importlib_resources is only needed in Python 3.8

Add type hints + fixes

lib/galaxy/config/__init__.py

@@ -59,11 +59,10 @@
 if TYPE_CHECKING:
     from galaxy.model import User
 
-try:
-    from importlib.resources import files  # type: ignore[attr-defined]
-except ImportError:
-    # Python < 3.9
-    from importlib_resources import files  # type: ignore[no-redef]
+if sys.version_info >= (3, 9):
+    from importlib.resources import files
+else:
+    from importlib_resources import files
 
 log = logging.getLogger(__name__)
 

lib/galaxy/config/templates.py

@@ -10,14 +10,17 @@
 
 from jinja2 import Environment
 
-from galaxy.util.resources import resource_path
+from galaxy.util.resources import (
+    resource_path,
+    Traversable,
+)
 
 TEMPLATE_SEP = ">>>>>>"  # Used to split templates into doc/body sections
 
 
 def render(template_path: str, context: dict, custom_templates_dir: str) -> str:
     """Read and return templated content as string."""
-    with open(_get_template_path(template_path, custom_templates_dir)) as f:
+    with _get_template_path(template_path, custom_templates_dir).open() as f:
         template_str = _get_template_body(f.read())
     tmpl = Environment().from_string(template_str)
     return tmpl.render(**context)
@@ -28,7 +31,7 @@ def _get_template_body(template: str) -> str:
     return template.split(TEMPLATE_SEP, 1)[-1].split("\n", 1)[1]
 
 
-def _get_template_path(relpath: str, custom_templates_dir: str) -> Path:
+def _get_template_path(relpath: str, custom_templates_dir: str) -> Traversable:
     """Return template file path."""
     default_path = resource_path("galaxy.config", "templates") / relpath
     custom_path = Path(custom_templates_dir) / relpath

lib/galaxy/util/resources.py

@@ -1,24 +1,38 @@
 """Provide a consistent interface into and utilities for importlib file resources.
 """
-try:
-    from importlib.abc import Traversable  # type: ignore[attr-defined]
-    from importlib.resources import files  # type: ignore[attr-defined]
-except ImportError:
-    # Python < 3.9
-    from importlib_resources import files  # type: ignore[no-redef]
-    from importlib_resources.abc import Traversable  # type: ignore[no-redef]
-
-
-def resource_path(package_or_requirement, resource_name):
+import sys
+
+if sys.version_info >= (3, 12):
+    from importlib.resources import (
+        Anchor,
+        as_file,
+        files,
+    )
+    from importlib.resources.abc import Traversable
+elif sys.version_info >= (3, 9):
+    from importlib.abc import Traversable
+    from importlib.resources import (
+        as_file,
+        files,
+        Package as Anchor,
+    )
+else:
+    from importlib_resources import (
+        as_file,
+        files,
+        Package as Anchor,
+    )
+    from importlib_resources.abc import Traversable
+
+
+def resource_path(package_or_requirement: Anchor, resource_name: str) -> Traversable:
     """
-    Return specified resource as a string.
-
-    Replacement function for pkg_resources.resource_string, but returns unicode string instead of bytestring.
+    Return specified resource as a Traversable.
     """
     return files(package_or_requirement).joinpath(resource_name)
 
 
-def resource_string(package_or_requirement, resource_name) -> str:
+def resource_string(package_or_requirement: Anchor, resource_name: str) -> str:
     """
     Return specified resource as a string.
 
@@ -28,6 +42,7 @@ def resource_string(package_or_requirement, resource_name) -> str:
 
 
 __all__ = (
+    "as_file",
     "files",
     "resource_string",
     "resource_path",

packages/util/setup.cfg

@@ -35,7 +35,7 @@ install_requires =
     bleach
     boltons
     docutils!=0.17,!=0.17.1
-    importlib_resources
+    importlib-resources;python_version<'3.9'
     packaging
     pyparsing
     PyYAML

packages/web_apps/setup.cfg

@@ -46,7 +46,7 @@ install_requires =
     fastapi-utils
     gunicorn
     gxformat2
-    importlib_resources
+    importlib-resources;python_version<'3.9'
     Mako
     MarkupSafe
     mercurial

pyproject.toml

@@ -69,7 +69,7 @@ gxformat2 = "*"
 h5grove = ">=1.2.1"
 h5py = "*"
 importlib-metadata = "<5"  # Work around https://github.com/celery/kombu/issues/1600
-importlib-resources = "*"
+importlib-resources = { version = "*", python = "<3.9" }  # for importlib.{abc.Traversable,resources.{files, Package}}
 isa-rwval = ">=0.10.10"
 kombu = "*"
 lagom = "*"
@@ -167,6 +167,7 @@ watchdog = "*"
 
 [tool.poetry.group.typecheck.dependencies]
 mypy = "*"
+lxml-stubs = "*"
 pydantic = "<2"  # for pydantic.mypy plugin
 types-bleach = "*"
 types-boto = "*"

test/unit/data/model/migrations/test_migrations.py

@@ -43,7 +43,10 @@
     drop_existing_database,
     url_factory,
 )
-from galaxy.util.resources import resource_path
+from galaxy.util.resources import (
+    as_file,
+    resource_path,
+)
 
 # Revision numbers from test versions directories
 GXY_REVISION_0 = "62695fac6cc0"  # oldest/base
@@ -1128,10 +1131,13 @@ def db_state6_gxy_state3_tsi_no_sam(url_factory, metadata_state6_gxy_state3_tsi_
 @pytest.fixture(autouse=True)
 def legacy_manage_db(monkeypatch):
     def get_alembic_cfg():
-        path = resource_path("galaxy.model.migrations", "alembic.ini")
-        config = Config(path)
-        path1, path2 = _get_paths_to_version_locations()
-        config.set_main_option("version_locations", f"{path1};{path2}")
+        traversable = resource_path("galaxy.model.migrations", "alembic.ini")
+        with as_file(traversable) as path:
+            config = Config(path)
+            path1, path2 = _get_paths_to_version_locations()
+            config.set_main_option("version_locations", f"{path1};{path2}")
+            # config.set_main_option() calls config.file_config() which memoizes
+            # the temporary file path from the as_file() contextmanager
         return config
 
     monkeypatch.setattr(galaxy.model.migrations.scripts, "get_alembic_cfg", get_alembic_cfg)

test/unit/tool_util/data/test_tool_data_bundles.py

@@ -15,7 +15,10 @@
     galaxy_directory,
     parse_xml,
 )
-from galaxy.util.resources import resource_path
+from galaxy.util.resources import (
+    as_file,
+    resource_path,
+)
 
 TOOLS_DIRECTORY = os.path.abspath(os.path.join(galaxy_directory(), "test/functional/tools/"))
 
@@ -51,8 +54,8 @@ def test_xml_parsing() -> None:
 
 
 def test_parsing_manual() -> None:
-    path = resource_path(__package__, "example_data_managers/manual.xml")
-    tree = parse_xml(path)
+    with as_file(resource_path(__package__, "example_data_managers/manual.xml")) as path:
+        tree = parse_xml(path)
     data_managers_el = tree.getroot()
     data_manager_el = data_managers_el.find("data_manager")
     description = convert_data_tables_xml(data_manager_el)
@@ -61,8 +64,8 @@ def test_parsing_manual() -> None:
 
 
 def test_parsing_mothur() -> None:
-    path = resource_path(__package__, "example_data_managers/mothur.xml")
-    tree = parse_xml(path)
+    with as_file(resource_path(__package__, "example_data_managers/mothur.xml")) as path:
+        tree = parse_xml(path)
     data_managers_el = tree.getroot()
     data_manager_el = data_managers_el.find("data_manager")
     description = convert_data_tables_xml(data_manager_el)