Drop support for Python 3.8

Drop Python 3.8 support in 5 Pulsar-compatible packages
(job_metrics, tool_util, tool_util_models, util, objectstore)
and run pyupgrade --py310-plus on their source code.

- Bump requires-python from >=3.8 to >=3.10 in all 5 packages
- Remove Python 3.8 and 3.9 classifiers
- Remove ruff per-file-ignores for UP rules on these paths
- Remove backports.zoneinfo conditional dependency
- Remove pydyf<0.11 pin from conditional-requirements.txt
- Update Makefile pyupgrade target (remove PY38_PYUPGRADE_PATHS)
- Update CI workflow to test with Python 3.10 instead of 3.8

Clean up unused deprecated typing imports after pyupgrade

Remove now-unused typing imports (Dict, List, Optional, Set, Tuple,
Type, Union) that became dead after pyupgrade --py310-plus converted
annotations to use built-in types and | syntax.

Also run ruff check --fix --select=UP007,UP045 across the entire
codebase to convert remaining Optional[X] -> X | None and
Union[X, Y] -> X | Y patterns.

Enable ruff UP007/UP045 for Python 3.10 union syntax

Remove UP007 (Union[X,Y] -> X | Y) and UP045 (Optional[X] -> X | None)
from the ruff ignore list and convert all type aliases across the
codebase. These rules were deferred while Python 3.9 was supported;
requires-python is now >=3.10.

A custom script was used because neither ruff --fix nor
pyupgrade --py310-plus converts Optional[X]/Union[X,Y] in type alias
positions (e.g. X = Union[A, B]) — they only handle annotation
positions (e.g. def f(x: Optional[int])). All 167 violations were
module-level type aliases. A few edge cases were fixed manually:
single-element Union[X,], typing.Union qualified refs, runtime
Optional[type] calls, and Annotated[Optional[...]] pydantic fields.

Fix UP007 autofix regression with string forward reference type aliases

Commit fa6bd955a0 enabled ruff UP007/UP045 and auto-fixed
module-level type aliases using Union with string forward
references, producing invalid 'str | str' expressions.

This was a known ruff bug (charliermarsh/ruff#826) that has since
been fixed in later ruff versions, but this codebase was
converted before the fix was in place.

Revert to Union syntax and restore TYPE_CHECKING imports that
ruff's TCH rule cleaned up as a side effect when it thought the
forward references were unused.

scripts/bootstrap_test_shed.py

@@ -12,7 +12,6 @@ import sys
 import tempfile
 from typing import (
     Any,
-    Optional,
 )
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
@@ -104,8 +103,8 @@ class RemoteToolShedPopulator(ToolShedPopulator):
     for tests.
     """
 
-    _categories_by_name: Optional[dict[str, Category]] = None
-    _users_by_username: Optional[dict[str, dict[str, Any]]] = None
+    _categories_by_name: dict[str, Category] | None = None
+    _users_by_username: dict[str, dict[str, Any]] | None = None
     _populators_by_username: dict[str, "RemoteToolShedPopulator"] = {}
 
     def __init__(self, admin_interactor: ShedApiInteractor, user_interactor: ShedApiInteractor):

scripts/check_and_update_purged_on_duplicated_uuid.py

@@ -28,7 +28,6 @@ from galaxy.model.orm.scripts import get_config
 from galaxy.objectstore import ObjectStore
 
 if __name__ == "__main__":
-
     from galaxy.celery import tasks  # noqa: F401
 
     config = get_config(sys.argv)

scripts/check_python.py

@@ -3,8 +3,6 @@ If the current installed Python version is not supported, prints an error
 message to stderr and returns 1
 """
 
-from __future__ import print_function
-
 import sys
 
 MIN_VERSION_TUPLE = (3, 10)
@@ -17,15 +15,12 @@ def check_python():
     else:
         version_string = ".".join(str(_) for _ in sys.version_info[:3])
         min_version_string = ".".join(str(_) for _ in MIN_VERSION_TUPLE)
-        msg = """ERROR: Your Python version is: {}
-Galaxy is currently supported on Python >={} .
+        msg = f"""ERROR: Your Python version is: {version_string}
+Galaxy is currently supported on Python >={min_version_string} .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
-on how to force Galaxy to use a different version.""".format(
-            version_string,
-            min_version_string,
-        )
+on how to force Galaxy to use a different version."""
         print(msg, file=sys.stderr)
         raise Exception(msg)
 

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -296,8 +296,7 @@ def _get_tool_id_for_hda(app, hda_id):
 
     job_query = select(Job.tool_id).join(JTODA).where(JTODA.dataset_id == hda_id)
 
-    tool_id = session.execute(job_query).scalars().first()
-    if tool_id is not None:
+    if (tool_id := session.execute(job_query).scalars().first()) is not None:
         return tool_id
 
     hda = session.get(HistoryDatasetAssociation, hda_id)

scripts/extract_tool_sections_from_api.py

@@ -16,7 +16,6 @@ import urllib.request
 from pathlib import Path
 from typing import (
     Any,
-    Optional,
 )
 
 import yaml
@@ -82,7 +81,7 @@ def represent_quoted_string(dumper: yaml.Dumper, data: str) -> yaml.ScalarNode:
 QuotingDumper.add_representer(QuotedString, represent_quoted_string)
 
 
-def fetch_tools(api_url: Optional[str] = None, timeout: float = DEFAULT_TIMEOUT_SECONDS) -> list[dict[str, Any]]:
+def fetch_tools(api_url: str | None = None, timeout: float = DEFAULT_TIMEOUT_SECONDS) -> list[dict[str, Any]]:
     """Fetch tools from a Galaxy `/api/tools` endpoint.
 
     Raises ``RuntimeError`` on transport / HTTP / decoding failures so the caller
@@ -274,7 +273,7 @@ def _build_arg_parser() -> argparse.ArgumentParser:
     return parser
 
 
-def main(argv: Optional[list[str]] = None) -> int:
+def main(argv: list[str] | None = None) -> int:
     args = _build_arg_parser().parse_args(argv)
 
     global API_URL, OUTPUT_FILE

scripts/fix_dm_versions.py

@@ -62,7 +62,7 @@ for guid in guid_mapping:
         tool_version = dm.find("./tool/version")
         tool_version = tool_version.text
 
-        new_guid = f"{guid[:guid.rfind('/')]}/{tool_version}"
+        new_guid = f"{guid[: guid.rfind('/')]}/{tool_version}"
         dm.attrib["guid"] = new_guid
         print(f"changing guid: {guid} -> {new_guid}")
         if "version" in dm.attrib:

scripts/mypy_config_utils.py

@@ -1,7 +1,6 @@
 import configparser
 import os
 from dataclasses import dataclass
-from typing import Optional
 
 
 @dataclass
@@ -29,7 +28,7 @@ def main():
             print(f"Warning section {entry.section_name} does not refer to existant files")
 
 
-def to_python_path(package_name: str) -> Optional[str]:
+def to_python_path(package_name: str) -> str | None:
     path = os.path.join("lib", package_name.replace(".", "/"))
     if os.path.exists(path + ".py"):
         path = f"{path}.py"

scripts/release-diff.py

@@ -105,7 +105,9 @@ def report_diff(added, changed, removed, new_files):
             "Changed",
             "The following configuration options have been changed",
             changed,
-            lambda x: f"-  {x[0]} has changed from\n\n   ::\n\n{_indent(x[1])}\n\n   to\n\n   ::\n\n{_indent(x[2])}\n\n",
+            lambda x: (
+                f"-  {x[0]} has changed from\n\n   ::\n\n{_indent(x[1])}\n\n   to\n\n   ::\n\n{_indent(x[2])}\n\n"
+            ),
         )
 
     if removed: