lnccbrown / lnccbrown/HSSM

Lift the pyrefly <1.3 cap: 1.3.0 reports 5 new type errors

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Description

pyrefly 1.3.0 (released 2026-09-11) reports 5 new errors on an unchanged `main` (fefed57d) under `[tool.pyrefly] preset = "legacy"`. It turned the weekly drift lint leg red on 2026-09-14 ([run](https://github.com/lnccbrown/HSSM/actions/runs/34808842835)). The last green lint run (2026-09-07) used pyrefly 1.2.0. mypy (2.3.1), xarray and arviz were unchanged between the two runs.

HSSM has no lockfile, so every PR's lint job gets 1.3.0 too. The companion PR caps `pyrefly<1.3` to unblock CI. This issue tracks the real migration and lifting that cap.

| Location | Error |
|---|---|
| `src/hssm/distribution_utils/onnx_utils/onnx2xla.py:49` | Class `AttributeType` has no class attribute `items` [missing-attribute] |
| `src/hssm/plotting/utils.py:592` | `not in` is not supported between `Literal['posterior_predictive']` and `None` [not-iterable] (and the same for `'prior_predictive'`) |
| `src/hssm/plotting/utils.py:604` | `None` is not subscriptable [unsupported-operation] |
| `src/hssm/utils.py:188` | Argument `DataArray \| DataTree` is not assignable to parameter `posterior` with type `DataArray` in `log_likelihood` [bad-argument-type] |

The two `plotting/utils.py` errors come from `dt = model.traces` right after an `is None` guard. 1.3.0 no longer narrows the attribute. The `utils.py` error is `dt["posterior"]`, which xarray types as `DataTree | DataArray`. None of these look like runtime bugs, but each one needs someone to decide between a narrowing fix (`assert`, `cast`, a local variable) and a suppression.

**Done when:** `uv run pyrefly check` passes on pyrefly 1.3.x and the `<1.3` cap is removed from `pyproject.toml`.

Refs #1302 (drift queue). Filed by the unattended spine drift-heal session.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with src/hssm/distribution_utils/onnx_utils/onnx2xla.py:49, src/hssm/plotting/utils.py:592 and 604, and src/hssm/utils.py:188; inspect the reported pyrefly 1.3.x errors and the surrounding type annotations. Run `uv run pyrefly check` while evaluating the narrowing or suppression approach for each location. Done means the check passes on pyrefly 1.3.x and the `<1.3` cap is removed from pyproject.toml.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
ci-cd, tooling
Issue type
Refactor
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Clearly specified
Newbie friendliness
72/100

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