diff --git a/lib/galaxy/schema/fields.py b/lib/galaxy/schema/fields.py
index 687785e6eff8..f5ff399a3995 100644
--- a/lib/galaxy/schema/fields.py
+++ b/lib/galaxy/schema/fields.py
@@ -1,13 +1,11 @@
 import re
+import typing
 
 from pydantic import Field
 from typing_extensions import get_args
 
-try:
+if typing.TYPE_CHECKING:
     from galaxy.security.idencoding import IdEncodingHelper
-except ImportError:
-    IdEncodingHelper = object  # type: ignore[assignment,misc]
-
 
 ENCODED_DATABASE_ID_PATTERN = re.compile("f?[0-9a-f]+")
 ENCODED_ID_LENGTH_MULTIPLE = 16
@@ -18,7 +16,7 @@ class BaseDatabaseIdField:
     Database ID validation.
     """
 
-    security: IdEncodingHelper
+    security: "IdEncodingHelper"
 
     @classmethod
     def __get_validators__(cls):
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 9d83144c258e..2323183bd178 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -33,6 +33,7 @@
 )
 from galaxy.tool_shed.util import dependency_display
 from galaxy.util import listify
+from galaxy.util.tool_shed.encoding_util import tool_shed_encode
 from tool_shed.context import (
     ProvidesRepositoriesContext,
     ProvidesUserContext,
@@ -40,10 +41,7 @@
 from tool_shed.metadata import repository_metadata_manager
 from tool_shed.repository_types import util as rt_util
 from tool_shed.structured_app import ToolShedApp
-from tool_shed.util import (
-    encoding_util,
-    hg_util,
-)
+from tool_shed.util import hg_util
 from tool_shed.util.metadata_util import (
     get_all_dependencies,
     get_current_repository_metadata_for_changeset_revision,
@@ -195,9 +193,9 @@ def check_updates(app: ToolShedApp, request: UpdatesRequest) -> Union[str, Dict[
                     tool_shed_status_dict["revision_upgrade"] = "False"
                 break
         return (
-            encoding_util.tool_shed_encode(tool_shed_status_dict) if hexlify_this else json.dumps(tool_shed_status_dict)
+            tool_shed_encode(tool_shed_status_dict) if hexlify_this else json.dumps(tool_shed_status_dict)
         )
-    return encoding_util.tool_shed_encode({}) if hexlify_this else json.dumps({})
+    return tool_shed_encode({}) if hexlify_this else json.dumps({})
 
 
 def guid_to_repository(app: ToolShedApp, tool_id: str) -> "Repository":
diff --git a/lib/tool_shed/test/functional/conftest.py b/lib/tool_shed/test/functional/conftest.py
index 2b547bfe4b51..37bcabc6d661 100644
--- a/lib/tool_shed/test/functional/conftest.py
+++ b/lib/tool_shed/test/functional/conftest.py
@@ -1,6 +1,7 @@
 import os
 from typing import (
     Any,
+    Callable,
     Dict,
     Generator,
 )
@@ -29,7 +30,7 @@ def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser,
 
 test_browser = os.environ.get("TOOL_SHED_TEST_BROWSER", DEFAULT_BROWSER)
 if test_browser == "twill":
-    shed_browser = pytest.fixture(scope="class")(twill_browser)
+    shed_browser: Callable[..., Generator[ShedBrowser, None, None]] = pytest.fixture(scope="class")(twill_browser)
 elif test_browser == "playwright":
     shed_browser = pytest.fixture(scope="class")(playwright_browser)
 else:
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index baee2f6123ba..688e2397525b 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -28,6 +28,7 @@
 from galaxy.model.base import transaction
 from galaxy.tool_shed.util import dependency_display
 from galaxy.tools.repositories import ValidationContext
+from galaxy.util.tool_shed import encoding_util
 from galaxy.web.form_builder import (
     CheckboxField,
     SelectField,
@@ -44,7 +45,6 @@
 from tool_shed.util import (
     basic_util,
     common_util,
-    encoding_util,
     hg_util,
     metadata_util,
     readme_util,
diff --git a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/common.mako b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/common.mako
index 1da62ed987fc..e775470d39bb 100644
--- a/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/common.mako
+++ b/lib/tool_shed/webapp/templates/webapps/tool_shed/repository/common.mako
@@ -820,7 +820,7 @@
 
 <%def name="render_repository_items( metadata, containers_dict, can_set_metadata=False, render_repository_actions_for='tool_shed' )">
     <%
-        from tool_shed.util.encoding_util import tool_shed_encode
+        from galaxy.util.tool_shed.encoding_util import tool_shed_encode
 
         has_datatypes = metadata and 'datatypes' in metadata
         has_readme_files = metadata and 'readme_files' in metadata
diff --git a/packages/packages_by_dep_dag.txt b/packages/packages_by_dep_dag.txt
index 3d9bc1f307aa..6c2547ff9fac 100644
--- a/packages/packages_by_dep_dag.txt
+++ b/packages/packages_by_dep_dag.txt
@@ -1,21 +1,27 @@
 util
-schema
+
 config
 files
 job_metrics
 navigation
 objectstore
+schema
 tool_util
+
 data
 selenium
 tours
+test_base
+
 auth
 job_execution
-web_stack
+test_api
 web_framework
+web_stack
+
 app
+
 web_apps
-test_base
+
 test_driver
-test_api
-tool_shed
\ No newline at end of file
+tool_shed
diff --git a/packages/test.sh b/packages/test.sh
index 87497a561e4f..2850a258e1bd 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -13,7 +13,9 @@ for arg in "$@"; do
 done
 
 # Don't display the pip progress bar when running under CI
-[ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
+if [ "$CI" = 'true' ]; then
+    export PIP_PROGRESS_BAR=off
+fi
 
 # Change to packages directory.
 cd "$(dirname "$0")"
@@ -30,7 +32,11 @@ if [ $FOR_PULSAR -eq 0 ]; then
 fi
 
 # ensure ordered by dependency DAG
-while read -r package_dir; do
+while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.com/questions/12916352/shell-script-read-missing-last-line
+    if [ -z "$package_dir" ]; then
+        # Skip empty lines
+        continue
+    fi
     printf "\n========= TESTING PACKAGE ${package_dir} =========\n\n"
 
     cd "$package_dir"
diff --git a/templates/webapps/tool_shed/repository/common.mako b/templates/webapps/tool_shed/repository/common.mako
index 88761598d423..d3fff587b61d 100644
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -1046,7 +1046,7 @@
 
 <%def name="render_repository_items( metadata, containers_dict, can_set_metadata=False, render_repository_actions_for='tool_shed' )">
     <%
-        from tool_shed.util.encoding_util import tool_shed_encode
+        from galaxy.util.tool_shed.encoding_util import tool_shed_encode
 
         has_datatypes = metadata and 'datatypes' in metadata
         has_readme_files = metadata and 'readme_files' in metadata