refactor: lots of typing updates, add pyright tests on CI

.github/workflows/ci.yml

@@ -18,6 +18,15 @@ jobs:
       - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
+  pyright:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - run: uv run pyright
+
   test:
     name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.gui }} ${{ matrix.canvas }}
     runs-on: ${{ matrix.os }}

.github_changelog_generator

@@ -3,4 +3,4 @@ project=ndv
 issues=false
 exclude-labels=duplicate,question,invalid,wontfix,hide
 add-sections={"tests":{"prefix":"**Tests & CI:**","labels":["tests"]}, "documentation":{"prefix":"**Documentation:**", "labels":["documentation"]}}
-exclude-tags-regex=.*rc
+exclude-tags-regex=.*rc

.pre-commit-config.yaml

@@ -4,6 +4,16 @@ ci:
   autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
 
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: ".*\\.md"
+      - id: end-of-file-fixer
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: check-added-large-files
+
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: v0.24.1
     hooks:
@@ -32,3 +42,17 @@ repos:
           - pydantic
           - psygnal
           - IPython
+          - types-wxpython
+          - qtpy
+          - git+https://github.com/tlambert03/PyQt6-stubs.git@v6.7.3
+
+  - repo: local
+    hooks:
+      - id: pyright
+        stages: [manual]
+        exclude: "^docs/"
+        name: pyright
+        language: system
+        types_or: [python, pyi]
+        require_serial: true
+        entry: uv run pyright

Makefile

@@ -40,5 +40,5 @@ docs:
 docs-serve:
 	uv run --group docs mkdocs serve --no-strict
 
-lint: 
-	uv run pre-commit run --all-files
+lint:
+	uv run pre-commit run --all-files

docs/css/material.css

@@ -2,25 +2,25 @@
 .md-main__inner {
     margin-bottom: 1.5rem;
   }
-  
+
   /* Custom admonition: preview */
   :root {
     --md-admonition-icon--preview: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M15.5 12a3.5 3.5 0 1 1-7 0 3.5 3.5 0 0 1 7 0Z"/><path d="M12 3.5c3.432 0 6.124 1.534 8.054 3.241 1.926 1.703 3.132 3.61 3.616 4.46a1.6 1.6 0 0 1 0 1.598c-.484.85-1.69 2.757-3.616 4.461-1.929 1.706-4.622 3.24-8.054 3.24-3.432 0-6.124-1.534-8.054-3.24C2.02 15.558.814 13.65.33 12.8a1.6 1.6 0 0 1 0-1.598c.484-.85 1.69-2.757 3.616-4.462C5.875 5.034 8.568 3.5 12 3.5ZM1.633 11.945a.115.115 0 0 0-.017.055c.001.02.006.039.017.056.441.774 1.551 2.527 3.307 4.08C6.691 17.685 9.045 19 12 19c2.955 0 5.31-1.315 7.06-2.864 1.756-1.553 2.866-3.306 3.307-4.08a.111.111 0 0 0 .017-.056.111.111 0 0 0-.017-.056c-.441-.773-1.551-2.527-3.307-4.08C17.309 6.315 14.955 5 12 5 9.045 5 6.69 6.314 4.94 7.865c-1.756 1.552-2.866 3.306-3.307 4.08Z"/></svg>');
   }
-  
+
   .md-typeset .admonition.preview,
   .md-typeset details.preview {
     border-color: rgb(220, 139, 240);
   }
-  
+
   .md-typeset .preview>.admonition-title,
   .md-typeset .preview>summary {
     background-color: rgba(142, 43, 155, 0.1);
   }
-  
+
   .md-typeset .preview>.admonition-title::before,
   .md-typeset .preview>summary::before {
     background-color: rgb(220, 139, 240);
     -webkit-mask-image: var(--md-admonition-icon--preview);
     mask-image: var(--md-admonition-icon--preview);
-  }
+  }

examples/cookbook/microscope_dashboard.py

@@ -14,6 +14,8 @@
 - move the stage in the x and y directions.
 """
 
+from __future__ import annotations
+
 from typing import Any, cast
 
 import astropy.units as u

pyproject.toml

@@ -64,15 +64,12 @@ pyside = [
     "superqt[iconify,pyside6] >=0.7.2",
     # https://github.com/pyapp-kit/ndv/issues/59
     "pyside6 ==6.6.3; sys_platform == 'win32'",
-    "numpy >=1.23,<2; sys_platform == 'win32'",  # needed for pyside6.6
+    "numpy >=1.23,<2; sys_platform == 'win32'", # needed for pyside6.6
     "pyside6 >=6.4",
     "pyside6 >=6.6; python_version >= '3.12'",
     "qtpy >=2",
 ]
-wxpython = [
-    "pyconify>=0.2.1",
-    "wxpython >=4.2.2",
-]
+wxpython = ["pyconify>=0.2.1", "wxpython >=4.2.2"]
 
 # Supported Canavs backends
 vispy = ["vispy>=0.14.3", "pyopengl >=3.1"]
@@ -110,7 +107,7 @@ dev = [
     # omitting wxpython from dev env for now
     # because `uv sync && pytest hangs` on a wx test in the "full" env
     # use `make test extras=wx,[pygfx|vispy] isolated=1` to test
-    "ndv[vispy,pygfx,pyqt,jupyter]",   
+    "ndv[vispy,pygfx,pyqt,jupyter]",
     "imageio[tifffile] >=2.20",
     "ipykernel>=6.29.5",
     "ipython>=8.18.1",
@@ -119,6 +116,9 @@ dev = [
     "pre-commit>=4.1.0",
     "rich>=13.9.4",
     "ruff>=0.9.4",
+    "pyright>=1.1.400",
+    "types-wxpython",
+    "pydevd",
 ]
 docs = [
     "mkdocs >=1.6.1",
@@ -189,6 +189,23 @@ plugins = ["pydantic.mypy"]
 module = ["jupyter_rfb.*", "vispy.*", "ipywidgets.*"]
 ignore_missing_imports = true
 
+# https://github.com/microsoft/pyright/blob/main/docs/configuration.md
+[tool.pyright]
+include = ["src"]
+pythonVersion = "3.9"
+enableExperimentalFeatures = true
+# reportMissingImports = false
+reportOptionalMemberAccess = "none"
+reportIncompatibleMethodOverride = "none"
+reportAttributeAccessIssue = "none"
+reportMissingModuleSource = "none"
+reportPrivateImportUsage = "none"
+reportMissingImports = "information"
+reportArgumentType = "none"               # because of pydantic
+reportCallIssue = "none"
+verboseOutput = true
+venv = ".venv"
+
 # https://docs.pytest.org/
 [tool.pytest.ini_options]
 addopts = ["-v"]

src/ndv/controllers/_array_viewer.py

@@ -19,6 +19,8 @@
     from concurrent.futures import Future
     from typing import Any, Unpack
 
+    import numpy.typing as npt
+
     from ndv._types import ChannelKey, MouseMoveEvent
     from ndv.models._array_display_model import ArrayDisplayModelKwargs
     from ndv.models._viewer_model import ArrayViewerModelKwargs
@@ -272,7 +274,7 @@ def _add_histogram(self, channel: ChannelKey = None) -> None:
         self._histograms[channel] = hist
 
     def _update_channel_dtype(
-        self, channel: ChannelKey, dtype: np.typing.DTypeLike | None = None
+        self, channel: ChannelKey, dtype: npt.DTypeLike | None = None
     ) -> None:
         if not (ctrl := self._lut_controllers.get(channel, None)):
             return

src/ndv/data.py

@@ -1,5 +1,6 @@
 """Sample data for testing and examples."""
 
+# pyright: reportMissingImports=none
 from __future__ import annotations
 
 from typing import Any
@@ -41,7 +42,6 @@ def nd_sine_wave(
                 angle = np.pi / angle_dim * angle_idx
                 # Rotate x and y coordinates
                 xr = np.cos(angle) * x - np.sin(angle) * y
-                np.sin(angle) * x + np.cos(angle) * y
 
                 # Compute the sine wave
                 sine_wave = (amplitude * 0.5) * np.sin(frequency * xr + phase)

src/ndv/models/_array_display_model.py

@@ -4,6 +4,7 @@
 from enum import Enum
 from typing import TYPE_CHECKING, Literal, Optional, TypedDict, Union, cast
 
+from cmap import Colormap
 from pydantic import Field, computed_field, model_validator
 from typing_extensions import Self, TypeAlias
 
@@ -27,21 +28,21 @@ class LutModelKwargs(TypedDict, total=False):
         """Keyword arguments for `LUTModel`."""
 
         visible: bool
-        cmap: cmap.Colormap | cmap._colormap.ColorStopsLike
-        clims: tuple[float, float] | None
+        cmap: "cmap.Colormap | cmap._colormap.ColorStopsLike"
+        clims: "tuple[float, float] | None"
         gamma: float
         autoscale: AutoscaleType
 
     class ArrayDisplayModelKwargs(TypedDict, total=False):
         """Keyword arguments for `ArrayDisplayModel`."""
 
-        visible_axes: tuple[AxisKey, AxisKey, AxisKey] | tuple[AxisKey, AxisKey]
+        visible_axes: "tuple[AxisKey, AxisKey, AxisKey] | tuple[AxisKey, AxisKey]"
         current_index: Mapping[AxisKey, Union[int, slice]]
-        channel_mode: "ChannelMode" | Literal["grayscale", "composite", "color", "rgba"]
+        channel_mode: 'ChannelMode | Literal["grayscale", "composite", "color", "rgba"]'
         channel_axis: Optional[AxisKey]
-        reducers: Mapping[AxisKey | None, ReducerType]
-        luts: Mapping[int | None, LUTModel | LutModelKwargs]
-        default_lut: LUTModel | LutModelKwargs
+        reducers: Mapping["AxisKey | None", ReducerType]
+        luts: Mapping["int | None", "LUTModel | LutModelKwargs"]
+        default_lut: "LUTModel | LutModelKwargs"
 
 
 # map of axis to index/slice ... i.e. the current subset of data being displayed
@@ -59,7 +60,7 @@ class ArrayDisplayModelKwargs(TypedDict, total=False):
 def _default_luts() -> LutMap:
     colors = ["green", "magenta", "cyan", "red", "blue", "yellow"]
     return ValidatedEventedDict(
-        (i, LUTModel(cmap=color)) for i, color in enumerate(colors)
+        (i, LUTModel(cmap=Colormap(color))) for i, color in enumerate(colors)
     )
 
 

src/ndv/models/_data_display_model.py

@@ -77,7 +77,7 @@ class _ArrayDataDisplayModel(NDVModel):
         The data wrapper. Provides the actual data to be displayed
     """
 
-    display: ArrayDisplayModel = Field(default_factory=ArrayDisplayModel)
+    display: ArrayDisplayModel = Field(default_factory=lambda: ArrayDisplayModel())
     data_wrapper: Optional[DataWrapper] = None
 
     def model_post_init(self, __context: Any) -> None:

src/ndv/models/_data_wrapper.py

@@ -1,5 +1,6 @@
 """In this module, we provide built-in support for many array types."""
 
+# pyright: reportMissingImports=none
 from __future__ import annotations
 
 import json
@@ -19,7 +20,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Container, Iterator
-    from typing import Any, TypeAlias, TypeGuard
+    from typing import Any, Union
 
     import dask.array.core as da
     import numpy.typing as npt
@@ -30,8 +31,9 @@
     import torch
     import xarray as xr
     from pydantic import GetCoreSchemaHandler
+    from typing_extensions import TypeAlias, TypeGuard
 
-    Index: TypeAlias = int | slice
+    Index: TypeAlias = Union[int, slice]
 
 
 class SupportsIndexing(Protocol):

src/ndv/models/_lut_model.py

@@ -127,8 +127,8 @@
     center: Optional[float] = None  # None means center around the mean
 
     def get_limits(self, data: npt.NDArray) -> tuple[float, float]:
-        center = np.nanmean(data) if self.center is None else self.center
-        diff = self.n_stdev * np.nanstd(data)
+        center = float(np.nanmean(data) if self.center is None else self.center)
+        diff = float(self.n_stdev * np.nanstd(data))
         return center - diff, center + diff
 
     def __eq__(self, other: object) -> bool:

src/ndv/models/_mapping.py

@@ -43,7 +43,7 @@ class ValidatedEventedDict(MutableMapping[_KT, _VT]):
     def __init__(self) -> None: ...
     @overload
     def __init__(  # type: ignore[misc]
-        self: dict[str, _VT],
+        self: dict,
         key_validator: Callable[[Any], _KT] | None = None,
         value_validator: Callable[[Any], _VT] | None = None,
         **kwargs: _VT,
@@ -58,10 +58,10 @@ def __init__(
     ) -> None: ...
     @overload
     def __init__(  # type: ignore[misc]
-        self: dict[str, _VT],
+        self: dict,
         map: SupportsKeysAndGetItem[str, _VT],
         /,
-        key_validator: Callable[[Any], _KT] | None = ...,
+        key_validator: Callable[[Any], _KT] | None = None,
         value_validator: Callable[[Any], _VT] | None = ...,
         validate_lookup: bool = ...,
         **kwargs: _VT,
@@ -77,10 +77,10 @@ def __init__(
     ) -> None: ...
     @overload
     def __init__(  # type: ignore[misc]
-        self: dict[str, _VT],
+        self: dict,
         iterable: Iterable[tuple[str, _VT]],
         /,
-        key_validator: Callable[[Any], _KT] | None = ...,
+        key_validator: Callable[[Any], _KT] | None = None,
         value_validator: Callable[[Any], _VT] | None = ...,
         validate_lookup: bool = ...,
         **kwargs: _VT,

src/ndv/models/_reducer.py

@@ -18,6 +18,7 @@ class Reducer(Protocol):
 
     def __call__(self, a: npt.ArrayLike, axis: _ShapeLike = ...) -> npt.ArrayLike:
         """Reduce an array along an axis."""
+        raise NotImplementedError()
 
 
 def _str_to_callable(obj: Any) -> Callable: