From 6ef21f745d852272c4a9cf4e48e5b63e226a167e Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 16:51:18 -0500 Subject: [PATCH 1/6] chore: different approach --- .gitignore | 1 + pyproject.toml | 37 +- uv.lock | 6732 ------------------------------------------------ 3 files changed, 14 insertions(+), 6756 deletions(-) delete mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index 13afad07..0ad7c448 100644 --- a/.gitignore +++ b/.gitignore @@ -109,3 +109,4 @@ ENV/ # IDE settings .vscode/ .idea/ +uv.lock diff --git a/pyproject.toml b/pyproject.toml index dfce64d8..097a4a90 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,19 +7,13 @@ build-backend = "hatchling.build" [tool.hatch.version] source = "vcs" -# read more about configuring hatch at: -# https://hatch.pypa.io/latest/config/build/ -[tool.hatch.build.targets.wheel] -only-include = ["src"] -sources = ["src"] - # https://peps.python.org/pep-0621/ [project] name = "ndv" dynamic = ["version"] description = "Simple, fast-loading, n-dimensional array viewer, with minimal dependencies." readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10" license = { text = "BSD-3-Clause" } authors = [ { name = "Talley Lambert", email = "talley.lambert@gmail.com" }, @@ -29,7 +23,6 @@ classifiers = [ "Development Status :: 3 - Alpha", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -39,9 +32,9 @@ classifiers = [ dependencies = [ "cmap >=0.3", "numpy >=1.23", - "psygnal >=0.10", - "pydantic >=2.9", - "typing_extensions >= 4.0", + "psygnal >=0.12", + "pydantic >=2.10", + "typing_extensions >= 4.10", ] # https://peps.python.org/pep-0621/#dependencies-optional-dependencies @@ -53,12 +46,7 @@ jupyter = [ "jupyter_rfb >=0.3.3", "glfw >=2.4", ] -pyqt = [ - "pyqt6 >=6.4,!=6.6", - "pyqt6 >=6.5.3; python_version >= '3.12'", - "qtpy >=2", - "superqt[iconify] >=0.7.2", -] +pyqt = ["pyqt6 >=6.7", "qtpy >=2", "superqt[iconify] >=0.7.2"] pyside = [ # defer to superqt's pyside6 restrictions "superqt[iconify,pyside6] >=0.7.2,<0.7.5", @@ -74,7 +62,7 @@ wxpython = ["pyconify>=0.2.1", "wxpython >=4.2.2"] # Supported Canavs backends vispy = ["vispy>=0.14.3", "pyopengl >=3.1"] -pygfx = ["pygfx>=0.8.0"] +pygfx = ["pygfx==0.9.0", "rendercanvas ==2.0.1", "wgpu==0.19.3"] # ready to go bundles with pygfx qt = ["ndv[pygfx,pyqt]", "imageio[tifffile] >=2.20"] @@ -113,13 +101,14 @@ dev = [ "ipykernel>=6.29.5", "ipython>=8.18.1", "mypy>=1.14.1", - 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{ url = "https://files.pythonhosted.org/packages/b7/1a/7e4798e9339adc931158c9d69ecc34f5e6791489d469f5e50ec15e35f458/zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630, upload-time = "2024-11-10T15:05:19.275Z" }, -] From de9692409d570612487070fd002617ada5c60412 Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 16:52:01 -0500 Subject: [PATCH 2/6] format for py310 --- src/ndv/_types.py | 3 +-- src/ndv/models/_array_display_model.py | 27 ++++++++++++++------------ src/ndv/models/_data_display_model.py | 14 ++++++------- src/ndv/models/_data_wrapper.py | 14 ++++++------- src/ndv/models/_lut_model.py | 20 +++++++++---------- src/ndv/models/_mapping.py | 3 +-- src/ndv/models/_reducer.py | 9 ++++----- src/ndv/models/_ring_buffer.py | 3 ++- src/ndv/views/_app.py | 4 ++-- src/ndv/views/_jupyter/_app.py | 4 +++- src/ndv/views/_pygfx/_array_canvas.py | 6 +++--- src/ndv/views/_qt/_app.py | 4 ++-- src/ndv/views/_qt/_main_thread.py | 4 +++- src/ndv/views/_wx/_app.py | 3 ++- src/ndv/views/_wx/_main_thread.py | 4 +++- src/ndv/views/bases/_app.py | 3 ++- tests/test_controller.py | 5 ++++- tests/test_ring_buffer.py | 2 +- 18 files changed, 72 insertions(+), 60 deletions(-) diff --git a/src/ndv/_types.py b/src/ndv/_types.py index 3716fa9a..8a99aafb 100644 --- a/src/ndv/_types.py +++ b/src/ndv/_types.py @@ -6,10 +6,9 @@ from contextlib import suppress from enum import Enum, IntFlag, auto from functools import cache -from typing import TYPE_CHECKING, Annotated, Any, NamedTuple, cast +from typing import TYPE_CHECKING, Annotated, Any, NamedTuple, TypeAlias, cast from pydantic import PlainSerializer, PlainValidator -from typing_extensions import TypeAlias if TYPE_CHECKING: from qtpy.QtCore import Qt diff --git a/src/ndv/models/_array_display_model.py b/src/ndv/models/_array_display_model.py index bfaa23a0..67976728 100644 --- a/src/ndv/models/_array_display_model.py +++ b/src/ndv/models/_array_display_model.py @@ -2,11 +2,11 @@ import warnings from enum import Enum -from typing import TYPE_CHECKING, Literal, Optional, TypedDict, Union, cast +from typing import TYPE_CHECKING, Literal, TypeAlias, TypedDict, cast from cmap import Colormap from pydantic import Field, computed_field, model_validator -from typing_extensions import Self, TypeAlias +from typing_extensions import Self from ndv._types import AxisKey, ChannelKey, Slice @@ -16,8 +16,11 @@ from ._reducer import ReducerType if TYPE_CHECKING: - from collections.abc import Hashable, Mapping # noqa: F401 # used for mkdocstrings - from typing import Callable # noqa: F401 # used for mkdocstrings + from collections.abc import ( # noqa: F401 # used for mkdocstrings + Callable, # used for mkdocstrings + Hashable, + Mapping, + ) import cmap import numpy.typing as npt # noqa: F401 # used for mkdocstrings @@ -37,24 +40,24 @@ class ArrayDisplayModelKwargs(TypedDict, total=False): """Keyword arguments for `ArrayDisplayModel`.""" visible_axes: "tuple[AxisKey, AxisKey, AxisKey] | tuple[AxisKey, AxisKey]" - current_index: Mapping[AxisKey, Union[int, slice]] + current_index: Mapping[AxisKey, int | slice] channel_mode: 'ChannelMode | Literal["grayscale", "composite", "color", "rgba"]' - channel_axis: Optional[AxisKey] + channel_axis: AxisKey | None 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 -IndexMap: TypeAlias = ValidatedEventedDict[AxisKey, Union[int, Slice]] +IndexMap: TypeAlias = ValidatedEventedDict[AxisKey, int | Slice] # map of index along channel axis to LUTModel object LutMap: TypeAlias = ValidatedEventedDict[ChannelKey, LUTModel] # map of axis to reducer -Reducers: TypeAlias = ValidatedEventedDict[Union[AxisKey, None], ReducerType] +Reducers: TypeAlias = ValidatedEventedDict[AxisKey | None, ReducerType] # used for visible_axes -TwoOrThreeAxisTuple: TypeAlias = Union[ - tuple[AxisKey, AxisKey, AxisKey], tuple[AxisKey, AxisKey] -] +TwoOrThreeAxisTuple: TypeAlias = ( + tuple[AxisKey, AxisKey, AxisKey] | tuple[AxisKey, AxisKey] +) def _default_luts() -> LutMap: @@ -183,7 +186,7 @@ class ArrayDisplayModel(NDVModel): default_reducer: ReducerType = "numpy.max" # type: ignore [assignment] # FIXME channel_mode: ChannelMode = ChannelMode.GRAYSCALE - channel_axis: Optional[AxisKey] = None + channel_axis: AxisKey | None = None # must come after channel_axis, since it is used to set default visible_axes visible_axes: TwoOrThreeAxisTuple = Field( default_factory=lambda k: (-3, -2) if k.get("channel_axis") == -1 else (-2, -1) diff --git a/src/ndv/models/_data_display_model.py b/src/ndv/models/_data_display_model.py index 320c0308..844b645d 100644 --- a/src/ndv/models/_data_display_model.py +++ b/src/ndv/models/_data_display_model.py @@ -9,7 +9,7 @@ ) from concurrent.futures import Future from dataclasses import dataclass, field -from typing import Any, Optional, Union, cast +from typing import Any, cast import numpy as np from pydantic import Field @@ -33,9 +33,9 @@ class DataRequest: """Request object for data slicing.""" wrapper: DataWrapper = field(repr=False) - index: Mapping[int, Union[int, slice]] + index: Mapping[int, int | slice] visible_axes: tuple[int, ...] - channel_axis: Optional[int] + channel_axis: int | None channel_mode: ChannelMode @@ -49,7 +49,7 @@ class DataResponse: # mapping of channel_key -> data n_visible_axes: int data: Mapping[ChannelKey, np.ndarray] = field(repr=False) - request: Optional[DataRequest] = None + request: DataRequest | None = None # NOTE: nobody particularly likes this class. It does important stuff, but we're @@ -78,7 +78,7 @@ class _ArrayDataDisplayModel(NDVModel): """ display: ArrayDisplayModel = Field(default_factory=lambda: ArrayDisplayModel()) - data_wrapper: Optional[DataWrapper] = None + data_wrapper: DataWrapper | None = None def model_post_init(self, __context: Any) -> None: # connect the channel mode change signal to the channel axis guessing method @@ -133,7 +133,7 @@ def normed_visible_axes(self) -> "tuple[int, int, int] | tuple[int, int]": ) @property - def normed_current_index(self) -> Mapping[int, Union[int, slice]]: + def normed_current_index(self) -> Mapping[int, int | slice]: """Return the current index with positive integer axis keys. This method has to handle cases where the the model current index is expressed @@ -149,7 +149,7 @@ def normed_current_index(self) -> Mapping[int, Union[int, slice]]: """ wrapper = self._ensure_wrapper() - output: MutableMapping[int, Union[int, slice]] = {} + output: MutableMapping[int, int | slice] = {} rev_map: dict[Hashable, Hashable] = {} to_remove: list[Hashable] = [] diff --git a/src/ndv/models/_data_wrapper.py b/src/ndv/models/_data_wrapper.py index 64663b43..c3704f49 100644 --- a/src/ndv/models/_data_wrapper.py +++ b/src/ndv/models/_data_wrapper.py @@ -20,7 +20,7 @@ if TYPE_CHECKING: from collections.abc import Container, Iterator - from typing import Any, Union + from typing import Any, TypeAlias, TypeGuard import dask.array.core as da import numpy.typing as npt @@ -31,9 +31,8 @@ import torch import xarray as xr from pydantic import GetCoreSchemaHandler - from typing_extensions import TypeAlias, TypeGuard - Index: TypeAlias = Union[int, slice] + Index: TypeAlias = int | slice class SupportsIndexing(Protocol): @@ -142,7 +141,7 @@ def coords(self) -> Mapping[Hashable, Sequence]: dims = self.dims # type ignore is asserted in the __init__ method - return {i: range(s) for i, s in zip(dims, self._data.shape)} # type: ignore [attr-defined] + return {i: range(s) for i, s in zip(dims, self._data.shape, strict=False)} # type: ignore [attr-defined] def isel(self, index: Mapping[int, int | slice]) -> np.ndarray: """Return a slice of the data as a numpy array. @@ -440,7 +439,8 @@ def __init__(self, data: Any) -> None: else: self._dims = tuple(range(len(self._data.domain))) self._coords: Mapping[Hashable, Sequence] = { - i: range(s) for i, s in zip(self._dims, self._data.domain.shape) + i: range(s) + for i, s in zip(self._dims, self._data.domain.shape, strict=False) } @property @@ -459,7 +459,7 @@ def coords(self) -> Mapping[Hashable, Sequence]: return self._coords def sizes(self) -> Mapping[Hashable, int]: - return dict(zip(self._dims, self._data.domain.shape)) + return dict(zip(self._dims, self._data.domain.shape, strict=False)) def isel(self, indexers: Mapping[int, int | slice]) -> np.ndarray: if not indexers: @@ -484,7 +484,7 @@ class TorchTensorWrapper(DataWrapper["torch.Tensor"]): @property def coords(self) -> Mapping[Hashable, Sequence]: dims = self.dims - return {i: range(s) for i, s in zip(dims, self.data.shape)} + return {i: range(s) for i, s in zip(dims, self.data.shape, strict=False)} @property def dims(self) -> tuple[Hashable, ...]: diff --git a/src/ndv/models/_lut_model.py b/src/ndv/models/_lut_model.py index 2f5366f9..22f4e512 100644 --- a/src/ndv/models/_lut_model.py +++ b/src/ndv/models/_lut_model.py @@ -1,5 +1,6 @@ from abc import ABC, abstractmethod -from typing import Annotated, Any, Callable, Literal, Optional, Union +from collections.abc import Callable +from typing import Annotated, Any, Literal, TypeAlias import numpy as np import numpy.typing as npt @@ -13,20 +14,19 @@ field_validator, model_validator, ) -from typing_extensions import TypeAlias from ._base_model import NDVModel -AutoscaleType: TypeAlias = Union[ - Callable[[npt.ArrayLike], tuple[float, float]], tuple[float, float], bool -] +AutoscaleType: TypeAlias = ( + Callable[[npt.ArrayLike], tuple[float, float]] | tuple[float, float] | bool +) class ClimPolicy(BaseModel, ABC): """ABC for contrast limit policies.""" model_config = ConfigDict(frozen=True, extra="forbid") - _cached_clims: Optional[tuple[float, float]] = PrivateAttr(None) + _cached_clims: tuple[float, float] | None = PrivateAttr(None) @abstractmethod def get_limits(self, image: npt.NDArray) -> tuple[float, float]: @@ -37,7 +37,7 @@ def calc_clims(self, image: npt.NDArray) -> tuple[float, float]: return value @property - def cached_clims(self) -> Optional[tuple[float, float]]: + def cached_clims(self) -> tuple[float, float] | None: """Return the last calculated clims.""" return self._cached_clims @@ -124,7 +124,7 @@ class ClimsStdDev(ClimPolicy): clim_type: Literal["stddev"] = "stddev" n_stdev: Annotated[float, Gt(0)] = 2 # number of standard deviations - center: Optional[float] = None # None means center around the mean + center: float | None = None # None means center around the mean def get_limits(self, data: npt.NDArray) -> tuple[float, float]: center = float(np.nanmean(data) if self.center is None else self.center) @@ -149,7 +149,7 @@ def __eq__(self, other: object) -> bool: # return self.func(data) -ClimsType = Union[ClimsManual, ClimsPercentile, ClimsStdDev, ClimsMinMax] +ClimsType: TypeAlias = ClimsManual | ClimsPercentile | ClimsStdDev | ClimsMinMax class LUTModel(NDVModel): @@ -178,7 +178,7 @@ class LUTModel(NDVModel): visible: bool = True cmap: Colormap = Field(default_factory=lambda: Colormap("gray")) clims: ClimsType = Field(discriminator="clim_type", default_factory=ClimsMinMax) - clim_bounds: tuple[Optional[float], Optional[float]] = (None, None) + clim_bounds: tuple[float | None, float | None] = (None, None) gamma: float = 1.0 @model_validator(mode="before") diff --git a/src/ndv/models/_mapping.py b/src/ndv/models/_mapping.py index d0bdc6dc..b9072beb 100644 --- a/src/ndv/models/_mapping.py +++ b/src/ndv/models/_mapping.py @@ -1,12 +1,11 @@ from __future__ import annotations -from collections.abc import Iterable, Iterator, MutableMapping +from collections.abc import Callable, Iterable, Iterator, MutableMapping from contextlib import suppress from functools import cached_property from typing import ( TYPE_CHECKING, Any, - Callable, Protocol, TypeVar, cast, diff --git a/src/ndv/models/_reducer.py b/src/ndv/models/_reducer.py index aa0f2aef..08fea418 100644 --- a/src/ndv/models/_reducer.py +++ b/src/ndv/models/_reducer.py @@ -1,12 +1,11 @@ -from collections.abc import Sequence -from typing import Any, Callable, Protocol, SupportsIndex, Union, cast +from collections.abc import Callable, Sequence +from typing import Any, Protocol, SupportsIndex, TypeAlias, cast import numpy as np import numpy.typing as npt from pydantic_core import core_schema -from typing_extensions import TypeAlias -_ShapeLike: TypeAlias = Union[SupportsIndex, Sequence[SupportsIndex]] +_ShapeLike: TypeAlias = SupportsIndex | Sequence[SupportsIndex] class Reducer(Protocol): @@ -42,7 +41,7 @@ def _str_to_callable(obj: Any) -> Callable: return cast("Callable", obj) -def _callable_to_str(obj: Union[str, Callable]) -> str: +def _callable_to_str(obj: str | Callable) -> str: """Serialize a callable to a string.""" if isinstance(obj, str): return obj diff --git a/src/ndv/models/_ring_buffer.py b/src/ndv/models/_ring_buffer.py index 43a2d685..a31ba8d6 100644 --- a/src/ndv/models/_ring_buffer.py +++ b/src/ndv/models/_ring_buffer.py @@ -37,7 +37,8 @@ from psygnal import Signal if TYPE_CHECKING: - from typing import Any, Callable, SupportsIndex + from collections.abc import Callable + from typing import Any, SupportsIndex import numpy.typing as npt diff --git a/src/ndv/views/_app.py b/src/ndv/views/_app.py index f72e5743..934b5e7d 100644 --- a/src/ndv/views/_app.py +++ b/src/ndv/views/_app.py @@ -5,10 +5,10 @@ import sys from enum import Enum from functools import wraps -from typing import TYPE_CHECKING, Any, Callable, Protocol, cast +from typing import TYPE_CHECKING, Any, Protocol, cast if TYPE_CHECKING: - from collections.abc import Iterator + from collections.abc import Callable, Iterator from concurrent.futures import Future from typing import Literal diff --git a/src/ndv/views/_jupyter/_app.py b/src/ndv/views/_jupyter/_app.py index 3835dab4..61f57644 100644 --- a/src/ndv/views/_jupyter/_app.py +++ b/src/ndv/views/_jupyter/_app.py @@ -2,7 +2,7 @@ import os from types import MethodType -from typing import TYPE_CHECKING, Any, Callable +from typing import TYPE_CHECKING, Any from jupyter_rfb import RemoteFrameBuffer @@ -15,6 +15,8 @@ from ndv.views.bases._app import NDVApp if TYPE_CHECKING: + from collections.abc import Callable + from ndv.views.bases import ArrayView from ndv.views.bases._graphics._mouseable import Mouseable diff --git a/src/ndv/views/_pygfx/_array_canvas.py b/src/ndv/views/_pygfx/_array_canvas.py index 6a2be785..498aefc7 100755 --- a/src/ndv/views/_pygfx/_array_canvas.py +++ b/src/ndv/views/_pygfx/_array_canvas.py @@ -1,7 +1,7 @@ from __future__ import annotations from contextlib import suppress -from typing import TYPE_CHECKING, Any, Callable, Literal, cast +from typing import TYPE_CHECKING, Any, Literal, cast from weakref import ReferenceType, WeakKeyDictionary, ref import cmap as _cmap @@ -24,11 +24,11 @@ from ._util import rendercanvas_class if TYPE_CHECKING: - from collections.abc import Sequence + from collections.abc import Callable, Sequence + from typing import TypeAlias from pygfx.materials import ImageBasicMaterial from pygfx.resources import Texture - from typing_extensions import TypeAlias from wgpu.gui.jupyter import JupyterWgpuCanvas from wgpu.gui.qt import QWgpuCanvas from wgpu.gui.wx import WxWgpuCanvas diff --git a/src/ndv/views/_qt/_app.py b/src/ndv/views/_qt/_app.py index d1157328..0b1cb814 100644 --- a/src/ndv/views/_qt/_app.py +++ b/src/ndv/views/_qt/_app.py @@ -1,7 +1,7 @@ from __future__ import annotations import sys -from typing import TYPE_CHECKING, Any, Callable, ClassVar +from typing import TYPE_CHECKING, Any, ClassVar from qtpy.QtCore import QEvent, QObject, Qt, QTimer from qtpy.QtGui import QMouseEvent @@ -17,7 +17,7 @@ from ndv.views.bases._app import NDVApp if TYPE_CHECKING: - from collections.abc import Container + from collections.abc import Callable, Container from concurrent.futures import Future from ndv.views.bases import ArrayView diff --git a/src/ndv/views/_qt/_main_thread.py b/src/ndv/views/_qt/_main_thread.py index 60bfdc1d..d41251a7 100644 --- a/src/ndv/views/_qt/_main_thread.py +++ b/src/ndv/views/_qt/_main_thread.py @@ -1,7 +1,7 @@ from __future__ import annotations from concurrent.futures import Future -from typing import TYPE_CHECKING, Callable +from typing import TYPE_CHECKING from qtpy.QtCore import ( # type: ignore[attr-defined] QCoreApplication, @@ -13,6 +13,8 @@ ) if TYPE_CHECKING: + from collections.abc import Callable + from typing_extensions import ParamSpec, TypeVar T = TypeVar("T") diff --git a/src/ndv/views/_wx/_app.py b/src/ndv/views/_wx/_app.py index 623a1924..139f7145 100644 --- a/src/ndv/views/_wx/_app.py +++ b/src/ndv/views/_wx/_app.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Any, Callable +from typing import TYPE_CHECKING, Any import wx from wx import ( @@ -19,6 +19,7 @@ from ._main_thread import call_in_main_thread if TYPE_CHECKING: + from collections.abc import Callable from concurrent.futures import Future from ndv.views.bases import ArrayView diff --git a/src/ndv/views/_wx/_main_thread.py b/src/ndv/views/_wx/_main_thread.py index f0013323..8d79778f 100644 --- a/src/ndv/views/_wx/_main_thread.py +++ b/src/ndv/views/_wx/_main_thread.py @@ -1,11 +1,13 @@ from __future__ import annotations from concurrent.futures import Future -from typing import TYPE_CHECKING, Callable +from typing import TYPE_CHECKING import wx if TYPE_CHECKING: + from collections.abc import Callable + from typing_extensions import ParamSpec, TypeVar T = TypeVar("T") diff --git a/src/ndv/views/bases/_app.py b/src/ndv/views/bases/_app.py index b48c211f..4e92d9a9 100644 --- a/src/ndv/views/bases/_app.py +++ b/src/ndv/views/bases/_app.py @@ -8,9 +8,10 @@ from contextlib import suppress from functools import cache from threading import Timer -from typing import TYPE_CHECKING, Any, Callable, ClassVar, Literal, cast +from typing import TYPE_CHECKING, Any, ClassVar, Literal, cast if TYPE_CHECKING: + from collections.abc import Callable from types import TracebackType import pydevd diff --git a/tests/test_controller.py b/tests/test_controller.py index 53a5964b..b60dcafd 100644 --- a/tests/test_controller.py +++ b/tests/test_controller.py @@ -3,7 +3,7 @@ from __future__ import annotations import os -from typing import Any, Callable, cast, no_type_check +from typing import TYPE_CHECKING, Any, cast, no_type_check from unittest.mock import MagicMock, Mock, patch import numpy as np @@ -27,6 +27,9 @@ from ndv.views.bases._graphics._canvas import ArrayCanvas, HistogramCanvas from ndv.views.bases._graphics._canvas_elements import ImageHandle +if TYPE_CHECKING: + from collections.abc import Callable + try: from qtpy import API_NAME except ImportError: diff --git a/tests/test_ring_buffer.py b/tests/test_ring_buffer.py index d00b9078..fe2792d9 100644 --- a/tests/test_ring_buffer.py +++ b/tests/test_ring_buffer.py @@ -179,7 +179,7 @@ def test_iter() -> None: rb = RingBuffer(5) for i in range(5): rb.append(i) - for i, j in zip(rb, range(5)): + for i, j in zip(rb, range(5), strict=False): assert i == j From 142376a3ab9b9b9e1237c9dcbd5d5715bd1aebe2 Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 16:54:22 -0500 Subject: [PATCH 3/6] update tests --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ecb62e72..717c330a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,6 @@ jobs: runs-on: ${{ matrix.os }} env: UV_PYTHON: ${{ matrix.python-version }} - UV_FROZEN: 1 strategy: fail-fast: false matrix: @@ -156,7 +155,6 @@ jobs: runs-on: ubuntu-latest env: UV_PYTHON: ${{ matrix.python-version }} - UV_FROZEN: 1 strategy: fail-fast: false matrix: From dab512f39c9a1fb01cdbd84526efdf95769ec6e5 Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 16:55:22 -0500 Subject: [PATCH 4/6] more 3.9 changes --- .github/workflows/ci.yml | 14 +------------- pyproject.toml | 2 +- src/ndv/models/_data_display_model.py | 6 ++---- 3 files changed, 4 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 717c330a..fc267b1a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -70,11 +70,6 @@ jobs: python-version: "3.13" gui: jupyter canvas: pygfx - # pyside6 is struggling with 3.9 - - os: ubuntu-latest - python-version: "3.9" - gui: pyqt - canvas: vispy - os: ubuntu-latest python-version: "3.11" gui: pyqt @@ -83,14 +78,7 @@ jobs: python-version: "3.13" gui: pyqt canvas: pygfx - - os: macos-15 - gui: wxpython - python-version: "3.9" - canvas: vispy - - os: windows-latest - gui: jupyter - python-version: "3.9" - canvas: pygfx + steps: - uses: actions/checkout@v6 diff --git a/pyproject.toml b/pyproject.toml index 097a4a90..d7a6376a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -185,7 +185,7 @@ ignore_missing_imports = true # https://github.com/microsoft/pyright/blob/main/docs/configuration.md [tool.pyright] include = ["src"] -pythonVersion = "3.9" +pythonVersion = "3.10" enableExperimentalFeatures = true # reportMissingImports = false reportOptionalMemberAccess = "none" diff --git a/src/ndv/models/_data_display_model.py b/src/ndv/models/_data_display_model.py index 844b645d..acd66d05 100644 --- a/src/ndv/models/_data_display_model.py +++ b/src/ndv/models/_data_display_model.py @@ -1,5 +1,4 @@ import logging -import sys from collections.abc import ( Hashable, Iterator, @@ -23,12 +22,11 @@ __all__ = ["DataRequest", "DataResponse", "_ArrayDataDisplayModel"] -SLOTS = {"slots": True} if sys.version_info >= (3, 10) else {} logger = logging.getLogger(__name__) -@dataclass(frozen=True, **SLOTS) +@dataclass(frozen=True, slots=True) class DataRequest: """Request object for data slicing.""" @@ -39,7 +37,7 @@ class DataRequest: channel_mode: ChannelMode -@dataclass(frozen=True, **SLOTS) +@dataclass(frozen=True, slots=True) class DataResponse: """Response object for data requests. From 7f24455e212ebf1550d6c5557aec9fd7cbbf5fa4 Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 16:59:22 -0500 Subject: [PATCH 5/6] remove dashboard --- docs/cookbook/embedding.md | 14 -- examples/cookbook/microscope_dashboard.py | 171 ---------------------- 2 files changed, 185 deletions(-) delete mode 100644 examples/cookbook/microscope_dashboard.py diff --git a/docs/cookbook/embedding.md b/docs/cookbook/embedding.md index 62da9f89..40d7214c 100644 --- a/docs/cookbook/embedding.md +++ b/docs/cookbook/embedding.md @@ -30,17 +30,3 @@ each one. ```` {{ screenshot: examples/cookbook/multi_ndv.py }} - -## A minimal microscope dashboard using `openwfs` - -You can use `ndv` to take an external image source (i.e. a widefield camera) and -show its content in real-time in a custom widget embedding `ArrayViewer`. The -script below uses [`openwfs`](https://github.com/IvoVellekoop/openwfs) to -generate synthetic images of a sample and continuously update the view, and -allows to move the field of view over the X and Y axis. - -````python title="examples/cookbook/microscope_dashboard.py" ---8<-- "examples/cookbook/microscope_dashboard.py" -```` - -{{ screenshot: examples/cookbook/microscope_dashboard.py }} diff --git a/examples/cookbook/microscope_dashboard.py b/examples/cookbook/microscope_dashboard.py deleted file mode 100644 index 9511d8d3..00000000 --- a/examples/cookbook/microscope_dashboard.py +++ /dev/null @@ -1,171 +0,0 @@ -# /// script -# dependencies = [ -# "ndv[vispy,pyqt]", -# "openwfs", -# ] -# /// -"""A minimal microscope dashboard. - -The `SyntheticManager` acts as an microscope simulator. -It generates images of a specimen and sends them to the `DashboardWidget`. - -The `DashboardWidget` is a simple GUI that displays the images and allows the user to: -- starts/stops the simulation; -- move the stage in the x and y directions. -""" - -from __future__ import annotations - -from typing import Any, cast - -import astropy.units as u -import numpy as np -from openwfs.simulation import Camera, Microscope, StaticSource -from qtpy import QtWidgets as QtW -from qtpy.QtCore import QObject, Qt, Signal - -from ndv import ArrayViewer - - -class SyntheticManager(QObject): - newFrame = Signal(np.ndarray) - - def __init__(self, parent: QObject | None = None) -> None: - super().__init__(parent) - - specimen_resolution = (1024, 1024) # (height, width) in pixels of the image - specimen_pixel_size = 60 * u.nm # resolution (pixel size) of the specimen image - magnification = 40 # magnification from object plane to camera. - numerical_aperture = 0.85 # numerical aperture of the microscope objective - wavelength = 532.8 * u.nm # wavelength of the light, for computing diffraction. - camera_resolution = (256, 256) # number of pixels on the camera - - img = np.random.randint(-10000, 10, specimen_resolution, dtype=np.int16) - img = np.maximum(img, 0) - src = StaticSource(img, pixel_size=specimen_pixel_size) - - self._microscope = Microscope( - src, - magnification=magnification, - numerical_aperture=numerical_aperture, - wavelength=wavelength, - ) - self._camera = Camera( - self._microscope, - analog_max=None, - shot_noise=True, - digital_max=255, - shape=camera_resolution, - ) - - def move_stage(self, axis: str, step: float) -> None: - if axis == "x": - self._microscope.xy_stage.x += step * u.um - if axis == "y": - self._microscope.xy_stage.y += step * u.um - - def toggle_simulation(self, start: bool) -> None: - if start: - self._timer_id = self.startTimer(100) - elif hasattr(self, "_timer_id"): - self.killTimer(self._timer_id) - - def timerEvent(self, e: Any) -> None: - self.emit_frame() - - def emit_frame(self) -> None: - self.newFrame.emit(self._camera.read()) - - -class StageWidget(QtW.QGroupBox): - stageMoved = Signal(str, int) - - def __init__(self, name: str, axes: list[str], parent: QtW.QWidget) -> None: - super().__init__(name, parent) - self._data_key = "data" - - def _make_button(txt: str, *data: Any) -> QtW.QPushButton: - btn = QtW.QPushButton(txt) - btn.setAutoRepeat(True) - btn.setProperty(self._data_key, data) - btn.clicked.connect(self._move_stage) - return btn - - layout = QtW.QVBoxLayout(self) - for ax in axes: - # spinbox showing stage position - spin = QtW.QDoubleSpinBox() - spin.setMinimumWidth(80) - spin.setAlignment(Qt.AlignmentFlag.AlignRight) - spin.setSuffix(" µm") - spin.setFocusPolicy(Qt.FocusPolicy.NoFocus) - spin.setButtonSymbols(QtW.QAbstractSpinBox.ButtonSymbols.NoButtons) - - # buttons to move the stage - down = _make_button("-", ax, spin) - up = _make_button("+", ax, spin) - - row = QtW.QHBoxLayout() - row.addWidget(QtW.QLabel(f"{ax}:"), 0) - row.addWidget(spin, 0, Qt.AlignmentFlag.AlignRight) - row.addWidget(down, 1) - row.addWidget(up, 1) - layout.addLayout(row) - - def _move_stage(self) -> None: - button = cast("QtW.QPushButton", self.sender()) - ax, spin = button.property(self._data_key) - step = 1 if button.text() == "+" else -1 - cast("QtW.QDoubleSpinBox", spin).stepBy(step) - self.stageMoved.emit(ax, step) - - -class DashboardWidget(QtW.QWidget): - simulationStarted = Signal(bool) - stageMoved = Signal(str, int) - - def __init__(self) -> None: - super().__init__() - - self._stage_widget = StageWidget("Stage", ["x", "y"], self) - self._stage_widget.setEnabled(False) - self._stage_widget.stageMoved.connect(self.stageMoved) - - self._viewer = ArrayViewer() - self._viewer._async = False # Disable async rendering for simplicity - - self._start_button = QtW.QPushButton("Start") - self._start_button.setMinimumWidth(120) - self._start_button.toggled.connect(self.start_simulation) - self._start_button.setCheckable(True) - - bottom = QtW.QHBoxLayout() - bottom.setContentsMargins(0, 0, 0, 0) - bottom.addWidget(self._start_button) - bottom.addSpacing(120) - bottom.addWidget(self._stage_widget) - - layout = QtW.QVBoxLayout(self) - layout.setSpacing(0) - layout.addWidget(self._viewer.widget(), 1) - layout.addLayout(bottom) - - def start_simulation(self, checked: bool) -> None: - self._stage_widget.setEnabled(checked) - self._start_button.setText("Stop" if checked else "Start") - self.simulationStarted.emit(checked) - - def set_data(self, frame: np.ndarray) -> None: - self._viewer.data = frame - - -app = QtW.QApplication([]) -manager = SyntheticManager() -wrapper = DashboardWidget() - -manager.newFrame.connect(wrapper.set_data) -wrapper.simulationStarted.connect(manager.toggle_simulation) -wrapper.stageMoved.connect(manager.move_stage) -manager.emit_frame() # just to populate the viewer with an image -wrapper.show() -app.exec() From ab3584009e02a9e0960efbad211fea3588e10f36 Mon Sep 17 00:00:00 2001 From: Talley Lambert Date: Wed, 4 Mar 2026 17:06:33 -0500 Subject: [PATCH 6/6] change numpy deps --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d7a6376a..d738fc36 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,8 @@ classifiers = [ ] dependencies = [ "cmap >=0.3", - "numpy >=1.23", + "numpy >=2.1.0; python_version >= '3.13'", + "numpy >=1.26.0; python_version >= '3.12'", "psygnal >=0.12", "pydantic >=2.10", "typing_extensions >= 4.10", @@ -52,7 +53,7 @@ pyside = [ "superqt[iconify,pyside6] >=0.7.2,<0.7.5", # 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' and python_version < '3.13'", # needed for pyside6.6 "pyside6 >=6.4", "pyside6 >=6.6; python_version >= '3.12' and sys_platform == 'win32'", "pyside6 >=6.7; python_version >= '3.12' and sys_platform != 'win32'", @@ -79,7 +80,6 @@ array-libs = [ "aiohttp>=3.11.11", "dask[array]>=2024.8.0", "jax[cpu]>=0.4.30", - "numpy>=1.23", "pooch>=1.8.2", "pyopencl>=2025.1", "pyopencl[pocl]>=2025.1 ; sys_platform == 'linux'",