diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml
index 4d654af6ddbb..a5702df1b6a7 100644
--- a/.github/workflows/mulled.yaml
+++ b/.github/workflows/mulled.yaml
@@ -41,6 +41,8 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
       - name: Install Apptainer's singularity
         uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6  # https://github.com/eWaterCycle/setup-apptainer/pull/68
       - name: Install tox
         run: pip install tox
       - name: Run tests
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index d1ce7e7aaa2f..3a7c79e4de31 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -28958,7 +28958,6 @@ export interface operations {
             };
             path: {
                 library_id: string;
-                /** @example F0123456789ABCDEF */
                 id: string;
             };
             cookie?: never;
diff --git a/doc/schema_template.md b/doc/schema_template.md
index d6577843ba2f..d3c2ac63bc77 100644
--- a/doc/schema_template.md
+++ b/doc/schema_template.md
@@ -21,6 +21,8 @@ number of tutorials on building Galaxy tools that would better serve that purpos
 $tag:tool://element[@name='tool']
 $tag:tool|description://element[@name='tool']//element[@name='description']
 $tag:tool|macros://complexType[@name='Macros']
+$tag:tool|entry_points://complexType[@name='EntryPoints']
+$tag:tool|entry_points|entry_point://complexType[@name='EntryPoint']
 $tag:tool|edam_topics://complexType[@name='EdamTopics']
 $tag:tool|edam_operations://complexType[@name='EdamOperations']
 $tag:tool|xrefs://complexType[@name='xrefs']
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index a1ae2de306a9..12b0806347f2 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -57,7 +57,6 @@
 APP_DESCRIPTION = """Application to target for operation (i.e. galaxy, tool_shed, or reports))"""
 DRY_RUN_DESCRIPTION = """If this action modifies files, just print what would be the result and continue."""
 UNKNOWN_OPTION_MESSAGE = "Option [%s] not found in schema - either it is invalid or the Galaxy team hasn't documented it. If invalid, you should manually remove it. If the option is valid but undocumented, please file an issue with the Galaxy team."
-USING_SAMPLE_MESSAGE = "Config file not found, using sample."
 NO_APP_MAIN_MESSAGE = "No app:main section found, using application defaults throughout."
 YAML_COMMENT_WRAPPER = TextWrapper(
     initial_indent="# ", subsequent_indent="# ", break_long_words=False, break_on_hyphens=False
@@ -306,9 +305,11 @@ def _find_config(args: Namespace, app_desc: App) -> str:
             if os.path.exists(possible_ini_config):
                 path = possible_ini_config
 
-    if not path:
-        _warn(USING_SAMPLE_MESSAGE)
+    if path:
+        print(f"Found config file {path}")
+    else:
         path = os.path.join(args.galaxy_root, app_desc.sample_destination)
+        _warn(f"Config file not found, using sample {path}")
 
     return path
 
@@ -354,8 +355,8 @@ def _validate(args: Namespace, app_desc: App) -> None:
     path = _find_config(args, app_desc)
     # Allow empty mapping (not allowed by pykwalify)
     raw_config = _order_load_path(path)
-    if raw_config.get(app_desc.app_name) is None:
-        raw_config[app_desc.app_name] = {}
+    # Drop top-level keys (e.g. "gravity") except for app_desc.app_name
+    raw_config = {app_desc.app_name: raw_config.get(app_desc.app_name) or {}}
     # Rewrite the file any way to merge any duplicate keys
     with tempfile.NamedTemporaryFile("w", delete=False, suffix=".yml") as config_p:
         ordered_dump(raw_config, config_p)
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index d1e55b6a6eac..a5609884a53e 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -1717,7 +1717,7 @@ mapping:
 
       helpsite_url:
         type: str
-        required: true
+        required: false
         default: https://help.galaxyproject.org/
         per_host: true
         desc: |
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 9bd5b323b8b7..e3b3cf102050 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -193,12 +193,7 @@ def set_meta(
     def displayable(self, dataset: DatasetProtocol) -> bool:
         try:
             return (
-                not dataset.deleted
-                and not dataset.dataset.purged
-                and dataset.has_data()
-                and dataset.state == dataset.states.OK
-                and dataset.metadata.columns > 0
-                and dataset.metadata.data_lines != 0
+                super().displayable(dataset)
                 and dataset.metadata.chromCol
                 and dataset.metadata.startCol
                 and dataset.metadata.endCol
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 2a150806d60b..6b06711c9c1f 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -258,13 +258,12 @@ def value_from_basic(self, value, app, ignore_errors=False):
         elif isinstance(value, MutableMapping) and value.get("__class__") == "UnvalidatedValue":
             return value["value"]
         # Delegate to the 'to_python' method
-        if ignore_errors:
-            try:
-                return self.to_python(value, app)
-            except Exception:
-                return value
-        else:
+        try:
             return self.to_python(value, app)
+        except Exception:
+            if not ignore_errors:
+                raise
+            return value
 
     def value_to_display_text(self, value) -> str:
         if is_runtime_value(value):
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index 26b4e171c0de..5a0e256fcbf2 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -161,9 +161,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                     else:
                         rval_dict[input.name] = input.value_from_basic(d[input.name], app, ignore_errors)
                 rval.append(rval_dict)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):
@@ -226,9 +226,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
             for input in self.inputs.values():
                 if not ignore_errors or input.name in value:
                     rval[input.name] = input.value_from_basic(value[input.name], app, ignore_errors)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):
@@ -389,9 +389,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                     else:
                         rval_dict[input.name] = input.value_from_basic(d[input.name], app, ignore_errors)
                 rval.append(rval_dict)
-            except Exception as e:
+            except Exception:
                 if not ignore_errors:
-                    raise e
+                    raise
         return rval
 
     def get_file_count(self, trans, context):
@@ -794,9 +794,9 @@ def value_from_basic(self, value, app, ignore_errors=False):
                 # conditional's values dictionary.
                 if not ignore_errors or input.name in value:
                     rval[input.name] = input.value_from_basic(value[input.name], app, ignore_errors)
-        except Exception as e:
+        except Exception:
             if not ignore_errors:
-                raise e
+                raise
         return rval
 
     def get_initial_value(self, trans, context):
diff --git a/lib/galaxy/webapps/galaxy/services/library_contents.py b/lib/galaxy/webapps/galaxy/services/library_contents.py
index 971c356f56d3..ee94caa1fba2 100644
--- a/lib/galaxy/webapps/galaxy/services/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/library_contents.py
@@ -58,7 +58,7 @@
     str,
     Path(
         title="The encoded ID of a library folder or dataset.",
-        example="F0123456789ABCDEF",
+        examples=["F0123456789ABCDEF"],
         min_length=16,
         pattern="F?[0-9a-fA-F]+",
     ),
diff --git a/pytest.ini b/pytest.ini
index 31665649c393..706dc325bb03 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,5 +1,5 @@
 [pytest]
-addopts = --doctest-continue-on-failure --verbosity=1
+addopts = --doctest-continue-on-failure --verbosity=1 --showlocals
 asyncio_mode = auto
 log_level = DEBUG
 # Install pytest-memray and set memray to true here to enable memory profiling of tests
diff --git a/test/unit/tool_shed/test_shed_index.py b/test/unit/tool_shed/test_shed_index.py
index bc929dcddfb1..880489151e2d 100644
--- a/test/unit/tool_shed/test_shed_index.py
+++ b/test/unit/tool_shed/test_shed_index.py
@@ -26,7 +26,9 @@ def whoosh_index_dir():
 @pytest.fixture(scope="module")
 def community_file_dir():
     extracted_archive_dir = tempfile.mkdtemp()
-    b = BytesIO(requests.get(URL).content)
+    response = requests.get(URL)
+    response.raise_for_status()
+    b = BytesIO(response.content)
     tarfile.open(fileobj=b, mode="r:gz").extractall(extracted_archive_dir)
     try:
         yield extracted_archive_dir
diff --git a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
index 728757b52f31..9ec4e47b44f8 100644
--- a/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
+++ b/test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py
@@ -46,6 +46,6 @@ def test_singularity_container_test(tmp_path) -> None:
         "singularity",
         tmp_path,
     )
-    assert "samtools:1.0--1" in results["passed"]
-    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
-    assert "yasm:1.3.0--0" in results["notest"]
+    assert "samtools:1.0--1" in results["passed"], results
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"], results
+    assert "yasm:1.3.0--0" in results["notest"], results