[hallelx2]

Nothing ran on a pull request. gh pr view returns statusCheckRollup: [] for every PR in this repo's history — #18 through #24 all merged CLEAN purely because nothing was configured to say otherwise. Green and absent are indistinguishable to gh, so a merge gate reading "merge once fully green" was vacuous. The 470 unit tests ran only when someone remembered to run them.

Two jobs

test — uv sync --frozen --group dev then pytest tests/unit.

--frozen is deliberate: a lockfile that has drifted from pyproject.toml fails the job rather than quietly resolving something different from what developers run. Python is pinned to 3.13 (what requires-python demands) so a runner image change cannot move it silently.

lint — ruff on the files the change touches, not the whole tree.

The tree carries ~140 pre-existing ruff errors. Gating on all of them would block every PR on work unrelated to it, and a check that cannot pass is a check that gets switched off. Gating the diff keeps new code clean while the backlog is paid down separately.

Verified before committing

Both branches of the diff step were run against real ranges:

$ # this PR — adds only YAML
base=b6862fb…
no Python files changed            → pass

$ # origin/main~2...origin/main
checking 4 files:
  src/cancerag/pipeline.py
  src/cancerag/preprocessing/binding_site.py
  tests/unit/test_pipeline_staleness.py
  tests/unit/test_receptor_repairs.py
All checks passed!                 → EXIT=0

The empty case matters because set -u plus an unset array is a common way for this exact step to break only on the PRs that touch no Python.

The workflow YAML parses, and uv sync --frozen succeeds against the current lock.

Not done here

• Making test a required status check on main — that is a repository setting, not a file, and it cannot be set from the PR. It needs doing once in Settings → Branches after this merges, or the checks will run and still not block anything. Flagging rather than silently leaving it.
• tests/integration — left out; it needs the docking stack, which is not available on a hosted runner.
• The ~140 pre-existing ruff errors, which are their own cleanup.

Closes HAL-4142