Gradually introduce mypy type checking (Phases 1-3)#48
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pskeshu merged 8 commits intoJun 15, 2026
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…t#46) Adds a lenient [tool.mypy] config with an explicit ignore_errors override list for the 113 modules that don't yet pass, runs mypy in the lint CI job and as a pre-commit hook, and adds mypy to the dev dependency group. New code is held to the standard; the override list shrinks as modules are cleaned up. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Annotates two implicit-Optional defaults and fixes a str/Path arg-type mismatch in create_timelapse_video. Removes the file from the mypy override list before it's even added. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Changes def f(x: T = None) to def f(x: T | None = None) to match PEP 484 / mypy's no_implicit_optional, matching the pattern already applied to bridge.py in gently-project#42. Removes 14 modules from the mypy ignore_errors override list (113 -> 99) that are now fully clean.
…errors The four ContextStore mixins (_intentions, _plans, _understanding, _ml_pipelines) call methods/attributes defined on the host class or sibling mixins (_conn, _tx, _now, _gen_id, get_plan_items, create_campaign, etc.), which mypy couldn't see on the mixins themselves. Add gently/harness/memory/_protocols.py declaring a StoreProtocol with these members and have each mixin inherit from it for typing only. Also fixes the remaining errors this didn't cover: two untyped dict literals in _plans.py needed explicit dict[str, Any] annotations, and three _ml_pipelines.py methods returning an Optional lookup right after an insert now assert the row exists. All four mixins are now mypy-clean; removes them from the ignore_errors override list (99 -> 95).
…y overrides Adds ctx_get(context, key) and retypes the require_* helpers in harness/tools/helpers.py to accept context: dict | None and return non-Optional success values, eliminating the dominant union-attr/arg-type pattern across the tool modules. Applies the same fix to memory_tools' local _get_memory and a handful of independent var-annotated/type issues. Removes all 16 gently.app.tools.* modules from the mypy override list (95 -> 79), cutting the underlying error count from 610 to 369. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
4 tasks
…ent crash and remaining type gaps - volume_tools.view_image: guard against a disconnected microscope client via require_microscope() instead of crashing on client.capture_bottom_image() - file_store/store register_volume: volume_data: np.ndarray = None -> np.ndarray | None = None (implicit-Optional missed in the earlier pass) - StoreProtocol: mark @runtime_checkable for consistency with gently.harness.protocols - TimelapseOrchestrator.start: embryo_ids: list[str] -> list[str] | None = None to match its actual None-handling and the docstring Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…onal CI installed mypy unpinned (`pip install mypy`) while the pre-commit hook pinned mirrors-mypy v2.1.0, so the two would diverge the moment a newer mypy released — "passes my pre-commit" would stop implying "passes CI". Pin all three sources to 2.1.0 (CI install, pyproject dev group, and the pre-commit rev) and cross-reference them so they move together. Also convert the one implicit-Optional missed in Phase 1: `view_image`'s `image: np.ndarray = None` in dispim/client.py (the other three params in that same signature were already converted). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
6 tasks
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Summary
Implements the incremental mypy-typing plan from #46: a lenient
[tool.mypy]config plus an explicit
[[tool.mypy.overrides]]ignore-list for currentlyfailing modules, wired into CI and pre-commit (#42's mypy scope), and then
progressively shrinking that list:
CONTRIBUTING.md(per Gradually introduce mypy type checking #46's task list).def f(x: str = None))across 45 modules, plus
gently/harness/bridge.py.StoreProtocolfor theContextStorememory mixins andfix the remaining errors it surfaced.
contextdict — newctx_get()helper plus retyped
require_agent/require_microscope/etc. ingently/harness/tools/helpers.py— clearing all 16gently.app.tools.*modules.
Results
mypy .passes cleanly against the remaining override list (300 source files)Test plan
.venv/bin/mypy .— success, no issues found in 300 source files.venv/bin/ruff check .— all checks passed.venv/bin/ruff format --check .— 300 files already formatted.venv/bin/pre-commit run --all-files— all hooks passProgress on #46 — 79 modules / 369 errors remain, scoped as a follow-up phase
in a separate issue.
🤖 Generated with Claude Code