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SET-1223: toolchain prep - #767

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set-1223-pr1-toolchain-prep
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SET-1223: toolchain prep#767
nevoodoo wants to merge 10 commits into
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set-1223-pr1-toolchain-prep

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@nevoodoo nevoodoo commented Aug 6, 2026

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First half of SET-1223. This is the in-place toolchain cleanup before the repo restructure, which will come in a follow-up PR.

Tests now run with pytest (the tests themselves are still unittest style, just the runner changed). Linting is ruff only now and the old pylint/flake8 configs are gone, ruff is bumped to 0.16 and its fixes are applied across scripts, server, web and the tests. Pre-commit hooks are bumped to latest and all the GitHub actions are pinned to commit SHAs.

setup.py, analysis_runner/ and .bumpversion.cfg are identical to main and the version hasn't changed, so merging this won't publish anything to PyPI. One thing to be aware of: ruff 0.16added some new rules that flag existing code inanalysis_runner/`, which this PR deliberately doesn't touch, so the ruff hook skips that directory for now. The restructure PR will swap that for per-file ignores and bring back full lint coverage of the package.

@nevoodoo nevoodoo changed the title SET-1223: toolchain prep — ruff-only lint, pytest runner, SHA-pinned actions SET-1223: toolchain prep Aug 6, 2026
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nevoodoo marked this pull request as ready for review August 6, 2026 11:12
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nevoodoo requested review from a team as code owners August 6, 2026 11:12
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nevoodoo requested review from jmarshall and removed request for jmarshall August 6, 2026 11:12
@nevoodoo nevoodoo assigned dancoates and unassigned dancoates Aug 6, 2026
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nevoodoo requested a review from dancoates August 12, 2026 00:50
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nevoodoo force-pushed the set-1223-pr1-toolchain-prep branch from faf8a52 to 3b65196 Compare August 12, 2026 01:15
Comment thread scripts/cromwell_status_parser.py Outdated


def copy_outputs_to_bucket(
def copy_outputs_to_bucket( # noqa: PLR0917

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This is added a few times. Should we suppress this one, or raise the limit via lint.pylint.max-positional-args?

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I think it would be good keep the limit fairly low to discourage future methods that have heaps of args, not against raising it above 5 though, 10 feels too high, 7 or 8?

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Looks fine to me

@nevoodoo
nevoodoo force-pushed the set-1223-pr1-toolchain-prep branch from 3b65196 to 013aed5 Compare August 16, 2026 05:57
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3 participants