Set up stubs for scipy and scikit-image as installable package (vreut…

…er#1)

* first-pass at basic installable

* need stubs suffix as hyphen to point to real package, and to be detected as stubs-only

* try removing added files that shouldn't really be needed

* bundle scipy and skimage stubs for installation per PEP 561

pyproject.toml

@@ -1,3 +1,38 @@
+[tool.poetry]
+name = "python-type-stubs"
+version = "0.1dev"
+description = "A set of type stubs for popular Python packages. These are works in progress from the Microsoft Python team and others, with the intent that they are contributed to typeshed or to the associated packages once sufficiently complete."
+authors = [
+    "microsoft",
+    "Vince Reuter <[email protected]>",
+]
+readme = "README.md"
+license = "MIT"
+repository = "https://github.com/gerlichlab/python-type-stubs"
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Software Development",
+    "Topic :: Software Development :: Build Tools",
+    "Topic :: Software Development :: Quality Assurance",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Utilities",
+]
+packages = [
+    { include = "scipy-stubs", from = "stubs" },
+    { include = "skimage-stubs", from = "stub-dist" },
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
 [tool.black]
 line_length = 130
 target_version = ["py37"]
@@ -85,4 +120,4 @@ strict_equality = true
 # Configuring error messages
 show_error_context = false
 show_column_numbers = false
-show_error_codes = true
+show_error_codes = true

stub-dist/skimage-stubs/__init__.pyi

@@ -0,0 +1,24 @@
+__version__: str = ...
+
+submodules: list = ...
+
+from ._shared.version_requirements import ensure_python_version as ensure_python_version
+
+from ._shared import lazy as lazy
+
+__getattr__, __lazy_dir__, _ = ...
+
+def __dir__(): ...
+
+# Logic for checking for improper install and importing while in the source
+# tree when package has not been installed inplace.
+# Code adapted from scikit-learn's __check_build module.
+_INPLACE_MSG: str = ...
+
+_STANDARD_MSG: str = ...
+
+def _raise_build_error(e): ...
+
+from skimage._shared.tester import PytestTester as PytestTester  # noqa
+
+test = ...

stub-dist/skimage-stubs/_shared/_dependency_checks.pyi

@@ -0,0 +1,3 @@
+from .version_requirements import is_installed
+
+has_mpl = ...

stub-dist/skimage-stubs/_shared/_geometry.pyi

@@ -0,0 +1,9 @@
+__all__ = ["polygon_clip", "polygon_area"]
+
+import numpy as np
+
+from .version_requirements import require
+
+@require("matplotlib", ">=3.0.3")
+def polygon_clip(rp, cp, r0, c0, r1, c1): ...
+def polygon_area(pr, pc) -> float: ...

stub-dist/skimage-stubs/_shared/_tempfile.pyi

@@ -0,0 +1,6 @@
+from tempfile import NamedTemporaryFile
+from contextlib import contextmanager
+import os
+
+@contextmanager
+def temporary_file(suffix: str = ""): ...

stub-dist/skimage-stubs/_shared/_warnings.pyi

@@ -0,0 +1,17 @@
+from contextlib import contextmanager
+import sys
+import warnings
+import re
+import functools
+import os
+
+__all__ = ["all_warnings", "expected_warnings", "warn"]
+
+# A version of `warnings.warn` with a default stacklevel of 2.
+# functool is used so as not to increase the call stack accidentally
+warn = ...
+
+@contextmanager
+def all_warnings(): ...
+@contextmanager
+def expected_warnings(matching): ...

stub-dist/skimage-stubs/_shared/coord.pyi

@@ -0,0 +1,13 @@
+import numpy as np
+from scipy.spatial import distance
+
+def _ensure_spacing(coord, spacing, p_norm, max_out): ...
+def ensure_spacing(
+    coords,
+    spacing: float = 1,
+    p_norm: float = ...,
+    min_split_size: int = 50,
+    max_out: int | None = None,
+    *,
+    max_split_size: int = 2000
+): ...

stub-dist/skimage-stubs/_shared/filters.pyi

@@ -0,0 +1,24 @@
+from skimage._typing import Scalar
+from numpy.typing import ArrayLike, NDArray
+from typing import Literal
+from collections.abc import Iterable
+
+import numpy as np
+from scipy import ndimage as ndi
+
+from .._shared import utils
+from .._shared.utils import _supported_float_type, convert_to_float, warn
+
+@utils.deprecate_multichannel_kwarg(multichannel_position=5)
+def gaussian(
+    image: ArrayLike,
+    sigma=1,
+    output: ArrayLike | None = None,
+    mode: Literal["reflect", "constant", "nearest", "mirror", "wrap"] = "nearest",
+    cval: Scalar = 0,
+    multichannel=None,
+    preserve_range: bool = False,
+    truncate: float = 4.0,
+    *,
+    channel_axis: int | None = None
+) -> NDArray: ...

stub-dist/skimage-stubs/_shared/lazy.pyi

@@ -0,0 +1,12 @@
+from typing import Mapping
+import importlib
+import importlib.util
+import os
+import sys
+
+def attach(
+    package_name: str,
+    submodules: set | None = None,
+    submod_attrs: Mapping | None = None,
+): ...
+def load(fullname: str): ...

stub-dist/skimage-stubs/_shared/setup.pyi

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+
+import os
+
+base_path = ...
+
+def configuration(parent_package="", top_path=None): ...

stub-dist/skimage-stubs/_shared/tester.pyi

@@ -0,0 +1,19 @@
+from numpy.typing import ArrayLike
+from typing import Literal
+import os
+import sys
+
+def _show_skimage_info(): ...
+
+class PytestTester(object):
+    def __init__(self, module_name): ...
+    def __call__(
+        self,
+        label: Literal["fast", "full"] = "fast",
+        verbose: int = 1,
+        extra_argv: ArrayLike | None = None,
+        doctests: bool = False,
+        coverage: bool = False,
+        durations: int = ...,
+        tests=None,
+    ) -> bool: ...

stub-dist/skimage-stubs/_shared/testing.pyi

@@ -0,0 +1,55 @@
+from numpy.typing import ArrayLike
+
+import os
+import re
+import struct
+import threading
+import functools
+from tempfile import NamedTemporaryFile
+
+import numpy as np
+from numpy import testing
+from numpy.testing import (
+    assert_array_equal,
+    assert_array_almost_equal,
+    assert_array_less,
+    assert_array_almost_equal_nulp,
+    assert_equal,
+    TestCase,
+    assert_allclose,
+    assert_almost_equal,
+    assert_,
+    assert_warns,
+    assert_no_warnings,
+)
+
+import warnings
+
+from ..data._fetchers import _fetch
+from ._warnings import expected_warnings
+
+SKIP_RE = ...
+
+skipif = ...
+xfail = ...
+parametrize = ...
+raises = ...
+fixture = ...
+
+# true if python is running in 32bit mode
+# Calculate the size of a void * pointer in bits
+# https://docs.python.org/3/library/struct.html
+arch32 = ...
+
+_error_on_warnings = ...
+
+def assert_less(a, b, msg=None): ...
+def assert_greater(a, b, msg=None): ...
+def doctest_skip_parser(func): ...
+def roundtrip(image, plugin, suffix): ...
+def color_check(plugin, fmt="png"): ...
+def mono_check(plugin, fmt="png"): ...
+def setup_test(): ...
+def teardown_test(): ...
+def fetch(data_filename): ...
+def test_parallel(num_threads: int = 2, warnings_matching: ArrayLike | None = None): ...

stub-dist/skimage-stubs/_shared/utils.pyi

@@ -0,0 +1,110 @@
+from collections.abc import Iterable
+from numpy.typing import ArrayLike, NDArray
+from typing import Any, Mapping, Literal
+import inspect
+import functools
+import sys
+import warnings
+from collections.abc import Iterable
+
+import numpy as np
+import scipy
+from numpy.lib import NumpyVersion
+
+from ._warnings import all_warnings, warn
+
+__all__ = [
+    "deprecated",
+    "get_bound_method_class",
+    "all_warnings",
+    "safe_as_int",
+    "check_shape_equality",
+    "check_nD",
+    "warn",
+    "reshape_nd",
+    "identity",
+    "slice_at_axis",
+]
+
+class skimage_deprecation(Warning):
+    pass
+
+def _get_stack_rank(func): ...
+def _is_wrapped(func): ...
+def _get_stack_length(func): ...
+
+class _DecoratorBaseClass:
+
+    _stack_length: dict = ...
+
+    def get_stack_length(self, func): ...
+
+class change_default_value(_DecoratorBaseClass):
+    def __init__(
+        self,
+        arg_name: str,
+        *,
+        new_value: Any,
+        changed_version: str,
+        warning_msg: str | None = None
+    ): ...
+    def __call__(self, func): ...
+
+class remove_arg(_DecoratorBaseClass):
+    def __init__(
+        self, arg_name: str, *, changed_version: str, help_msg: str | None = None
+    ): ...
+    def __call__(self, func): ...
+
+def docstring_add_deprecated(
+    func, kwarg_mapping: Mapping, deprecated_version: str
+) -> str: ...
+
+class deprecate_kwarg(_DecoratorBaseClass):
+    def __init__(
+        self,
+        kwarg_mapping: Mapping,
+        deprecated_version: str,
+        warning_msg: str | None = None,
+        removed_version: str | None = None,
+    ): ...
+    def __call__(self, func): ...
+
+class deprecate_multichannel_kwarg(deprecate_kwarg):
+    def __init__(self, removed_version: str = "1.0", multichannel_position=None): ...
+    def __call__(self, func): ...
+
+class channel_as_last_axis:
+    def __init__(
+        self,
+        channel_arg_positions: tuple[int, ...] = ...,
+        channel_kwarg_names: tuple[str, ...] = ...,
+        multichannel_output: bool = True,
+    ): ...
+    def __call__(self, func): ...
+
+class deprecated:
+    def __init__(
+        self,
+        alt_func: str | None = None,
+        behavior: Literal["warn", "raise"] = "warn",
+        removed_version: str | None = None,
+    ): ...
+    def __call__(self, func): ...
+
+def get_bound_method_class(m): ...
+def safe_as_int(val, atol: float = 1e-3): ...
+def check_shape_equality(im1, im2): ...
+def slice_at_axis(sl, axis: int): ...
+def reshape_nd(arr, ndim: int, dim: int): ...
+def check_nD(array: ArrayLike, ndim: int | Iterable[int], arg_name: str = "image"): ...
+def convert_to_float(image: NDArray, preserve_range: bool) -> NDArray: ...
+def _validate_interpolation_order(image_dtype, order): ...
+def _to_np_mode(mode): ...
+def _to_ndimage_mode(mode): ...
+def _fix_ndimage_mode(mode): ...
+
+new_float_type: dict = ...
+
+def _supported_float_type(input_dtype, allow_complex=False): ...
+def identity(image, *args, **kwargs): ...

stub-dist/skimage-stubs/_shared/version_requirements.pyi

@@ -0,0 +1,10 @@
+import sys
+
+from packaging import version as _version
+
+def ensure_python_version(min_version): ...
+def _check_version(actver, version, cmp_op): ...
+def get_module_version(module_name): ...
+def is_installed(name: str, version: str | None = None) -> bool: ...
+def require(name: str, version: str | None = None): ...
+def get_module(module_name: str, version: str | None = None): ...

stub-dist/skimage-stubs/_typing.pyi

@@ -0,0 +1,25 @@
+import decimal
+import io
+import numpy.typing
+import pandas as pd
+
+Decimal = decimal.Decimal
+PythonScalar = str | int | float | bool
+
+ArrayLike = numpy.typing.ArrayLike
+FileLike = io.IOBase
+PathLike = str
+
+PandasScalar = pd.Period | pd.Timestamp | pd.Timedelta | pd.Interval
+Scalar = PythonScalar | PandasScalar
+
+Color = tuple[float, float, float] | str
+
+__all__ = [
+    "ArrayLike",
+    "Color",
+    "Decimal",
+    "FileLike",
+    "PathLike",
+    "Scalar",
+]

stub-dist/skimage-stubs/data/__init__.pyi

@@ -0,0 +1,3 @@
+from .._shared import lazy as lazy
+
+__getattr__, __dir__, __all__ = ...