @@ class TestSetSqliteConnectArgs:
         set_sqlite_connect_args(engine_options, SQLITE_URL)
         assert len(engine_options) == 2
         assert engine_options["foo"] == "some foo"
-        assert engine_options["connect_args"] == {"check_same_thread": False}  # type:ignore[comparison-overlap]
+        assert engine_options["connect_args"] == {"check_same_thread": False}  # type: ignore[comparison-overlap]
 
     def test_overwrite_connect_args(self):
         engine_options = {"foo": "some foo", "connect_args": {"check_same_thread": True}}
@@ -30,5 +30,5 @@ class TestSetSqliteConnectArgs:
         assert len(engine_options) == 2
         assert engine_options["foo"] == "some foo"
         assert len(engine_options["connect_args"]) == 2
-        assert engine_options["connect_args"]["check_same_thread"] is False  # type:ignore[index]
-        assert engine_options["connect_args"]["bar"] == "some bar"  # type:ignore[index]
+        assert engine_options["connect_args"]["check_same_thread"] is False  # type: ignore[index]
+        assert engine_options["connect_args"]["bar"] == "some bar"  # type: ignore[index]
diff --git a/test/unit/tool_util/mulled/test_mulled_build_files.py b/test/unit/tool_util/mulled/test_mulled_build_files.py
index c3fb4d84ca0..7e013743091 100644
--- a/test/unit/tool_util/mulled/test_mulled_build_files.py
+++ b/test/unit/tool_util/mulled/test_mulled_build_files.py
@@ -9,8 +9,7 @@ from galaxy.tool_util.deps.mulled.mulled_build_files import (
     Target,
 )
 
-TESTCASES = yaml.safe_load(
-    r"""
+TESTCASES = yaml.safe_load(r"""
 - test_legacy_files_package_only:
     content: samtools
     equals:
@@ -53,8 +52,7 @@ TESTCASES = yaml.safe_load(
       image_build: '10'
       name_override: image_name
       targets: samtools
-"""
-)
+""")
 TEST_IDS = [next(iter(k.keys())) for k in TESTCASES]
 
 
diff --git a/test/unit/tool_util/test_assertion_models.py b/test/unit/tool_util/test_assertion_models.py
index 26af471f8ec..93d5fb7a656 100644
--- a/test/unit/tool_util/test_assertion_models.py
+++ b/test/unit/tool_util/test_assertion_models.py
@@ -179,8 +179,7 @@ invalid_xml_assertions = [
 ]
 
 
-TOOL_TEMPLATE = Template(
-    """
+TOOL_TEMPLATE = Template("""
 <tool id="gx_test" name="gx_test" version="1.0.0">
     <command><![CDATA[
 echo '$parameter' >> '$output'
@@ -202,8 +201,7 @@ echo '$parameter' >> '$output'
         </test>
     </tests>
 </tool>
-"""
-)
+""")
 
 
 def test_valid_json_models_validate():
diff --git a/test/unit/tool_util/test_conda_resolution.py b/test/unit/tool_util/test_conda_resolution.py
index 5e4084e70da..ce043ee7958 100644
--- a/test/unit/tool_util/test_conda_resolution.py
+++ b/test/unit/tool_util/test_conda_resolution.py
@@ -152,18 +152,18 @@ def test_best_search_result(tmp_path) -> None:
         condarc_override=os.path.join(tmp_path, "_condarc"),
     )
     install_conda(conda_context)
-    (hit, exact) = best_search_result(CondaTarget("samtools"), conda_context)
+    hit, exact = best_search_result(CondaTarget("samtools"), conda_context)
     assert hit is not None
     assert hit["name"] == "samtools"
     assert exact is True
-    (hit, exact) = best_search_result(CondaTarget("samtools", version="1.3.1", build="h0cf4675_11"), conda_context)
+    hit, exact = best_search_result(CondaTarget("samtools", version="1.3.1", build="h0cf4675_11"), conda_context)
     assert hit is not None
     assert hit["name"] == "samtools"
     assert hit["version"] == "1.3.1"
     assert hit["build"] == "h0cf4675_11"
     assert exact is True
     # Search non-existent version
-    (hit, exact) = best_search_result(CondaTarget("samtools", version="1.16"), conda_context)
+    hit, exact = best_search_result(CondaTarget("samtools", version="1.16"), conda_context)
     assert hit is not None
     assert hit["name"] == "samtools"
     assert exact is False
diff --git a/test/unit/tool_util/test_loader_directory.py b/test/unit/tool_util/test_loader_directory.py
index 08ec1f5a51c..270bec83cb9 100644
--- a/test/unit/tool_util/test_loader_directory.py
+++ b/test/unit/tool_util/test_loader_directory.py
@@ -6,8 +6,7 @@ from galaxy.tool_util.loader_directory import is_a_yaml_with_class
 def test_is_a_yaml_with_class():
     with tempfile.NamedTemporaryFile("w", suffix=".yaml") as tf:
         fname = tf.name
-        tf.write(
-            """class: GalaxyWorkflow
+        tf.write("""class: GalaxyWorkflow
 name: "Test Workflow"
 inputs:
   - id: input1
@@ -18,7 +17,6 @@ steps:
   - tool_id: cat
     label: first_cat
     in:
-      input1: input1"""
-        )
+      input1: input1""")
         tf.flush()
         assert is_a_yaml_with_class(fname, ["GalaxyWorkflow"])
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index 0815dda0dc9..b416a30243f 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -452,26 +452,22 @@ class TestXmlLoader(BaseLoaderTestCase):
         assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
 
     def test_exit_code(self):
-        tool_source = self._get_tool_source(
-            source_contents="""<tool id="bwa" name="bwa">
+        tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
             <command detect_errors="exit_code">
                 ls
             </command>
         </tool>
-        """
-        )
+        """)
         exit, regexes = tool_source.parse_stdio()
         assert len(exit) == 2, exit
         assert len(regexes) == 0, regexes
 
-        tool_source = self._get_tool_source(
-            source_contents="""<tool id="bwa" name="bwa">
+        tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
             <command detect_errors="aggressive">
                 ls
             </command>
         </tool>
-        """
-        )
+        """)
         exit, regexes = tool_source.parse_stdio()
         assert len(exit) == 2, exit
         # error:, exception: various memory exception...
diff --git a/test/unit/tool_util/test_test_parsing.py b/test/unit/tool_util/test_test_parsing.py
index ca6765d598c..3ee76b2c1a7 100644
--- a/test/unit/tool_util/test_test_parsing.py
+++ b/test/unit/tool_util/test_test_parsing.py
@@ -3,23 +3,19 @@ import yaml
 from galaxy.tool_util.parser.yaml import to_test_assert_list
 
 # Legacy style
-ASSERT_THAT_LIST = yaml.safe_load(
-    """
+ASSERT_THAT_LIST = yaml.safe_load("""
 - that: "has_text"
   text: "Number of input reads |\t1051466"
 - that: "has_text"
   text: "Uniquely mapped reads number |\t871202"
-"""
-)
+""")
 # New list of assertion style
-ASSERT_LIST = yaml.safe_load(
-    """
+ASSERT_LIST = yaml.safe_load("""
 - has_text:
     text: "Number of input reads |\t1051466"
 - has_text:
     text: "Uniquely mapped reads number |\t871202"
-"""
-)
+""")
 # Singleton assertion
 SIMPLE_ASSERT = {"has_text": {"text": "Number of input reads |\t1051466"}}
 
@@ -40,8 +36,7 @@ def test_assert_legacy_same_as_new_list_style():
     assert to_test_assert_list(ASSERT_THAT_LIST) == to_test_assert_list(ASSERT_THAT_LIST)
 
 
-NESTED_ASSERT_LIST = yaml.safe_load(
-    """
+NESTED_ASSERT_LIST = yaml.safe_load("""
 - has_archive_member:
     path: ".*"
     asserts:
@@ -49,8 +44,7 @@ NESTED_ASSERT_LIST = yaml.safe_load(
           text: "a text"
       - has_text:
           text: "another text"
-"""
-)
+""")
 
 
 def test_nested_asserts():
diff --git a/test/unit/tool_util/test_tool_deps.py b/test/unit/tool_util/test_tool_deps.py
index 84ae3fa28a0..172b7d25623 100644
--- a/test/unit/tool_util/test_tool_deps.py
+++ b/test/unit/tool_util/test_tool_deps.py
@@ -218,12 +218,10 @@ blast/2.24
         )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write(
-                """
+            f.write("""
 - from: blast+
   to: blast
-"""
-            )
+""")
 
         resolver = ModuleDependencyResolver(
             _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
@@ -247,16 +245,14 @@ blast/2.24
         )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write(
-                """
+            f.write("""
 - from:
     name: blast
     unversioned: true
   to:
     name: blast
     version: 2.24
-"""
-            )
+""")
 
         resolver = ModuleDependencyResolver(
             _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
@@ -285,8 +281,7 @@ blast/2.24.0-mpi
         )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write(
-                """
+            f.write("""
 - from:
     name: blast+
     version: 2.24
@@ -298,8 +293,7 @@ blast/2.24.0-mpi
     version: 2.22
   to:
     version: 2.22.0-mpi
-"""
-            )
+""")
 
         resolver = ModuleDependencyResolver(
             _SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file
@@ -473,8 +467,7 @@ Mothur/1.38.1.1
         )
         mapping_file = os.path.join(temp_directory, "mapping")
         with open(mapping_file, "w") as f:
-            f.write(
-                """
+            f.write("""
 - from:
     name: blast+
     unversioned: true
@@ -486,8 +479,7 @@ Mothur/1.38.1.1
     version: 1.38
   to:
     version: 1.38.1.1
-"""
-            )
+""")
 
         resolver = LmodDependencyResolver(
             _SimpleDependencyManager(),
@@ -665,45 +657,37 @@ def __test_base_path():
 
 
 def test_parse():
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <tool_shed_packages />
   <galaxy_packages />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         assert "ToolShed" in dependency_resolvers[0].__class__.__name__
         assert "Galaxy" in dependency_resolvers[1].__class__.__name__
 
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         assert "Galaxy" in dependency_resolvers[0].__class__.__name__
         assert "ToolShed" in dependency_resolvers[1].__class__.__name__
 
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
   <galaxy_packages versionless="true" />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         assert not dependency_resolvers[0].versionless
         assert dependency_resolvers[2].versionless
 
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <galaxy_packages />
   <tool_shed_packages />
   <galaxy_packages base_path="/opt/galaxy/legacy/"/>
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         # Unspecified base_paths are both default_base_paths
         assert dependency_resolvers[0].base_path == dependency_resolvers[1].base_path
         # Can specify custom base path...
@@ -713,30 +697,24 @@ def test_parse():
 
 
 def test_uses_tool_shed_dependencies():
-    with __dependency_manager(
-        """<dependency_resolvers>
+    with __dependency_manager("""<dependency_resolvers>
   <galaxy_packages />
 </dependency_resolvers>
-"""
-    ) as dm:
+""") as dm:
         assert not dm.uses_tool_shed_dependencies()
 
-    with __dependency_manager(
-        """<dependency_resolvers>
+    with __dependency_manager("""<dependency_resolvers>
   <tool_shed_packages />
 </dependency_resolvers>
-"""
-    ) as dm:
+""") as dm:
         assert dm.uses_tool_shed_dependencies()
 
 
 def test_config_module_defaults():
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <modules prefetch="false" />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.__class__.__name__ == "AvailModuleChecker"
 
@@ -753,12 +731,10 @@ def test_config_module_defaults():
 
 def test_config_modulepath():
     # Test reads and splits MODULEPATH if modulepath is not specified.
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <modules find_by="directory" modulepath="/opt/modules/modulefiles:/usr/local/modules/modulefiles" />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         assert dependency_resolvers[0].module_checker.directories == [
             "/opt/modules/modulefiles",
             "/usr/local/modules/modulefiles",
@@ -768,12 +744,10 @@ def test_config_modulepath():
 def test_config_MODULEPATH():
     # Test reads and splits MODULEPATH if modulepath is not specified.
     with modify_environ({"MODULEPATH": "/opt/modules/modulefiles:/usr/local/modules/modulefiles"}):
-        with __parse_resolvers(
-            """<dependency_resolvers>
+        with __parse_resolvers("""<dependency_resolvers>
   <modules find_by="directory" />
 </dependency_resolvers>
-"""
-        ) as dependency_resolvers:
+""") as dependency_resolvers:
             assert dependency_resolvers[0].module_checker.directories == [
                 "/opt/modules/modulefiles",
                 "/usr/local/modules/modulefiles",
@@ -784,22 +758,18 @@ def test_config_MODULESHOME():
     # Test fallbacks to read MODULESHOME if modulepath is not specified and
     # neither is MODULEPATH.
     with modify_environ({"MODULESHOME": "/opt/modules"}, keys_to_remove=["MODULEPATH"]):
-        with __parse_resolvers(
-            """<dependency_resolvers>
+        with __parse_resolvers("""<dependency_resolvers>
   <modules find_by="directory" />
 </dependency_resolvers>
-"""
-        ) as dependency_resolvers:
+""") as dependency_resolvers:
             assert dependency_resolvers[0].module_checker.directories == ["/opt/modules/modulefiles"]
 
 
 def test_config_module_directory_searcher():
-    with __parse_resolvers(
-        """<dependency_resolvers>
+    with __parse_resolvers("""<dependency_resolvers>
   <modules find_by="directory" modulepath="/opt/Modules/modulefiles" />
 </dependency_resolvers>
-"""
-    ) as dependency_resolvers:
+""") as dependency_resolvers:
         module_resolver = dependency_resolvers[0]
         assert module_resolver.module_checker.directories == ["/opt/Modules/modulefiles"]
 
diff --git a/test/unit/tool_util/test_tool_loader.py b/test/unit/tool_util/test_tool_loader.py
index b506ca98610..80767898cf8 100644
--- a/test/unit/tool_util/test_tool_loader.py
+++ b/test/unit/tool_util/test_tool_loader.py
@@ -54,8 +54,7 @@ def test_loader_simple():
     Test simple macro replacement.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs" />
     <macros>
@@ -63,8 +62,7 @@ def test_loader_simple():
             <inputs />
         </macro>
     </macros>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load(preprocess=False)
         assert xml.find("inputs") is None
         xml = tool_dir.load(preprocess=True)
@@ -88,8 +86,7 @@ def test_loader_external():
 def test_loader_unnamed_yield():
     # Test macros with unnamed yield statements.
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -112,8 +109,7 @@ def test_loader_unnamed_yield():
             </inputs>
         </macro>
     </macros>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load()
         assert xml.find("/inputs[1]/input").get("name") == "first_input"
         assert xml.find("/inputs[2]/input").get("name") == "second_input"
@@ -125,8 +121,7 @@ def test_loader_unnamed_yield_nested():
     Test nested macro with yield statements
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <macro name="paired_options">
@@ -151,8 +146,7 @@ def test_loader_unnamed_yield_nested():
         </expand>
     </inputs>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         # assert the both yields in the inner macro (paired_options) are expanded
         assert xml.find('/inputs/conditional[@name="library"]/when[@value="paired"]/param[@name="test"]') is not None
@@ -167,8 +161,7 @@ def test_loader_recursive():
     Test recursive macro applications.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -185,8 +178,7 @@ def test_loader_recursive():
             <input name="second_input" />
         </macro>
     </macros>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load()
         assert xml.find("/inputs/input[1]").get("name") == "first_input"
         assert xml.find("/inputs/input[2]").get("name") == "second_input"
@@ -198,8 +190,7 @@ def test_loader_recursive2():
     Test recursive macro applications.
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs">
         <input name="first_input" />
@@ -219,8 +210,7 @@ def test_loader_recursive2():
             <input name="second_input" />
         </macro>
     </macros>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load()
         assert xml.find("/inputs/input[1]").get("name") == "first_input"
         assert xml.find("/inputs/input[2]").get("name") == "second_input"
@@ -232,8 +222,7 @@ def test_loader_toplevel_yield():
     test expansion of top level (ie child of <macro>) yields
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool id="issue_647">
     <macros>
         <macro name="a">
@@ -246,8 +235,7 @@ def test_loader_toplevel_yield():
             <param name="b" type="text" value="b" label="b" />
         </expand>
     </inputs>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load()
         assert xml.find("/inputs/param[1]").get("name") == "a1"
         assert xml.find("/inputs/param[2]").get("name") == "b"
@@ -258,8 +246,7 @@ def test_loader_shortcut():
     Test <xml> is shortcut for macro type="xml"
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs" />
     <macros>
@@ -267,16 +254,14 @@ def test_loader_shortcut():
             <inputs />
         </xml>
     </macros>
-</tool>"""
-        )
+</tool>""")
         xml = tool_dir.load()
         assert xml.find("inputs") is not None
 
 
 def test_loader_template():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <command interpreter="python">tool_wrapper.py
     #include source=$tool_params
@@ -285,8 +270,7 @@ def test_loader_template():
         <template name="tool_params">-a 1 -b 2</template>
     </macros>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         params_dict = template_macro_params(xml.getroot())
         assert params_dict["tool_params"] == "-a 1 -b 2"
@@ -294,8 +278,7 @@ def test_loader_template():
 
 def test_loader_token_text():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="@CITATION@">The citation.</token>
@@ -305,8 +288,7 @@ def test_loader_token_text():
         <tag />
     </another>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         help_el = xml.find("help")
         assert help_el.text == "The citation.", help_el.text
@@ -314,8 +296,7 @@ def test_loader_token_text():
 
 def test_loader_token_nested():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="@WIZARD@">Ab@HELPER@ra</token>
@@ -327,8 +308,7 @@ def test_loader_token_nested():
         <tag />
     </another>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         help_el = xml.find("help")
         assert help_el.text == "Abracadabra", help_el.text
@@ -339,8 +319,7 @@ def test_loader_token_cycle():
     test if cycles in nested tokens are detected
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="@A@">a @ROSE@</token>
@@ -352,8 +331,7 @@ def test_loader_token_cycle():
         <tag />
     </another>
 </tool>
-"""
-        )
+""")
         try:
             tool_dir.load()
         except Exception as e:
@@ -367,8 +345,7 @@ def test_loader_token_attribute_name():
     test the repacement of an attribute name by a token
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="__ATTR_NAME">name</token>
@@ -377,8 +354,7 @@ def test_loader_token_attribute_name():
         <tag __ATTR_NAME="blah" />
     </another>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         assert xml.find('/another/tag[@name="blah"]') is not None
 
@@ -388,8 +364,7 @@ def test_loader_token_attribute_value():
     test the repacement of an attribute value by a token
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="@TAG_VAL@">The value.</token>
@@ -398,16 +373,14 @@ def test_loader_token_attribute_value():
         <tag value="@TAG_VAL@" />
     </another>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         assert xml.find('/another/tag[@value="The value."]') is not None
 
 
 def test_loader_token_empty():
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <token name="@TAG_VAL@"><![CDATA[]]></token>
@@ -416,8 +389,7 @@ def test_loader_token_empty():
         <tag value="@TAG_VAL@" />
     </another>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         assert xml.find('/another/tag[@value=""]') is not None
 
@@ -427,8 +399,7 @@ def test_loader_macro_token_quote():
     Test macros XML macros with $$ expansions in attributes
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs" bar="hello" />
     <expand macro="inputs" bar="my awesome" />
@@ -439,8 +410,7 @@ def test_loader_macro_token_quote():
         </xml>
     </macros>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -454,8 +424,7 @@ def test_loader_macro_token():
     Test macros XML macros with @ expansions in text
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs" foo="hello" />
     <expand macro="inputs" foo="world" />
@@ -466,8 +435,7 @@ def test_loader_macro_token():
         </xml>
     </macros>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -481,8 +449,7 @@ def test_loader_macro_token_recursive():
     Test macros XML macros with @ expansions and recursive
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <expand macro="inputs" foo="hello" />
     <expand macro="inputs" foo="world" />
@@ -496,8 +463,7 @@ def test_loader_macro_token_recursive():
         </xml>
     </macros>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
         input_els = xml.findall("inputs")
         assert len(input_els) == 3
@@ -513,8 +479,7 @@ def test_loader_macro_named_yield():
     - unnamed yields are replaced by all non-token elements of the expand tag
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <xml name="test">
@@ -541,12 +506,9 @@ def test_loader_macro_named_yield():
         <sub_of_expand_2/>
     </expand>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
-        assert (
-            xml_to_string(xml, pretty=True)
-            == """<?xml version="1.0" ?>
+        assert xml_to_string(xml, pretty=True) == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <A>
@@ -562,7 +524,6 @@ def test_loader_macro_named_yield():
         <more_content_of_token2/>
     </B>
 </tool>"""
-        )
 
 
 def test_loader_macro_multiple_toplevel_yield():
@@ -570,8 +531,7 @@ def test_loader_macro_multiple_toplevel_yield():
     test replacement of multiple top level yield
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <xml name="test">
@@ -596,12 +556,9 @@ def test_loader_macro_multiple_toplevel_yield():
         <sub_of_expand_2/>
     </expand>
 </tool>
-"""
-        )
+""")
         xml = tool_dir.load()
-        assert (
-            xml_to_string(xml, pretty=True)
-            == """<?xml version="1.0" ?>
+        assert xml_to_string(xml, pretty=True) == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <blah/>
@@ -614,7 +571,6 @@ def test_loader_macro_multiple_toplevel_yield():
     <content_of_token2/>
     <more_content_of_token2/>
 </tool>"""
-        )
 
 
 def test_loader_macro_recursive_named_yield():
@@ -627,8 +583,7 @@ def test_loader_macro_recursive_named_yield():
     - replacing unnamed yield gives the only non-token element of the expand
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <xml name="test">
@@ -650,13 +605,10 @@ def test_loader_macro_recursive_named_yield():
         </token>
         <T/>
     </expand>
-</tool>"""
-        )
+</tool>""")
 
         xml = tool_dir.load()
-        assert (
-            xml_to_string(xml, pretty=True)
-            == """<?xml version="1.0" ?>
+        assert xml_to_string(xml, pretty=True) == """<?xml version="1.0" ?>
 <tool>
     <macros/>
     <A>
@@ -667,7 +619,6 @@ def test_loader_macro_recursive_named_yield():
         </T1>
     </A>
 </tool>"""
-        )
 
 
 def test_loader_specify_nested_macro_by_token():
@@ -677,16 +628,14 @@ def test_loader_specify_nested_macro_by_token():
     of the outer macro
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <import>external.xml</import>
     </macros>
     <expand macro="testp" token_name="a"/>
     <expand macro="testp" token_name="b"/>
-</tool>"""
-        )
+</tool>""")
         tool_dir.write(
             """
 <macros>
@@ -726,8 +675,7 @@ def test_loader_circular_macros():
     check the cycles in nested macros are detected
     """
     with TestToolDirectory() as tool_dir:
-        tool_dir.write(
-            """
+        tool_dir.write("""
 <tool>
     <macros>
         <xml name="a">
@@ -742,8 +690,7 @@ def test_loader_circular_macros():
         </xml>
     </macros>
     <expand macro="a"/>
-</tool>"""
-        )
+</tool>""")
         try:
             tool_dir.load()
         except AssertionError as a:
diff --git a/test/unit/tool_util/test_toolbox_view_sources.py b/test/unit/tool_util/test_toolbox_view_sources.py
index 72479548733..9bc1cb579dc 100644
--- a/test/unit/tool_util/test_toolbox_view_sources.py
+++ b/test/unit/tool_util/test_toolbox_view_sources.py
@@ -24,15 +24,13 @@ def test_from_directory():
     with open(os.path.join(dir_1, "foo.json"), "w") as f:
         json.dump(EXAMPLE_1, f)
     with open(os.path.join(dir_2, "seqanalysis.yml"), "w") as f:
-        f.write(
-            """
+        f.write("""
 name: Sequence Analysis
 type: generic
 items:
 - type: workflow
   id: 12345abcd
-"""
-        )
+""")
 
     config_param = f"{os.path.abspath(dir_1)},{os.path.abspath(dir_2)}"
     try:
diff --git a/test/unit/util/test_properties.py b/test/unit/util/test_properties.py
index d643876961a..7990b5fb611 100644
--- a/test/unit/util/test_properties.py
+++ b/test/unit/util/test_properties.py
@@ -139,14 +139,12 @@ def test_dont_read_properties_from_other_format(mock_properties):
 
 def test_nice_config_parser(tmp_path):
     conf_path = tmp_path / "config.ini"
-    conf_path.write_text(
-        """
+    conf_path.write_text("""
 [main]
 foo_path = %(here)s/cow
 FOO_PATH123 = hackedtonotchangecase
 config_file = %(__file__)s
-"""
-    )
+""")
     config_parser = nice_config_parser(conf_path)
     foo_path = config_parser.get("main", "foo_path")
     assert foo_path == str(tmp_path / "cow")
@@ -156,12 +154,10 @@ config_file = %(__file__)s
 
 def test_nice_config_parser_custom_exceptions(tmp_path):
     conf_path = tmp_path / "config.ini"
-    conf_path.write_text(
-        """
+    conf_path.write_text("""
 [main]
 foo_var = %(foobar)s/cow
-"""
-    )
+""")
     config_parser = nice_config_parser(conf_path)
     exc = None
     try:
diff --git a/test/unit/util/test_utils.py b/test/unit/util/test_utils.py
index b56efd24e8d..a645cee3c0f 100644
--- a/test/unit/util/test_utils.py
+++ b/test/unit/util/test_utils.py
@@ -79,13 +79,11 @@ def test_parse_xml_enoent():
 
 
 def test_clean_multiline_string():
-    x = util.clean_multiline_string(
-        """
+    x = util.clean_multiline_string("""
         a
         b
         c
-"""
-    )
+""")
     assert x == "a\nb\nc\n"
 
 
diff --git a/test/unit/webapps/api/test_fetch_schema.py b/test/unit/webapps/api/test_fetch_schema.py
index d871a3c87b1..d3919fafa84 100644
--- a/test/unit/webapps/api/test_fetch_schema.py
+++ b/test/unit/webapps/api/test_fetch_schema.py
@@ -123,8 +123,7 @@ nested_element_regression_payload = {
     "auto_decompress": True,
 }
 
-library_payload = yaml.safe_load(
-    """
+library_payload = yaml.safe_load("""
 destination:
   type: library
   name: "Cool Training Library"
@@ -147,8 +146,7 @@ items:
         src: url
         ext: xml
 
-"""
-)
+""")
 
 
 def test_fetch_data_schema():
diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py
index 08cc8c057f4..3324d07ef40 100644
--- a/test/unit/workflows/test_workflow_progress.py
+++ b/test/unit/workflows/test_workflow_progress.py
@@ -200,7 +200,7 @@ class TestWorkflowProgress(TestCase):
         session.commit()
         progress = self._new_workflow_progress()
         remaining_steps = progress.remaining_steps()
-        (subworkflow_step, subworkflow_invocation_step) = remaining_steps[0]
+        subworkflow_step, subworkflow_invocation_step = remaining_steps[0]
         subworkflow_progress = progress.subworkflow_progress(subworkflow_invocation, subworkflow_step, {})
         subworkflow = subworkflow_step.subworkflow
         assert subworkflow_progress.workflow_invocation == subworkflow_invocation
diff --git a/tools/data_source/import.py b/tools/data_source/import.py
index 0e7d1b4af33..09ec03de9e1 100644
--- a/tools/data_source/import.py
+++ b/tools/data_source/import.py
@@ -3,6 +3,7 @@
 Script that imports locally stored data as a new dataset for the user
 Usage: import id outputfile
 """
+
 from __future__ import print_function
 
 import os
diff --git a/tools/data_source/microbial_import.py b/tools/data_source/microbial_import.py
index 8de22b1e693..8cdbd213666 100644
--- a/tools/data_source/microbial_import.py
+++ b/tools/data_source/microbial_import.py
@@ -3,6 +3,7 @@
 Script that imports locally stored data as a new dataset for the user
 Usage: import id outputfile
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py
index e5155503fcc..dc621c5fb1b 100755
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -9,6 +9,7 @@ usage: %prog $input $out_file1
     -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction
     -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
 """
+
 from __future__ import print_function
 
 import os
diff --git a/tools/filters/axt_to_concat_fasta.py b/tools/filters/axt_to_concat_fasta.py
index c1e9eb9a022..48694e00052 100644
--- a/tools/filters/axt_to_concat_fasta.py
+++ b/tools/filters/axt_to_concat_fasta.py
@@ -2,6 +2,7 @@
 """
 Adapted from bx/scripts/axt_to_concat_fasta.py
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/filters/axt_to_fasta.py b/tools/filters/axt_to_fasta.py
index 3b949fb7782..a173237201b 100644
--- a/tools/filters/axt_to_fasta.py
+++ b/tools/filters/axt_to_fasta.py
@@ -2,6 +2,7 @@
 """
 Adapted from bx/scripts/axt_to_fasta.py
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/filters/axt_to_lav.py b/tools/filters/axt_to_lav.py
index 5bf973a2657..bc1d5c648cd 100644
--- a/tools/filters/axt_to_lav.py
+++ b/tools/filters/axt_to_lav.py
@@ -9,6 +9,7 @@ Application to convert AXT file to LAV file
 The application reads an AXT file from standard input and writes a LAV file to
 standard out;  some statistics are written to standard error.
 """
+
 from __future__ import print_function
 
 import sys
@@ -84,12 +85,12 @@ def main():
         usage("missing secondary file name and length")
 
     try:
-        (primaryFile, primary, primaryLengths) = parse_spec(primary)
+        primaryFile, primary, primaryLengths = parse_spec(primary)
     except Exception:
         usage("bad primary spec (must be seq_file[:species_name]:lengths_file")
 
     try:
-        (secondaryFile, secondary, secondaryLengths) = parse_spec(secondary)
+        secondaryFile, secondary, secondaryLengths = parse_spec(secondary)
     except Exception:
         usage("bad secondary spec (must be seq_file[:species_name]:lengths_file")
 
diff --git a/tools/filters/convert_characters.py b/tools/filters/convert_characters.py
index a0c9ae83616..a69a0dc2192 100644
--- a/tools/filters/convert_characters.py
+++ b/tools/filters/convert_characters.py
@@ -10,7 +10,7 @@ def __main__():
     parser = optparse.OptionParser()
     parser.add_option("--strip", action="store_true", help="strip leading and trailing whitespaces")
     parser.add_option("--condense", action="store_true", help="condense consecutive delimiters")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     if len(args) != 3:
         parser.error("usage: convert_characters.py infile from_char outfile")
 
diff --git a/tools/filters/gff/extract_GFF_Features.py b/tools/filters/gff/extract_GFF_Features.py
index 34c002b04cf..61eb1fd371c 100644
--- a/tools/filters/gff/extract_GFF_Features.py
+++ b/tools/filters/gff/extract_GFF_Features.py
@@ -5,6 +5,7 @@ Extract features from GFF file.
 
 usage: %prog input1 out_file1 column features
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py
index f53b52db3e3..7e00887dbe0 100644
--- a/tools/filters/gff/gff_filter_by_feature_count.py
+++ b/tools/filters/gff/gff_filter_by_feature_count.py
@@ -5,6 +5,7 @@ Filter a gff file using a criterion based on feature counts for a transcript.
 Usage:
 %prog input_name output_name feature_name condition
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/filters/join.py b/tools/filters/join.py
index 670921554f4..5e472f3b370 100644
--- a/tools/filters/join.py
+++ b/tools/filters/join.py
@@ -6,6 +6,7 @@ Script to Join Two Files on specified columns.
 Takes two tab delimited files, two column numbers (base 1) and outputs a new tab delimited file with lines joined by tabs.
 User can also opt to have have non-joining rows of file1 echoed.
 """
+
 from __future__ import print_function
 
 import json
diff --git a/tools/filters/random_lines_two_pass.py b/tools/filters/random_lines_two_pass.py
index 66262074bf2..21a75916a20 100644
--- a/tools/filters/random_lines_two_pass.py
+++ b/tools/filters/random_lines_two_pass.py
@@ -86,7 +86,7 @@ def __main__():
     parser.add_option(
         "-s", "--seed", dest="seed", action="store", type="string", default=None, help="Set the random seed."
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     assert len(args) == 3, "Invalid command line specified."
 
diff --git a/tools/filters/secure_hash_message_digest.py b/tools/filters/secure_hash_message_digest.py
index 6834fafff68..0f9dece529b 100644
--- a/tools/filters/secure_hash_message_digest.py
+++ b/tools/filters/secure_hash_message_digest.py
@@ -3,6 +3,7 @@
 """
 A script for calculating secure hashes / message digests.
 """
+
 import hashlib
 import optparse
 from collections import OrderedDict
@@ -24,7 +25,7 @@ def __main__():
     )
     parser.add_option("-i", "--input", dest="input", action="store", type="string", help="Input filename")
     parser.add_option("-o", "--output", dest="output", action="store", type="string", help="Output filename")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     algorithms = OrderedDict()
     for algorithm in options.algorithms:
diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index 6fda50ef252..41bf7ef08f2 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -1319,7 +1319,7 @@ def read_config():
     parser.set_defaults(pelinker_fname=def_pelinker_fname)
 
     # we parse the cmd line
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     # we put the result in a dict
     global config
diff --git a/tools/filters/ucsc_gene_bed_to_exon_bed.py b/tools/filters/ucsc_gene_bed_to_exon_bed.py
index e40a353faa5..f86b6e78690 100755
--- a/tools/filters/ucsc_gene_bed_to_exon_bed.py
+++ b/tools/filters/ucsc_gene_bed_to_exon_bed.py
@@ -13,6 +13,7 @@ options:
   -i, --input=inputfile       input file
   -o, --output=outputfile     output file
 """
+
 from __future__ import print_function
 
 import optparse
diff --git a/tools/filters/ucsc_gene_bed_to_intron_bed.py b/tools/filters/ucsc_gene_bed_to_intron_bed.py
index 54de6bddc8f..04f7e07993f 100755
--- a/tools/filters/ucsc_gene_bed_to_intron_bed.py
+++ b/tools/filters/ucsc_gene_bed_to_intron_bed.py
@@ -13,6 +13,7 @@ options:
   -i, --input=inputfile       input file
   -o, --output=outputfile     output file
 """
+
 from __future__ import print_function
 
 import optparse
diff --git a/tools/filters/ucsc_gene_table_to_intervals.py b/tools/filters/ucsc_gene_table_to_intervals.py
index f23a9fce211..1e2d7574cdf 100755
--- a/tools/filters/ucsc_gene_table_to_intervals.py
+++ b/tools/filters/ucsc_gene_table_to_intervals.py
@@ -13,6 +13,7 @@ options:
   -i, --input=inputfile       input file
   -o, --output=outputfile     output file
 """
+
 from __future__ import print_function
 
 import optparse
diff --git a/tools/filters/wiggle_to_simple.py b/tools/filters/wiggle_to_simple.py
index ae1953f7745..2ec08c33dab 100755
--- a/tools/filters/wiggle_to_simple.py
+++ b/tools/filters/wiggle_to_simple.py
@@ -4,6 +4,7 @@ Read a wiggle track and print out a series of lines containing
 "chrom position score". Ignores track lines, handles bed, variableStep
 and fixedStep wiggle lines.
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/maf/interval2maf.py b/tools/maf/interval2maf.py
index dd2641d6ea6..c8a4672b61e 100755
--- a/tools/maf/interval2maf.py
+++ b/tools/maf/interval2maf.py
@@ -24,6 +24,7 @@ usage: %prog maf_file [options]
    -l, --indexLocation=l: Override default maf_index.loc file
    -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/interval_maf_to_merged_fasta.py b/tools/maf/interval_maf_to_merged_fasta.py
index 133eba3e881..57b6bc75f63 100644
--- a/tools/maf/interval_maf_to_merged_fasta.py
+++ b/tools/maf/interval_maf_to_merged_fasta.py
@@ -23,6 +23,7 @@ usage: %prog maf_file [options]
 
 usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_by_block_number.py b/tools/maf/maf_by_block_number.py
index 5f023cd99f4..d81438aca49 100644
--- a/tools/maf/maf_by_block_number.py
+++ b/tools/maf/maf_by_block_number.py
@@ -4,6 +4,7 @@
 Reads a list of block numbers and a maf. Produces a new maf containing the
 blocks specified by number.
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/maf/maf_limit_size.py b/tools/maf/maf_limit_size.py
index a2aa3f0d3c2..5b8a750587d 100644
--- a/tools/maf/maf_limit_size.py
+++ b/tools/maf/maf_limit_size.py
@@ -3,6 +3,7 @@
 """
 Removes blocks that fall outside of specified size range.
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/maf/maf_limit_to_species.py b/tools/maf/maf_limit_to_species.py
index 28c70f5d8ac..ac1f706dcf6 100644
--- a/tools/maf/maf_limit_to_species.py
+++ b/tools/maf/maf_limit_to_species.py
@@ -6,6 +6,7 @@ columns containing only gaps.
 
 usage: %prog species,species2,... input_maf output_maf allow_partial min_species_per_block
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_reverse_complement.py b/tools/maf/maf_reverse_complement.py
index a80efb6c6c6..a3df5e58bfb 100644
--- a/tools/maf/maf_reverse_complement.py
+++ b/tools/maf/maf_reverse_complement.py
@@ -5,6 +5,7 @@ the reverse complement for each block in the source file.
 
 usage: %prog input_maf_file output_maf_file
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_split_by_species.py b/tools/maf/maf_split_by_species.py
index eeb6f36ad98..cc6794eb623 100644
--- a/tools/maf/maf_split_by_species.py
+++ b/tools/maf/maf_split_by_species.py
@@ -2,6 +2,7 @@
 """
 Read a maf and split blocks by unique species combinations
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/maf/maf_stats.py b/tools/maf/maf_stats.py
index 2d5772cee10..b67d2e132d7 100644
--- a/tools/maf/maf_stats.py
+++ b/tools/maf/maf_stats.py
@@ -3,6 +3,7 @@
 """
 Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
 """
+
 from __future__ import print_function
 
 import sys
diff --git a/tools/maf/maf_thread_for_species.py b/tools/maf/maf_thread_for_species.py
index 67a53394790..e9316692c6b 100644
--- a/tools/maf/maf_thread_for_species.py
+++ b/tools/maf/maf_thread_for_species.py
@@ -7,6 +7,7 @@ which are adjacent after the unwanted species have been dropped.
 
 usage: %prog input_maf output_maf species1,species2
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_to_bed.py b/tools/maf/maf_to_bed.py
index 3122501f5a7..b159f278506 100644
--- a/tools/maf/maf_to_bed.py
+++ b/tools/maf/maf_to_bed.py
@@ -2,6 +2,7 @@
 """
 Read a maf and output intervals for specified list of species.
 """
+
 from __future__ import print_function
 
 import os
diff --git a/tools/maf/maf_to_fasta_concat.py b/tools/maf/maf_to_fasta_concat.py
index 4dc174e9c3e..1f0c38f0f92 100755
--- a/tools/maf/maf_to_fasta_concat.py
+++ b/tools/maf/maf_to_fasta_concat.py
@@ -4,6 +4,7 @@ Read a maf and output a single block fasta file, concatenating blocks
 
 usage %prog species1,species2 maf_file out_file
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_to_fasta_multiple_sets.py b/tools/maf/maf_to_fasta_multiple_sets.py
index a08d2e8abc0..5993bcc069e 100755
--- a/tools/maf/maf_to_fasta_multiple_sets.py
+++ b/tools/maf/maf_to_fasta_multiple_sets.py
@@ -2,6 +2,7 @@
 """
 Read a maf and output a multiple block fasta file.
 """
+
 # Dan Blankenberg
 from __future__ import print_function
 
diff --git a/tools/maf/maf_to_interval.py b/tools/maf/maf_to_interval.py
index fd7b18ae3d4..88fa8bcb365 100644
--- a/tools/maf/maf_to_interval.py
+++ b/tools/maf/maf_to_interval.py
@@ -3,6 +3,7 @@
 """
 Read a maf and output intervals for specified list of species.
 """
+
 import os
 import sys
 
diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py
index 22c629400ab..0383999a1da 100644
--- a/tools/maf/vcf_to_maf_customtrack.py
+++ b/tools/maf/vcf_to_maf_customtrack.py
@@ -77,7 +77,7 @@ def main():
         default=False,
         help="Tool is being executed by Galaxy (adds extra error messaging).",
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     if len(args) < 3:
         if options.galaxy:
diff --git a/tools/metag_tools/shrimp_wrapper.py b/tools/metag_tools/shrimp_wrapper.py
index fc5ea7abf04..d617cb42482 100644
--- a/tools/metag_tools/shrimp_wrapper.py
+++ b/tools/metag_tools/shrimp_wrapper.py
@@ -42,6 +42,7 @@ SHRiMP output:
 >7:2:1147:982/1 chr3    +   95338194    95338225    4   35  36  2700    9T7C14
 >7:2:587:93/1   chr3    +   14913541    14913577    1   35  36  2960    19--16
 """
+
 from __future__ import print_function
 
 import os
diff --git a/tools/next_gen_conversion/solid2fastq.py b/tools/next_gen_conversion/solid2fastq.py
index d763375983e..61eab98b0e4 100644
--- a/tools/next_gen_conversion/solid2fastq.py
+++ b/tools/next_gen_conversion/solid2fastq.py
@@ -165,15 +165,13 @@ def main():
     options, args = parser.parse_args()
 
     if not (options.fout and options.fr and options.fq):
-        parser.error(
-            """
+        parser.error("""
         One or more of the three required paremetrs is missing:
         (1) --fr F3.csfasta file
         (2) --fq F3.qual file
         (3) --fout name of output file
         Use --help for more info
-        """
-        )
+        """)
 
     fr = open(options.fr)
     fq = open(options.fq)
diff --git a/tools/ngs_simulation/ngs_simulation.py b/tools/ngs_simulation/ngs_simulation.py
index fc6a226d603..7ccd5a155f8 100644
--- a/tools/ngs_simulation/ngs_simulation.py
+++ b/tools/ngs_simulation/ngs_simulation.py
@@ -16,6 +16,7 @@ usage: %prog [options]
    -m, --output_summary=m: File name for output summary of all simulations
    -f, --new_file_path=f: Directory for summary output files
 """
+
 # removed output of all simulation results on request (not working)
 #   -r, --sim_results=r: Output all tabular simulation results (number of polymorphisms times number of detection thresholds)
 #   -o, --output=o: Base name for summary output for each run
@@ -187,15 +188,12 @@ def __main__():
             output.close()
 
     # Parameters (heteroplasmy, error threshold, colours)
-    r(
-        """
+    r("""
     het=c(%s)
     err=c(%s)
     grade = (0:32)/32
     hues = rev(gray(grade))
-    """
-        % (",".join(str(p) for p in polymorphisms), ",".join(str(d) for d in detection_threshes))
-    )
+    """ % (",".join(str(p) for p in polymorphisms), ",".join(str(d) for d in detection_threshes)))
 
     # Suppress warnings
     r("options(warn=-1)")
@@ -228,80 +226,62 @@ def __main__():
         r('write.table(summary(ngsum), file="%s", quote=FALSE, sep="\t", row.names=FALSE)' % options.output_summary)
 
     # Summary objects (these could be printed)
-    r(
-        """
+    r("""
     tr_pos <- tapply(allsum$fprate,list(allsum$hetcol,allsum$errcol), mean)
     tr_neg <- tapply(allsum$FN,list(allsum$hetcol,allsum$errcol), mean)
     cat('\nFalse Positive Rate Summary\n\t', file='%s', append=T, sep='\t')
     write.table(format(tr_pos, digits=4), file='%s', append=T, quote=F, sep='\t')
     cat('\nFalse Negative Rate Summary\n\t', file='%s', append=T, sep='\t')
     write.table(format(tr_neg, digits=4), file='%s', append=T, quote=F, sep='\t')
-    """
-        % tuple([options.output_summary] * 4)
-    )
+    """ % tuple([options.output_summary] * 4))
 
     # Setup graphs
-    r(
-        """
+    r("""
     png('%s', width=800, height=500, units='px', res=250)
     layout(matrix(data=c(1,2,1,3,1,4), nrow=2, ncol=3), widths=c(4,6,2), heights=c(1,10,10))
-    """
-        % options.output_png
-    )
+    """ % options.output_png)
 
     # Main title
     genome = ""
     if options.genome:
         genome = "%s: " % options.genome
-    r(
-        """
+    r("""
     par(mar=c(0,0,0,0))
     plot(1, type='n', axes=F, xlab='', ylab='')
     text(1,1,paste('%sVariation in False Positives and Negatives (', %s, ' simulations, coverage ', %s,')', sep=''), font=2, family='sans', cex=0.7)
-    """
-        % (genome, options.num_sims, options.avg_coverage)
-    )
+    """ % (genome, options.num_sims, options.avg_coverage))
 
     # False positive boxplot
-    r(
-        """
+    r("""
     par(mar=c(5,4,2,2), las=1, cex=0.35)
     boxplot(allsum$fprate ~ allsum$errcol, horizontal=T, ylim=rev(range(allsum$fprate)), cex.axis=0.85)
     title(main='False Positives', xlab='false positive rate', ylab='')
-    """
-    )
+    """)
 
     # False negative heatmap (note zlim command!)
     num_polys = len(polymorphisms)
     num_dets = len(detection_threshes)
-    r(
-        """
+    r("""
     par(mar=c(5,4,2,1), las=1, cex=0.35)
     image(1:%s, 1:%s, tr_neg, zlim=c(0,1), col=hues, xlab='', ylab='', axes=F, border=1)
     axis(1, at=1:%s, labels=rownames(tr_neg), lwd=1, cex.axis=0.85, axs='i')
     axis(2, at=1:%s, labels=colnames(tr_neg), lwd=1, cex.axis=0.85)
     title(main='False Negatives', xlab='minor allele frequency', ylab='detection threshold')
-    """
-        % (num_polys, num_dets, num_polys, num_dets)
-    )
+    """ % (num_polys, num_dets, num_polys, num_dets))
 
     # Scale alongside
-    r(
-        """
+    r("""
     par(mar=c(2,2,2,3), las=1)
     image(1, grade, matrix(grade, ncol=length(grade), nrow=1), col=hues, xlab='', ylab='', xaxt='n', las=1, cex.axis=0.85)
     title(main='Key', cex=0.35)
     mtext('false negative rate', side=1, cex=0.35)
-    """
-    )
+    """)
 
     # Close graphics
-    r(
-        """
+    r("""
     layout(1)
     dev.off()
-    """
-    )
+    """)
 
 
 if __name__ == "__main__":
diff --git a/tools/phenotype_association/pagetag.py b/tools/phenotype_association/pagetag.py
index 7cd7e1fdcc1..07dfe81a4cc 100755
--- a/tools/phenotype_association/pagetag.py
+++ b/tools/phenotype_association/pagetag.py
@@ -37,6 +37,7 @@ b) a file where each line has the following:
 where SNP is one of  the SNPs and the "list" is a comma separated list of SNPs
 that exceed the rsquare threshold with the first SNP.
 """
+
 from __future__ import print_function
 
 from getopt import (
diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py
index 577225d8d58..5cbc4bf397d 100755
--- a/tools/phenotype_association/senatag.py
+++ b/tools/phenotype_association/senatag.py
@@ -21,6 +21,7 @@ d) Mark that SNP and all the snps connected to it as "visited". This should be
 done for each population.
 e) Continue steps b-e until all SNPs, in all populations have been visited.
 """
+
 from __future__ import print_function
 
 import heapq
diff --git a/tools/sr_assembly/velvetg_wrapper.py b/tools/sr_assembly/velvetg_wrapper.py
index a6ef93e4116..c9573599d6a 100644
--- a/tools/sr_assembly/velvetg_wrapper.py
+++ b/tools/sr_assembly/velvetg_wrapper.py
@@ -3,6 +3,7 @@
 Classes encapsulating decypher tool.
 James E Johnson - University of Minnesota
 """
+
 from __future__ import print_function
 
 import os
diff --git a/tools/sr_assembly/velveth_wrapper.py b/tools/sr_assembly/velveth_wrapper.py
index 42d49fce862..f83bb8ae31c 100644
--- a/tools/sr_assembly/velveth_wrapper.py
+++ b/tools/sr_assembly/velveth_wrapper.py
@@ -3,6 +3,7 @@
 Classes encapsulating decypher tool.
 James E Johnson - University of Minnesota
 """
+
 import os
 import subprocess
 import sys
diff --git a/tools/sr_mapping/bfast_wrapper.py b/tools/sr_mapping/bfast_wrapper.py
index 7685652e975..b3035b1e734 100644
--- a/tools/sr_mapping/bfast_wrapper.py
+++ b/tools/sr_mapping/bfast_wrapper.py
@@ -213,7 +213,7 @@ def __main__():
         help="output a random best scoring alignment",
     )
 
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     # output version # of tool
     try:
diff --git a/tools/sr_mapping/srma_wrapper.py b/tools/sr_mapping/srma_wrapper.py
index 0d52547f5a1..8c258c942e5 100644
--- a/tools/sr_mapping/srma_wrapper.py
+++ b/tools/sr_mapping/srma_wrapper.py
@@ -67,7 +67,7 @@ def __main__():
     parser.add_option("-p", "--params", dest="params", help="Parameter setting to use (pre_set or full)")
     parser.add_option("-j", "--jarBin", dest="jarBin", default="", help="The path to where jars are stored")
     parser.add_option("-f", "--jarFile", dest="jarFile", help="The file name of the jar file to use")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     # make temp directory for srma
     tmp_dir = tempfile.mkdtemp()
diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py
index 7cefe1b2587..f966c6b8a29 100644
--- a/tools/stats/grouping.py
+++ b/tools/stats/grouping.py
@@ -11,6 +11,7 @@ Arguments:
     5 ascii to delete (comma separated list)
     6... op,col,do_round,default
 """
+
 from __future__ import print_function
 
 import random