mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 22:06:53 +08:00
paperbenni
bec3d3ad9c
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.
81 lines
2.6 KiB
Python
Executable File
81 lines
2.6 KiB
Python
Executable File
#!/usr/bin/env python
|
|
import argparse
|
|
import shutil
|
|
from datetime import datetime
|
|
|
|
from lxml import etree
|
|
|
|
desc = """
|
|
Fix shed_data_manager_conf.xml
|
|
|
|
Modifies the guid and version attribute of data_manager tags:
|
|
|
|
- the version in the guid (text after the last slash) is replaced
|
|
by the data manager tool version
|
|
- the version attribute is set to the data manager tool version
|
|
|
|
By default only data managers with duplicated guid are modified
|
|
and version attributes are not added if absent.
|
|
|
|
A copy of the original file with a time stamp appended to the name
|
|
is created.
|
|
|
|
Note, if there are versions of the data manager tool that have the
|
|
same version there will still be DMs with duplicated guids. These
|
|
need to be corrected manually.
|
|
"""
|
|
|
|
parser = argparse.ArgumentParser(description=desc)
|
|
parser.add_argument(
|
|
"shed_data_manager_conf",
|
|
metavar="CONFIG_FILE",
|
|
type=str,
|
|
default="config/shed_data_manager_conf.xml",
|
|
help="an integer for the accumulator",
|
|
)
|
|
parser.add_argument(
|
|
"--all-entries", action="store_true", help="modify all entries (default only those with duplicated guid)"
|
|
)
|
|
parser.add_argument("--add-version", action="store_true", help="also add version attribute if absent")
|
|
parser.add_argument("--dry-run", action="store_true", help="do not write resulting config file")
|
|
args = parser.parse_args()
|
|
|
|
with open(args.shed_data_manager_conf) as fh:
|
|
tree = etree.parse(args.shed_data_manager_conf)
|
|
root = tree.getroot()
|
|
|
|
guid_mapping = {}
|
|
for dm in root.iter("data_manager"):
|
|
guid = dm.attrib["guid"]
|
|
if guid not in guid_mapping:
|
|
guid_mapping[guid] = [dm]
|
|
else:
|
|
guid_mapping[guid].append(dm)
|
|
|
|
for guid in guid_mapping:
|
|
if len(guid_mapping[guid]) > 1:
|
|
print(f"{guid} found {len(guid_mapping[guid])}x")
|
|
elif not args.all_entries:
|
|
continue
|
|
|
|
for dm in guid_mapping[guid]:
|
|
tool_version = dm.find("./tool/version")
|
|
tool_version = tool_version.text
|
|
|
|
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:
|
|
print(f"changing version: {dm.attrib['version']} -> {tool_version}")
|
|
dm.attrib["version"] = tool_version
|
|
elif args.add_version:
|
|
print(f"adding version: {tool_version}")
|
|
dm.attrib["version"] = tool_version
|
|
|
|
if not args.dry_run:
|
|
nfn = args.shed_data_manager_conf + datetime.now().isoformat()
|
|
print(f"save copy at {nfn}")
|
|
shutil.copyfile(args.shed_data_manager_conf, nfn)
|
|
print(f"saving {args.shed_data_manager_conf}")
|
|
tree.write(args.shed_data_manager_conf)
|