From d9d63dc9247971e51afb6bab76f95e1e1411d344 Mon Sep 17 00:00:00 2001
From: David Stansby <dstansby@gmail.com>
Date: Thu, 26 Dec 2024 17:24:39 +0000
Subject: [PATCH] Add recommended mypy config (#71)

* Improve TOC structure

* Add recommended mypy config

* Add pytest to mypy deps

* Fix unreachable messages

* Add pydantic zarr to type checking

* Remove unused comments

* Add a py.typed file

* Ignore subclssing any warnings
---
 .pre-commit-config.yaml                | 9 +++++++++
 pyproject.toml                         | 2 ++
 src/ome_zarr_models/py.typed           | 0
 src/ome_zarr_models/v04/hcs.py         | 2 +-
 src/ome_zarr_models/v04/image.py       | 2 +-
 src/ome_zarr_models/v04/image_label.py | 2 +-
 src/ome_zarr_models/v04/labels.py      | 2 +-
 src/ome_zarr_models/v04/well.py        | 2 +-
 tests/v04/test_multiscales.py          | 2 +-
 9 files changed, 17 insertions(+), 6 deletions(-)
 create mode 100644 src/ome_zarr_models/py.typed

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 170b66a..8f23ec5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -38,3 +38,12 @@ repos:
     rev: 0.7.21 # 0.7.19
     hooks:
     - id: mdformat
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: f56614daa94d5cd733d3b7004c5df9caad267b4a # 1.13.0
+    hooks:
+    -   id: mypy
+        additional_dependencies:
+        - pydantic
+        - pytest
+        - pydantic-zarr
diff --git a/pyproject.toml b/pyproject.toml
index 4de4244..73a89a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -95,7 +95,9 @@ skip-magic-trailing-comma = false # default is false
 [tool.mypy]
 
 strict = true
+warn_unreachable = true
 plugins = ['pydantic.mypy']
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 
 [[tool.mypy.overrides]]
 module = ["zarr.*", "pydantic_zarr.*"]
diff --git a/src/ome_zarr_models/py.typed b/src/ome_zarr_models/py.typed
new file mode 100644
index 0000000..e69de29
diff --git a/src/ome_zarr_models/v04/hcs.py b/src/ome_zarr_models/v04/hcs.py
index c460d67..6690432 100644
--- a/src/ome_zarr_models/v04/hcs.py
+++ b/src/ome_zarr_models/v04/hcs.py
@@ -19,7 +19,7 @@ class HCSAttrs(Base):
     plate: Plate
 
 
-class HCS(GroupSpec[HCSAttrs, ArraySpec | GroupSpec]):
+class HCS(GroupSpec[HCSAttrs, ArraySpec | GroupSpec]):  # type: ignore[misc]
     """
     An OME-zarr high-content screening (HCS) dataset representing a single plate.
     """
diff --git a/src/ome_zarr_models/v04/image.py b/src/ome_zarr_models/v04/image.py
index a85aee5..80fc399 100644
--- a/src/ome_zarr_models/v04/image.py
+++ b/src/ome_zarr_models/v04/image.py
@@ -74,7 +74,7 @@ class ImageAttrs(Base):
     omero: Omero | None = None
 
 
-class Image(GroupSpec[ImageAttrs, ArraySpec | GroupSpec]):
+class Image(GroupSpec[ImageAttrs, ArraySpec | GroupSpec]):  # type: ignore[misc]
     """
     An OME-zarr multiscale dataset.
     """
diff --git a/src/ome_zarr_models/v04/image_label.py b/src/ome_zarr_models/v04/image_label.py
index c992add..22c8725 100644
--- a/src/ome_zarr_models/v04/image_label.py
+++ b/src/ome_zarr_models/v04/image_label.py
@@ -119,7 +119,7 @@ class ImageLabelAttrs(Base):
     multiscales: list[Multiscale]
 
 
-class ImageLabel(GroupSpec[ImageLabelAttrs, ArraySpec | GroupSpec]):
+class ImageLabel(GroupSpec[ImageLabelAttrs, ArraySpec | GroupSpec]):  # type: ignore[misc]
     _check_arrays_compatible = model_validator(mode="after")(_check_arrays_compatible)
 
     @classmethod
diff --git a/src/ome_zarr_models/v04/labels.py b/src/ome_zarr_models/v04/labels.py
index 5dd88e9..db81728 100644
--- a/src/ome_zarr_models/v04/labels.py
+++ b/src/ome_zarr_models/v04/labels.py
@@ -20,7 +20,7 @@ class LabelsAttrs(Base):
     )
 
 
-class Labels(GroupSpec[LabelsAttrs, ArraySpec | GroupSpec]):
+class Labels(GroupSpec[LabelsAttrs, ArraySpec | GroupSpec]):  # type: ignore[misc]
     """
     An OME-zarr labels dataset.
     """
diff --git a/src/ome_zarr_models/v04/well.py b/src/ome_zarr_models/v04/well.py
index 1822187..179b6ce 100644
--- a/src/ome_zarr_models/v04/well.py
+++ b/src/ome_zarr_models/v04/well.py
@@ -72,7 +72,7 @@ class WellAttrs(Base):
     well: Well
 
 
-class WellGroup(GroupSpec[WellAttrs, ArraySpec | GroupSpec]):
+class WellGroup(GroupSpec[WellAttrs, ArraySpec | GroupSpec]):  # type: ignore[misc]
     def get_image(self, i: int) -> Image:
         """
         Get a single image from this well.
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 0614989..833a6a5 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -273,7 +273,7 @@ def test_transform_invalid_second_element(
         match="The second element of `coordinateTransformations` "
         "must be a translation transform",
     ):
-        Dataset(path="foo", coordinateTransformations=transforms)  # type: ignore[arg-type]
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 def test_validate_axes_top_transforms() -> None: