TYP: Annotate deprecation, one-time property, and optional package tooling

nibabel/deprecated.py

@@ -2,12 +2,15 @@
 """
 from __future__ import annotations
 
+import typing as ty
 import warnings
-from typing import Type
 
 from .deprecator import Deprecator
 from .pkg_info import cmp_pkg_version
 
+if ty.TYPE_CHECKING:  # pragma: no cover
+    P = ty.ParamSpec('P')
+
 
 class ModuleProxy:
     """Proxy for module that may not yet have been imported
@@ -30,14 +33,14 @@ class ModuleProxy:
     module.
     """
 
-    def __init__(self, module_name):
+    def __init__(self, module_name: str) -> None:
         self._module_name = module_name
 
-    def __getattr__(self, key):
+    def __getattr__(self, key: str) -> ty.Any:
         mod = __import__(self._module_name, fromlist=[''])
         return getattr(mod, key)
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return f'<module proxy for {self._module_name}>'
 
 
@@ -60,7 +63,7 @@ class FutureWarningMixin:
 
     warn_message = 'This class will be removed in future versions'
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self, *args: P.args, **kwargs: P.kwargs) -> None:
         warnings.warn(self.warn_message, FutureWarning, stacklevel=2)
         super().__init__(*args, **kwargs)
 
@@ -85,12 +88,12 @@ def alert_future_error(
     msg: str,
     version: str,
     *,
-    warning_class: Type[Warning] = FutureWarning,
-    error_class: Type[Exception] = RuntimeError,
+    warning_class: type[Warning] = FutureWarning,
+    error_class: type[Exception] = RuntimeError,
     warning_rec: str = '',
     error_rec: str = '',
     stacklevel: int = 2,
-):
+) -> None:
     """Warn or error with appropriate messages for changing functionality.
 
     Parameters

nibabel/deprecator.py

@@ -1,10 +1,16 @@
 """Class for recording and reporting deprecations
 """
+from __future__ import annotations
 
 import functools
 import re
+import typing as ty
 import warnings
 
+if ty.TYPE_CHECKING:  # pragma: no cover
+    T = ty.TypeVar('T')
+    P = ty.ParamSpec('P')
+
 _LEADING_WHITE = re.compile(r'^(\s*)')
 
 TESTSETUP = """
@@ -38,15 +44,20 @@ class ExpiredDeprecationError(RuntimeError):
     pass
 
 
-def _ensure_cr(text):
+def _ensure_cr(text: str) -> str:
     """Remove trailing whitespace and add carriage return
 
     Ensures that `text` always ends with a carriage return
     """
     return text.rstrip() + '\n'
 
 
-def _add_dep_doc(old_doc, dep_doc, setup='', cleanup=''):
+def _add_dep_doc(
+    old_doc: str,
+    dep_doc: str,
+    setup: str = '',
+    cleanup: str = '',
+) -> str:
     """Add deprecation message `dep_doc` to docstring in `old_doc`
 
     Parameters
@@ -55,6 +66,10 @@ def _add_dep_doc(old_doc, dep_doc, setup='', cleanup=''):
         Docstring from some object.
     dep_doc : str
         Deprecation warning to add to top of docstring, after initial line.
+    setup : str, optional
+        Doctest setup text
+    cleanup : str, optional
+        Doctest teardown text
 
     Returns
     -------
@@ -76,7 +91,9 @@ def _add_dep_doc(old_doc, dep_doc, setup='', cleanup=''):
     if next_line >= len(old_lines):
         # nothing following first paragraph, just append message
         return old_doc + '\n' + dep_doc
-    indent = _LEADING_WHITE.match(old_lines[next_line]).group()
+    leading_white = _LEADING_WHITE.match(old_lines[next_line])
+    assert leading_white is not None  # Type narrowing, since this always matches
+    indent = leading_white.group()
     setup_lines = [indent + L for L in setup.splitlines()]
     dep_lines = [indent + L for L in [''] + dep_doc.splitlines() + ['']]
     cleanup_lines = [indent + L for L in cleanup.splitlines()]
@@ -113,15 +130,15 @@ class Deprecator:
 
     def __init__(
         self,
-        version_comparator,
-        warn_class=DeprecationWarning,
-        error_class=ExpiredDeprecationError,
-    ):
+        version_comparator: ty.Callable[[str], int],
+        warn_class: type[Warning] = DeprecationWarning,
+        error_class: type[Exception] = ExpiredDeprecationError,
+    ) -> None:
         self.version_comparator = version_comparator
         self.warn_class = warn_class
         self.error_class = error_class
 
-    def is_bad_version(self, version_str):
+    def is_bad_version(self, version_str: str) -> bool:
         """Return True if `version_str` is too high
 
         Tests `version_str` with ``self.version_comparator``
@@ -139,7 +156,14 @@ def is_bad_version(self, version_str):
         """
         return self.version_comparator(version_str) == -1
 
-    def __call__(self, message, since='', until='', warn_class=None, error_class=None):
+    def __call__(
+        self,
+        message: str,
+        since: str = '',
+        until: str = '',
+        warn_class: type[Warning] | None = None,
+        error_class: type[Exception] | None = None,
+    ) -> ty.Callable[[ty.Callable[P, T]], ty.Callable[P, T]]:
         """Return decorator function function for deprecation warning / error
 
         Parameters
@@ -164,8 +188,8 @@ def __call__(self, message, since='', until='', warn_class=None, error_class=Non
         deprecator : func
             Function returning a decorator.
         """
-        warn_class = warn_class or self.warn_class
-        error_class = error_class or self.error_class
+        exception = error_class if error_class is not None else self.error_class
+        warning = warn_class if warn_class is not None else self.warn_class
         messages = [message]
         if (since, until) != ('', ''):
             messages.append('')
@@ -174,19 +198,21 @@ def __call__(self, message, since='', until='', warn_class=None, error_class=Non
         if until:
             messages.append(
                 f"* {'Raises' if self.is_bad_version(until) else 'Will raise'} "
-                f'{error_class} as of version: {until}'
+                f'{exception} as of version: {until}'
             )
         message = '\n'.join(messages)
 
-        def deprecator(func):
+        def deprecator(func: ty.Callable[P, T]) -> ty.Callable[P, T]:
             @functools.wraps(func)
-            def deprecated_func(*args, **kwargs):
+            def deprecated_func(*args: P.args, **kwargs: P.kwargs) -> T:
                 if until and self.is_bad_version(until):
-                    raise error_class(message)
-                warnings.warn(message, warn_class, stacklevel=2)
+                    raise exception(message)
+                warnings.warn(message, warning, stacklevel=2)
                 return func(*args, **kwargs)
 
             keep_doc = deprecated_func.__doc__
+            if keep_doc is None:
+                keep_doc = ''
             setup = TESTSETUP
             cleanup = TESTCLEANUP
             # After expiration, remove all but the first paragraph.

nibabel/onetime.py

@@ -19,6 +19,12 @@
 
 [2] Python data model, https://docs.python.org/reference/datamodel.html
 """
+from __future__ import annotations
+
+import typing as ty
+
+InstanceT = ty.TypeVar('InstanceT')
+T = ty.TypeVar('T')
 
 from nibabel.deprecated import deprecate_with_version
 
@@ -96,26 +102,24 @@ class ResetMixin:
     10.0
     """
 
-    def reset(self):
+    def reset(self) -> None:
         """Reset all OneTimeProperty attributes that may have fired already."""
-        instdict = self.__dict__
-        classdict = self.__class__.__dict__
         # To reset them, we simply remove them from the instance dict.  At that
         # point, it's as if they had never been computed.  On the next access,
         # the accessor function from the parent class will be called, simply
         # because that's how the python descriptor protocol works.
-        for mname, mval in classdict.items():
-            if mname in instdict and isinstance(mval, OneTimeProperty):
+        for mname, mval in self.__class__.__dict__.items():
+            if mname in self.__dict__ and isinstance(mval, OneTimeProperty):
                 delattr(self, mname)
 
 
-class OneTimeProperty:
+class OneTimeProperty(ty.Generic[T]):
     """A descriptor to make special properties that become normal attributes.
 
     This is meant to be used mostly by the auto_attr decorator in this module.
     """
 
-    def __init__(self, func):
+    def __init__(self, func: ty.Callable[[InstanceT], T]) -> None:
         """Create a OneTimeProperty instance.
 
         Parameters
@@ -128,24 +132,35 @@ def __init__(self, func):
         """
         self.getter = func
         self.name = func.__name__
+        self.__doc__ = func.__doc__
+
+    @ty.overload
+    def __get__(
+        self, obj: None, objtype: type[InstanceT] | None = None
+    ) -> ty.Callable[[InstanceT], T]:
+        ...  # pragma: no cover
+
+    @ty.overload
+    def __get__(self, obj: InstanceT, objtype: type[InstanceT] | None = None) -> T:
+        ...  # pragma: no cover
 
-    def __get__(self, obj, type=None):
+    def __get__(
+        self, obj: InstanceT | None, objtype: type[InstanceT] | None = None
+    ) -> T | ty.Callable[[InstanceT], T]:
         """This will be called on attribute access on the class or instance."""
         if obj is None:
             # Being called on the class, return the original function. This
             # way, introspection works on the class.
-            # return func
             return self.getter
 
-        # Errors in the following line are errors in setting a
-        # OneTimeProperty
+        # Errors in the following line are errors in setting a OneTimeProperty
         val = self.getter(obj)
 
-        setattr(obj, self.name, val)
+        obj.__dict__[self.name] = val
         return val
 
 
-def auto_attr(func):
+def auto_attr(func: ty.Callable[[InstanceT], T]) -> OneTimeProperty[T]:
     """Decorator to create OneTimeProperty attributes.
 
     Parameters

nibabel/optpkg.py

@@ -1,20 +1,31 @@
 """Routines to support optional packages"""
+from __future__ import annotations
+
+import typing as ty
+from types import ModuleType
+
 from packaging.version import Version
 
 from .tripwire import TripWire
 
 
-def _check_pkg_version(pkg, min_version):
-    # Default version checking function
-    if isinstance(min_version, str):
-        min_version = Version(min_version)
-    try:
-        return min_version <= Version(pkg.__version__)
-    except AttributeError:
+def _check_pkg_version(min_version: str | Version) -> ty.Callable[[ModuleType], bool]:
+    min_ver = Version(min_version) if isinstance(min_version, str) else min_version
+
+    def check(pkg: ModuleType) -> bool:
+        pkg_ver = getattr(pkg, '__version__', None)
+        if isinstance(pkg_ver, str):
+            return min_ver <= Version(pkg_ver)
         return False
 
+    return check
+
 
-def optional_package(name, trip_msg=None, min_version=None):
+def optional_package(
+    name: str,
+    trip_msg: str | None = None,
+    min_version: str | Version | ty.Callable[[ModuleType], bool] | None = None,
+) -> tuple[ModuleType | TripWire, bool, ty.Callable[[], None]]:
     """Return package-like thing and module setup for package `name`
 
     Parameters
@@ -81,7 +92,7 @@ def optional_package(name, trip_msg=None, min_version=None):
     elif min_version is None:
         check_version = lambda pkg: True
     else:
-        check_version = lambda pkg: _check_pkg_version(pkg, min_version)
+        check_version = _check_pkg_version(min_version)
     # fromlist=[''] results in submodule being returned, rather than the top
     # level module.  See help(__import__)
     fromlist = [''] if '.' in name else []
@@ -107,11 +118,11 @@ def optional_package(name, trip_msg=None, min_version=None):
         trip_msg = (
             f'We need package {name} for these functions, but ``import {name}`` raised {exc}'
         )
-    pkg = TripWire(trip_msg)
+    trip = TripWire(trip_msg)
 
-    def setup_module():
+    def setup_module() -> None:
         import unittest
 
         raise unittest.SkipTest(f'No {name} for these tests')
 
-    return pkg, False, setup_module
+    return trip, False, setup_module

nibabel/pkg_info.py

@@ -14,7 +14,7 @@
 COMMIT_HASH = '$Format:%h$'
 
 
-def _cmp(a, b) -> int:
+def _cmp(a: Version, b: Version) -> int:
     """Implementation of ``cmp`` for Python 3"""
     return (a > b) - (a < b)
 
@@ -113,7 +113,7 @@ def pkg_commit_hash(pkg_path: str | None = None) -> tuple[str, str]:
     return '(none found)', '<not found>'
 
 
-def get_pkg_info(pkg_path: str) -> dict:
+def get_pkg_info(pkg_path: str) -> dict[str, str]:
     """Return dict describing the context of this package
 
     Parameters

nibabel/processing.py

@@ -20,7 +20,7 @@
 
 from .optpkg import optional_package
 
-spnd, _, _ = optional_package('scipy.ndimage')
+spnd = optional_package('scipy.ndimage')[0]
 
 from .affines import AffineError, append_diag, from_matvec, rescale_affine, to_matvec
 from .imageclasses import spatial_axes_first

nibabel/testing/helpers.py

@@ -6,7 +6,7 @@
 
 from ..optpkg import optional_package
 
-_, have_scipy, _ = optional_package('scipy.io')
+have_scipy = optional_package('scipy.io')[1]
 
 from numpy.testing import assert_array_equal