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.
I think this fixes https://github.com/galaxyproject/galaxy/issues/18770
? I did manage to get the redirect to Galaxy, however the user interface
looks pretty weird to me, so I'm not sure this is how it is meant to be
?
Allows moving all data source tools using the script to profile 20.09.
For more recent profiles data_source.py would have to work outside of
Galaxy's Python environment.
- Drop support for very old format of specifying execution params in a
tabular file instead of a json one
- Use O_TRUNC to discard previous file contents instead of opening for
writing, then closing
- Do not silently ignore non-integer values for max_file_size
with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
The value of this can be seen for instance in unpack_tar_gz_archive - which should have nothing to do with datatypes and now doesn't need to load the whole datatypes module.
Use this in workflows API to allow downloading workflow files from configured URIs.
paperbenni