From 78234720c4e25dc07dd056570fb216bb69feb0ee Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 13 Dec 2024 12:41:28 +0000
Subject: [PATCH] Replace deprecated ``__package__`` with ``__name__`

`__package__` is deprecated since Python 3.13, see
https://docs.python.org/3/reference/datamodel.html#module.__package__

`importlib.resources.files()` can be passed a non-package module
since Python 3.12 (or importlib-resources 5.10.0, see
https://importlib-resources.readthedocs.io/en/latest/history.html#v5-10-0 ),
so we can use `__name__` instead of `__package__`.

Also, I noticed that in lib/galaxy/config/__init__.py we are passing
a directory to `importlib.resources.as_file()`, which is supported
only since Python 3.12 (or importlib-resources 5.9.0).

For the reasons above:
- Update conditional imports in `lib/galaxy/util/resources.py` to
  import from `importlib.resources` only for Python 3.12,
  otherwise from the importlib-resources package.
- Update importlib-resources requirement in galaxy-util package.
- Drop importlib-resources requirement from galaxy-web-apps as it's
  not imported directly from its code any more.
---
 lib/galaxy/authnz/managers.py                 |  2 +-
 lib/galaxy/config/__init__.py                 |  2 +-
 lib/galaxy/config/templates.py                |  2 +-
 lib/galaxy/exceptions/error_codes.py          |  2 +-
 .../files/templates/examples/__init__.py      |  2 +-
 lib/galaxy/managers/licenses.py               |  2 +-
 lib/galaxy/managers/markdown_util.py          |  2 +-
 lib/galaxy/navigation/data.py                 |  2 +-
 lib/galaxy/objectstore/examples/__init__.py   |  2 +-
 .../templates/examples/__init__.py            |  2 +-
 lib/galaxy/tool_util/client/landing.py        |  2 +-
 lib/galaxy/tool_util/linters/datatypes.py     |  2 +-
 .../tool_util/ontologies/ontology_data.py     |  2 +-
 lib/galaxy/tool_util/upgrade/__init__.py      |  2 +-
 lib/galaxy/util/resources.py                  | 22 +++++++++++--------
 lib/galaxy/util/rules_dsl.py                  |  2 +-
 lib/galaxy/web/framework/base.py              |  2 +-
 lib/galaxy/webapps/base/webapp.py             |  2 +-
 lib/galaxy_test/base/populators.py            |  6 ++---
 lib/tool_shed/test/base/populators.py         |  2 +-
 .../test/functional/test_shed_repositories.py |  2 +-
 packages/util/setup.cfg                       |  2 +-
 packages/web_apps/setup.cfg                   |  1 -
 .../tool_util/data/test_tool_data_bundles.py  |  4 ++--
 .../tool_util/test_parameter_specification.py |  4 ++--
 25 files changed, 40 insertions(+), 37 deletions(-)

diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 8a1145b9fd46..1d6ba0592e5f 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -26,7 +26,7 @@
     PSAAuthnz,
 )
 
-OIDC_BACKEND_SCHEMA = resource_path(__package__, "xsd/oidc_backends_config.xsd")
+OIDC_BACKEND_SCHEMA = resource_path(__name__, "xsd/oidc_backends_config.xsd")
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index ef284bae1158..14bc863f19cc 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -70,7 +70,7 @@
 ISO_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
 
 GALAXY_APP_NAME = "galaxy"
-GALAXY_SCHEMAS_PATH = resource_path(__package__, "schemas")
+GALAXY_SCHEMAS_PATH = resource_path(__name__, "schemas")
 GALAXY_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "config_schema.yml"
 REPORTS_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "reports_config_schema.yml"
 TOOL_SHED_CONFIG_SCHEMA_PATH = GALAXY_SCHEMAS_PATH / "tool_shed_config_schema.yml"
diff --git a/lib/galaxy/config/templates.py b/lib/galaxy/config/templates.py
index fc4b473ce7cc..04bf69adad14 100644
--- a/lib/galaxy/config/templates.py
+++ b/lib/galaxy/config/templates.py
@@ -33,7 +33,7 @@ def _get_template_body(template: str) -> str:
 
 def _get_template_path(relpath: str, custom_templates_dir: str) -> Traversable:
     """Return template file path."""
-    default_path = resource_path("galaxy.config", "templates") / relpath
+    default_path = resource_path(__name__, "templates") / relpath
     custom_path = Path(custom_templates_dir) / relpath
     if custom_path.exists():
         return custom_path
diff --git a/lib/galaxy/exceptions/error_codes.py b/lib/galaxy/exceptions/error_codes.py
index fe6c3e575177..0f978bcd4a24 100644
--- a/lib/galaxy/exceptions/error_codes.py
+++ b/lib/galaxy/exceptions/error_codes.py
@@ -43,7 +43,7 @@ def _from_dict(entry):
     return (name, ErrorCode(code, message))
 
 
-error_codes_json = resource_string(__package__, "error_codes.json")
+error_codes_json = resource_string(__name__, "error_codes.json")
 error_codes_by_name: Dict[str, ErrorCode] = {}
 error_codes_by_int_code: Dict[int, ErrorCode] = {}
 
diff --git a/lib/galaxy/files/templates/examples/__init__.py b/lib/galaxy/files/templates/examples/__init__.py
index 3220cb7423f2..1bbf5b4b46fb 100644
--- a/lib/galaxy/files/templates/examples/__init__.py
+++ b/lib/galaxy/files/templates/examples/__init__.py
@@ -2,4 +2,4 @@
 
 
 def get_example(filename) -> str:
-    return resource_string("galaxy.files.templates.examples", filename)
+    return resource_string(__name__, filename)
diff --git a/lib/galaxy/managers/licenses.py b/lib/galaxy/managers/licenses.py
index 47613aa739a8..f1c3b8f92585 100644
--- a/lib/galaxy/managers/licenses.py
+++ b/lib/galaxy/managers/licenses.py
@@ -65,7 +65,7 @@ class LicenseMetadataModel(BaseModel):
     "MPL-2.0",
     "PDDL-1.0",
 ]
-SPDX_LICENSES_STRING = resource_string(__package__, "licenses.json")
+SPDX_LICENSES_STRING = resource_string(__name__, "licenses.json")
 SPDX_LICENSES = json.loads(SPDX_LICENSES_STRING)
 for license in SPDX_LICENSES["licenses"]:
     license["recommended"] = license["licenseId"] in RECOMMENDED_LICENSES
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index ba32b6489624..be670bcc917c 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -767,7 +767,7 @@ def to_pdf_raw(basic_markdown: str, css_paths: Optional[List[str]] = None) -> by
         output_file.write(as_html)
         output_file.close()
         html = weasyprint.HTML(filename=index)
-        stylesheets = [weasyprint.CSS(string=resource_string(__package__, "markdown_export_base.css"))]
+        stylesheets = [weasyprint.CSS(string=resource_string(__name__, "markdown_export_base.css"))]
         for css_path in css_paths:
             with open(css_path) as f:
                 css_content = f.read()
diff --git a/lib/galaxy/navigation/data.py b/lib/galaxy/navigation/data.py
index 31b8b0d3c9ed..9af996c2ac29 100644
--- a/lib/galaxy/navigation/data.py
+++ b/lib/galaxy/navigation/data.py
@@ -5,6 +5,6 @@
 
 
 def load_root_component() -> Component:
-    new_data_yaml = resource_string(__package__, "navigation.yml")
+    new_data_yaml = resource_string(__name__, "navigation.yml")
     navigation_raw = yaml.safe_load(new_data_yaml)
     return Component.from_dict("root", navigation_raw)
diff --git a/lib/galaxy/objectstore/examples/__init__.py b/lib/galaxy/objectstore/examples/__init__.py
index 42b05b2d6eb2..ea099b6dcbcf 100644
--- a/lib/galaxy/objectstore/examples/__init__.py
+++ b/lib/galaxy/objectstore/examples/__init__.py
@@ -2,4 +2,4 @@
 
 
 def get_example(filename: str) -> str:
-    return resource_string("galaxy.objectstore.examples", filename)
+    return resource_string(__name__, filename)
diff --git a/lib/galaxy/objectstore/templates/examples/__init__.py b/lib/galaxy/objectstore/templates/examples/__init__.py
index 2bcbd0645c79..1bbf5b4b46fb 100644
--- a/lib/galaxy/objectstore/templates/examples/__init__.py
+++ b/lib/galaxy/objectstore/templates/examples/__init__.py
@@ -2,4 +2,4 @@
 
 
 def get_example(filename) -> str:
-    return resource_string("galaxy.objectstore.templates.examples", filename)
+    return resource_string(__name__, filename)
diff --git a/lib/galaxy/tool_util/client/landing.py b/lib/galaxy/tool_util/client/landing.py
index e089ae268689..63f5d7c7bc0f 100644
--- a/lib/galaxy/tool_util/client/landing.py
+++ b/lib/galaxy/tool_util/client/landing.py
@@ -24,7 +24,7 @@
 
 
 def load_default_catalog():
-    catalog_yaml = resource_string("galaxy.tool_util.client", "landing_catalog.sample.yml")
+    catalog_yaml = resource_string(__name__, "landing_catalog.sample.yml")
     return yaml.safe_load(catalog_yaml)
 
 
diff --git a/lib/galaxy/tool_util/linters/datatypes.py b/lib/galaxy/tool_util/linters/datatypes.py
index f05ae5c7ab23..63866cf0f84c 100644
--- a/lib/galaxy/tool_util/linters/datatypes.py
+++ b/lib/galaxy/tool_util/linters/datatypes.py
@@ -18,7 +18,7 @@
     from galaxy.tool_util.parser import ToolSource
     from galaxy.util.resources import Traversable
 
-DATATYPES_CONF = resource_path(__package__, "datatypes_conf.xml.sample")
+DATATYPES_CONF = resource_path(__name__, "datatypes_conf.xml.sample")
 
 
 def _parse_datatypes(datatype_conf_path: Union[str, "Traversable"]) -> Set[str]:
diff --git a/lib/galaxy/tool_util/ontologies/ontology_data.py b/lib/galaxy/tool_util/ontologies/ontology_data.py
index 63a4d573b4d7..cb5f7b093965 100644
--- a/lib/galaxy/tool_util/ontologies/ontology_data.py
+++ b/lib/galaxy/tool_util/ontologies/ontology_data.py
@@ -27,7 +27,7 @@ def _multi_dict_mapping(content: str) -> Dict[str, List[str]]:
 
 
 def _read_ontology_data_text(filename: str) -> str:
-    return resource_string(__package__, filename)
+    return resource_string(__name__, filename)
 
 
 BIOTOOLS_MAPPING_FILENAME = "biotools_mappings.tsv"
diff --git a/lib/galaxy/tool_util/upgrade/__init__.py b/lib/galaxy/tool_util/upgrade/__init__.py
index 41be4988d0c4..299062f03b19 100644
--- a/lib/galaxy/tool_util/upgrade/__init__.py
+++ b/lib/galaxy/tool_util/upgrade/__init__.py
@@ -46,7 +46,7 @@ class AdviceCode(TypedDict):
     url: NotRequired[str]
 
 
-upgrade_codes_json = resource_string(__package__, "upgrade_codes.json")
+upgrade_codes_json = resource_string(__name__, "upgrade_codes.json")
 upgrade_codes_by_name: Dict[str, AdviceCode] = {}
 
 for name, upgrade_object in loads(upgrade_codes_json).items():
diff --git a/lib/galaxy/util/resources.py b/lib/galaxy/util/resources.py
index f40a9b6071b3..60944e3f3ee8 100644
--- a/lib/galaxy/util/resources.py
+++ b/lib/galaxy/util/resources.py
@@ -3,17 +3,17 @@
 
 import sys
 
-if sys.version_info >= (3, 9):
+if sys.version_info >= (3, 12):
     from importlib.resources import (
         as_file,
         files,
-        Package as Anchor,
     )
+    from importlib.resources.abc import Traversable
 
-    if sys.version_info >= (3, 12):
-        from importlib.resources.abc import Traversable
+    if sys.version_info >= (3, 13):
+        from importlib.resources import Anchor
     else:
-        from importlib.abc import Traversable
+        from importlib.resources import Package as Anchor
 else:
     from importlib_resources import (
         as_file,
@@ -23,20 +23,24 @@
     from importlib_resources.abc import Traversable
 
 
-def resource_path(package_or_requirement: Anchor, resource_name: str) -> Traversable:
+def resource_path(anchor: Anchor, resource_name: str) -> Traversable:
     """
     Return specified resource as a Traversable.
+
+    anchor is either a module object or a module name as a string.
     """
-    return files(package_or_requirement).joinpath(resource_name)
+    return files(anchor).joinpath(resource_name)
 
 
-def resource_string(package_or_requirement: Anchor, resource_name: str) -> str:
+def resource_string(anchor: Anchor, resource_name: str) -> str:
     """
     Return specified resource as a string.
 
     Replacement function for pkg_resources.resource_string, but returns unicode string instead of bytestring.
+
+    anchor is either a module object or a module name as a string.
     """
-    return resource_path(package_or_requirement, resource_name).read_text()
+    return resource_path(anchor, resource_name).read_text()
 
 
 __all__ = (
diff --git a/lib/galaxy/util/rules_dsl.py b/lib/galaxy/util/rules_dsl.py
index ebea78be82a1..83aca4560ec2 100644
--- a/lib/galaxy/util/rules_dsl.py
+++ b/lib/galaxy/util/rules_dsl.py
@@ -12,7 +12,7 @@
 
 
 def get_rules_specification():
-    return yaml.safe_load(resource_string(__package__, "rules_dsl_spec.yml"))
+    return yaml.safe_load(resource_string(__name__, "rules_dsl_spec.yml"))
 
 
 def _ensure_rule_contains_keys(rule, keys):
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index 875494d3a378..dced82598fd6 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -35,7 +35,7 @@
 #: time of the most recent server startup
 server_starttime = int(time.time())
 try:
-    meta_json = json.loads(resource_string(__package__, "meta.json"))
+    meta_json = json.loads(resource_string(__name__, "meta.json"))
     server_starttime = meta_json.get("epoch") or server_starttime
 except Exception:
     meta_json = {}
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index f2be00448f20..611f4fa02c9a 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -181,7 +181,7 @@ def build_apispec(self):
     def create_mako_template_lookup(self, galaxy_app, name):
         paths = []
         base_package = (
-            "tool_shed.webapp" if galaxy_app.name == "tool_shed" else "galaxy.webapps.base"
+            "tool_shed.webapp" if galaxy_app.name == "tool_shed" else __name__
         )  # reports has templates in galaxy package
         base_template_path = resource_path(base_package, "templates")
         with ExitStack() as stack:
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 3f9a3043fd8a..ee32c27b822c 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -136,10 +136,10 @@
 CWL_TOOL_DIRECTORY = os.path.join(galaxy_root_path, "test", "functional", "tools", "cwl_tools")
 
 # Simple workflow that takes an input and call cat wrapper on it.
-workflow_str = resource_string(__package__, "data/test_workflow_1.ga")
+workflow_str = resource_string(__name__, "data/test_workflow_1.ga")
 # Simple workflow that takes an input and filters with random lines twice in a
 # row - first grabbing 8 lines at random and then 6.
-workflow_random_x2_str = resource_string(__package__, "data/test_workflow_2.ga")
+workflow_random_x2_str = resource_string(__name__, "data/test_workflow_2.ga")
 
 DEFAULT_TIMEOUT = 60  # Secs to wait for state to turn ok
 
@@ -1821,7 +1821,7 @@ def load_random_x2_workflow(self, name: str) -> dict:
     def load_workflow_from_resource(self, name: str, filename: Optional[str] = None) -> dict:
         if filename is None:
             filename = f"data/{name}.ga"
-        content = resource_string(__package__, filename)
+        content = resource_string(__name__, filename)
         return self.load_workflow(name, content=content)
 
     def simple_workflow(self, name: str, **create_kwds) -> str:
diff --git a/lib/tool_shed/test/base/populators.py b/lib/tool_shed/test/base/populators.py
index 642c1b76b9ac..7c2c31aba727 100644
--- a/lib/tool_shed/test/base/populators.py
+++ b/lib/tool_shed/test/base/populators.py
@@ -53,7 +53,7 @@
 HasRepositoryId = Union[str, Repository]
 
 DEFAULT_PREFIX = "repofortest"
-TEST_DATA_REPO_FILES = resource_path(__package__, "../test_data")
+TEST_DATA_REPO_FILES = resource_path(__name__, "../test_data")
 COLUMN_MAKER_PATH = TEST_DATA_REPO_FILES.joinpath("column_maker/column_maker.tar")
 COLUMN_MAKER_1_1_1_PATH = TEST_DATA_REPO_FILES.joinpath("column_maker/column_maker_1.1.1.tar")
 DEFAULT_COMMIT_MESSAGE = "a test commit message"
diff --git a/lib/tool_shed/test/functional/test_shed_repositories.py b/lib/tool_shed/test/functional/test_shed_repositories.py
index bd4e88d26567..6d7cd61262c6 100644
--- a/lib/tool_shed/test/functional/test_shed_repositories.py
+++ b/lib/tool_shed/test/functional/test_shed_repositories.py
@@ -20,7 +20,7 @@
     skip_if_api_v2,
 )
 
-COLUMN_MAKER_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar")
+COLUMN_MAKER_PATH = resource_path(__name__, "../test_data/column_maker/column_maker.tar")
 
 
 # test_0000 tests commit_message  - find a way to test it here
diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
index 808606b77042..b52765c23c45 100644
--- a/packages/util/setup.cfg
+++ b/packages/util/setup.cfg
@@ -36,7 +36,7 @@ install_requires =
     bleach
     boltons
     docutils!=0.17,!=0.17.1
-    importlib-resources;python_version<'3.9'
+    importlib-resources>=5.10.0;python_version<'3.12'
     packaging
     pyparsing
     PyYAML
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 19ddb35ae0b3..fceb66451cc4 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -46,7 +46,6 @@ install_requires =
     fastapi>=0.101.0
     gunicorn
     gxformat2
-    importlib-resources;python_version<'3.9'
     Mako
     MarkupSafe
     Paste
diff --git a/test/unit/tool_util/data/test_tool_data_bundles.py b/test/unit/tool_util/data/test_tool_data_bundles.py
index 616323946a7f..b449178b316c 100644
--- a/test/unit/tool_util/data/test_tool_data_bundles.py
+++ b/test/unit/tool_util/data/test_tool_data_bundles.py
@@ -55,7 +55,7 @@ def test_xml_parsing() -> None:
 
 
 def test_parsing_manual() -> None:
-    with as_file(resource_path(__package__, "example_data_managers/manual.xml")) as path:
+    with as_file(resource_path(__name__, "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")
@@ -66,7 +66,7 @@ def test_parsing_manual() -> None:
 
 
 def test_parsing_mothur() -> None:
-    with as_file(resource_path(__package__, "example_data_managers/mothur.xml")) as path:
+    with as_file(resource_path(__name__, "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")
diff --git a/test/unit/tool_util/test_parameter_specification.py b/test/unit/tool_util/test_parameter_specification.py
index ed4b437449b5..41ec1fc9a95a 100644
--- a/test/unit/tool_util/test_parameter_specification.py
+++ b/test/unit/tool_util/test_parameter_specification.py
@@ -41,7 +41,7 @@
 
 def specification_object():
     try:
-        yaml_str = resource_string(__package__, "parameter_specification.yml")
+        yaml_str = resource_string(__name__, "parameter_specification.yml")
     except AttributeError:
         # hack for the main() function below where this file is interpreted as part of the
         # Galaxy tree.
@@ -54,7 +54,7 @@ def framework_tool_checks():
     # There is something beautiful about a targeted tool for every parameter feature but realistically
     # we've been doing a version of the for a decade with tool tests and we can leverage those also.
     try:
-        yaml_str = resource_string(__package__, "framework_tool_checks.yml")
+        yaml_str = resource_string(__name__, "framework_tool_checks.yml")
     except AttributeError:
         # hack for the main() function below where this file is interpreted as part of the
         # Galaxy tree.