diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 449402cb7bc..a864a68b05c 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -158,7 +158,7 @@ https://help.github.com/en/github/getting-started-with-github/git-and-github-lea
   particular emphasis on readability being the ultimate goal:
   - 4 spaces (not tabs!) per indentation level
   - divergences from PEP-8 are listed in the `[flake8]` section of the
-    `setup.cfg` file
+    `.flake8` file
   - The Python code base is automatically formatted using
     [isort](https://pycqa.github.io/isort/) (for imports) and
     [black](https://black.readthedocs.io). To easily format your Python code
diff --git a/contrib/galaxy_config_merger.py b/contrib/galaxy_config_merger.py
index f7d60f183aa..229fb57af6b 100644
--- a/contrib/galaxy_config_merger.py
+++ b/contrib/galaxy_config_merger.py
@@ -6,21 +6,6 @@ Created by Anne Pajon on 31 Jan 2012
 
 Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute.
 
-This source file is licensed under the Academic Free License version
-3.0 available at http://www.opensource.org/licenses/AFL-3.0.
-
-Permission is hereby granted to reproduce, translate, adapt, alter,
-transform, modify, or arrange this source file (the "Original Work");
-to distribute or communicate copies of it under any license of your
-choice that does not contradict the terms and conditions; to perform
-or display the Original Work publicly.
-
-THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS
-AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT
-LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR
-FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF
-THE ORIGINAL WORK IS WITH YOU.
-
 Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample
 """
 
diff --git a/lib/galaxy/job_execution/output_collect.py b/lib/galaxy/job_execution/output_collect.py
index a06c9c231e8..066681c2eb0 100644
--- a/lib/galaxy/job_execution/output_collect.py
+++ b/lib/galaxy/job_execution/output_collect.py
@@ -646,7 +646,7 @@ class DatasetCollector:
     def __init__(self, dataset_collection_description):
         self.discover_via = dataset_collection_description.discover_via
         # dataset_collection_description is an abstract description
-        # built from the tool parsing module - see galaxy.tool_util.parser.output_colleciton_def
+        # built from the tool parsing module - see galaxy.tool_util.parser.output_collection_def
         self.sort_key = dataset_collection_description.sort_key
         self.sort_reverse = dataset_collection_description.sort_reverse
         self.sort_comp = dataset_collection_description.sort_comp
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 07f912d45b5..b6d99043eba 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2128,10 +2128,8 @@ class MinimalJobWrapper(HasResourceParameters):
             raise Exception(f"Unknown target type [{target}]")
 
     def get_tool_provided_job_metadata(self):
-        if self.tool_provided_job_metadata is not None:
-            return self.tool_provided_job_metadata
-
-        self.tool_provided_job_metadata = self.tool.tool_provided_metadata(self)
+        if self.tool_provided_job_metadata is None:
+            self.tool_provided_job_metadata = self.tool.tool_provided_metadata(self)
         return self.tool_provided_job_metadata
 
     def get_dataset_finish_context(self, job_context, output_dataset_assoc):
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index d32754f782d..d606a493cdf 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -1322,9 +1322,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
 
     def _tool_from_lineage_version(self, lineage_tool_version):
         if lineage_tool_version.id_based:
-            return self._tools_by_id.get(lineage_tool_version.id, None)
+            return self._tools_by_id.get(lineage_tool_version.id)
         else:
-            return self._tool_versions_by_id.get(lineage_tool_version.id, {}).get(lineage_tool_version.version, None)
+            return self._tool_versions_by_id.get(lineage_tool_version.id, {}).get(lineage_tool_version.version)
 
     def _build_filter_method(self, trans):
         context = Bunch(toolbox=self, trans=trans)
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 7b8ccd52f8a..28627ac8d0c 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1332,14 +1332,6 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
 
     job_stdio = galaxy_interactor.get_job_stdio(job["id"])
 
-    if testdef.num_outputs is not None:
-        expected = testdef.num_outputs
-        actual = len(data_list) + len(data_collection_list)
-        if expected != actual:
-            message = f"Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}"
-            error = AssertionError(message)
-            register_exception(error)
-
     if testdef.num_outputs is not None:
         expected = testdef.num_outputs
         actual = len(data_list) + len(data_collection_list)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index aa1255d592c..988a040e36c 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -3528,7 +3528,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
                 add_copied_value_to_new_elements(new_labels[i], dce_object)
         for key in new_elements.keys():
             if not re.match(r"^[\w\- \.,]+$", key):
-                raise Exception(f"Invalid new colleciton identifier [{key}]")
+                raise Exception(f"Invalid new collection identifier [{key}]")
         self._add_datasets_to_history(history, new_elements.values())
         output_collections.create_collection(
             next(iter(self.outputs.values())), "output", elements=new_elements, propagate_hda_tags=False
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index b64f91ec873..f0bb67bcb9b 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -33,7 +33,7 @@ if typing.TYPE_CHECKING:
 log = logging.getLogger(__name__)
 
 SINGLE_EXECUTION_SUCCESS_MESSAGE = "Tool ${tool_id} created job ${job_id}"
-BATCH_EXECUTION_MESSAGE = "Executed ${job_count} job(s) for tool ${tool_id} request"
+BATCH_EXECUTION_MESSAGE = "Created ${job_count} job(s) for tool ${tool_id} request"
 
 
 class PartialJobExecution(Exception):
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 2ac753025e5..19b6f457313 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -19,6 +19,7 @@ from urllib.parse import urlparse
 import mako.lookup
 import mako.runtime
 from apispec import APISpec
+from paste.urlmap import URLMap
 from sqlalchemy import (
     and_,
     true,
@@ -47,6 +48,7 @@ from galaxy.web.framework import (
     helpers,
     url_for,
 )
+from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
 
 try:
     from importlib.resources import files  # type: ignore[attr-defined]
@@ -1114,10 +1116,6 @@ def default_url_path(path):
 
 
 def build_url_map(app, global_conf, **local_conf):
-    from paste.urlmap import URLMap
-
-    from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
-
     urlmap = URLMap()
     # Merge the global and local configurations
     conf = global_conf.copy()
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index d418ce5b3cf..4dfb1bfc9e9 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -260,7 +260,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         return {"has_empty_inputs": has_empty_inputs, "has_duplicate_inputs": has_duplicate_inputs}
 
     @expose_api
-    def inputs(self, trans: ProvidesUserContext, id, **kwd):
+    def inputs(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
         """
         GET /api/jobs/{id}/inputs
 
@@ -269,14 +269,14 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :type   id: string
         :param  id: Encoded job id
 
-        :rtype:     dictionary
-        :returns:   dictionary containing input dataset associations
+        :rtype:     list of dicts
+        :returns:   list of dictionaries containing input dataset associations
         """
         job = self.__get_job(trans, id)
         return self.__dictify_associations(trans, job.input_datasets, job.input_library_datasets)
 
     @expose_api
-    def outputs(self, trans: ProvidesUserContext, id, **kwd):
+    def outputs(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
         """
         outputs( trans, id )
         * GET /api/jobs/{id}/outputs
@@ -285,8 +285,8 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :type   id: string
         :param  id: Encoded job id
 
-        :rtype:     dictionary
-        :returns:   dictionary containing output dataset associations
+        :rtype:     list of dicts
+        :returns:   list of dictionaries containing output dataset associations
         """
         job = self.__get_job(trans, id)
         return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
@@ -309,7 +309,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         return self.job_manager.stop(job, message=message)
 
     @expose_api
-    def resume(self, trans: ProvidesUserContext, id, **kwd):
+    def resume(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
         """
         * PUT /api/jobs/{id}/resume
             Resumes a paused job
@@ -317,8 +317,8 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
         :type   id: string
         :param  id: Encoded job id
 
-        :rtype:     dictionary
-        :returns:   dictionary containing output dataset associations
+        :rtype:     list of dicts
+        :returns:   list of dictionaries containing output dataset associations
         """
         job = self.__get_job(trans, id)
         if not job:
@@ -425,13 +425,13 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
             raise exceptions.ConfigDoesNotAllowException(f"Tool '{job.tool_id}' cannot be rerun.")
         return tool.to_json(trans, {}, job=job)
 
-    def __dictify_associations(self, trans, *association_lists):
-        rval = []
+    def __dictify_associations(self, trans, *association_lists) -> List[dict]:
+        rval: List[dict] = []
         for association_list in association_lists:
             rval.extend(self.__dictify_association(trans, a) for a in association_list)
         return rval
 
-    def __dictify_association(self, trans, job_dataset_association):
+    def __dictify_association(self, trans, job_dataset_association) -> dict:
         dataset_dict = None
         dataset = job_dataset_association.dataset
         if dataset:
diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py
index fc6beed6627..50bb1ea9b25 100644
--- a/lib/galaxy_test/api/test_history_contents.py
+++ b/lib/galaxy_test/api/test_history_contents.py
@@ -434,7 +434,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
         assert post_combined_count == pre_combined_count + 1
         assert pre_dataset_count == post_dataset_count
 
-        # Test show dataset colleciton.
+        # Test show dataset collection.
         collection_url = f"histories/{self.history_id}/contents/dataset_collections/{dataset_collection['id']}"
         show_response = self._get(collection_url)
         self._assert_status_code_is(show_response, 200)
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index f7a7c188c64..5971780112a 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -2662,7 +2662,7 @@ class BaseDatasetCollectionPopulator:
         return element_identifiers
 
     def __create(self, payload, wait=False):
-        # Create a colleciton - either from existing datasets using collection creation API
+        # Create a collection - either from existing datasets using collection creation API
         # or from direct uploads with the fetch API. Dispatch on "targets" keyword in payload
         # to decide which to use.
         if "targets" not in payload:
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index de90dcf0d0b..403af4d246c 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -43,8 +43,6 @@ from . import (
 # Set a 10 minute timeout for repository installation.
 repository_installation_timeout = 600
 
-# Dial ClientCookie logging down (very noisy)
-logging.getLogger("ClientCookie.cookies").setLevel(logging.WARNING)
 log = logging.getLogger(__name__)
 tc.options["equiv_refresh_interval"] = 0
 
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 070917f05a9..68ae530f123 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -212,16 +212,17 @@ def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
     elif checkers.check_binary(file_path):
         return "<br/>Binary file<br/>"
     else:
-        for line in open(file_path):
-            safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
-            # Stop reading after string is larger than MAX_CONTENT_SIZE.
-            if len(safe_str) > MAX_CONTENT_SIZE:
-                large_str = (
-                    "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
-                    % util.nice_size(MAX_CONTENT_SIZE)
-                )
-                safe_str = f"{safe_str}{large_str}"
-                break
+        with open(file_path) as fh:
+            for line in fh:
+                safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
+                # Stop reading after string is larger than MAX_CONTENT_SIZE.
+                if len(safe_str) > MAX_CONTENT_SIZE:
+                    large_str = (
+                        "<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
+                        % util.nice_size(MAX_CONTENT_SIZE)
+                    )
+                    safe_str = f"{safe_str}{large_str}"
+                    break
 
         if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
             # Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 52def04404b..e0989af283c 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -11,6 +11,10 @@ from typing import (
     TYPE_CHECKING,
 )
 
+from mercurial import (
+    hg,
+    ui,
+)
 from sqlalchemy import (
     Boolean,
     Column,
@@ -414,11 +418,6 @@ class Repository(Base, Dictifiable, _HasTable):
 
     @property
     def hg_repo(self):
-        from mercurial import (
-            hg,
-            ui,
-        )
-
         if not WEAK_HG_REPO_CACHE.get(self):
             WEAK_HG_REPO_CACHE[self] = hg.cachedlocalrepo(hg.repository(ui.ui(), self.repo_path().encode("utf-8")))
         return WEAK_HG_REPO_CACHE[self].fetch()[0]
diff --git a/pyproject.toml b/pyproject.toml
index 96be89e3f10..29425a1bc79 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,7 +49,7 @@ cwltool = "==3.1.20211107152837"
 dictobj = "*"
 docutils = "!=0.17, !=0.17.1"
 edam-ontology = "*"
-fastapi = ">=0.68.2, !=0.69.0, !=0.70.0, !=0.70.1"  # https://github.com/tiangolo/fastapi/issues/4041
+fastapi = ">=0.71.0"  # https://github.com/tiangolo/fastapi/issues/4041
 fastapi-utils = "*"
 fs = "*"
 future = "*"