Merge pull request #1338 from effigies/mnt/coverage-fixes

MNT: Update coverage config

.coveragerc

@@ -1,9 +1,18 @@
 [run]
 branch = True
 source = nibabel
-include = */nibabel/*
 omit =
     */externals/*
     */benchmarks/*
-    */tests/*
     nibabel/_version.py
+
+[report]
+exclude_also =
+    def __repr__
+    if (ty\.|typing\.)?TYPE_CHECKING:
+    class .*\((ty\.|typing\.)Protocol\):
+    @(ty\.|typing\.)overload
+    if 0:
+    if __name__ == .__main__.:
+    @(abc\.)?abstractmethod
+    raise NotImplementedError

nibabel/_compression.py

@@ -17,7 +17,7 @@
 
 from .optpkg import optional_package
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import indexed_gzip  # type: ignore[import]
     import pyzstd
 

nibabel/arrayproxy.py

@@ -57,7 +57,7 @@
 KEEP_FILE_OPEN_DEFAULT = False
 
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
     from typing_extensions import Self  # PY310
 
@@ -75,19 +75,17 @@ class ArrayLike(ty.Protocol):
     shape: tuple[int, ...]
 
     @property
-    def ndim(self) -> int: ...  # pragma: no cover
+    def ndim(self) -> int: ...
 
     # If no dtype is passed, any dtype might be returned, depending on the array-like
     @ty.overload
-    def __array__(
-        self, dtype: None = ..., /
-    ) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...  # pragma: no cover
+    def __array__(self, dtype: None = ..., /) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...
 
     # Any dtype might be passed, and *that* dtype must be returned
     @ty.overload
-    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...  # pragma: no cover
+    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...
 
-    def __getitem__(self, key, /) -> npt.NDArray: ...  # pragma: no cover
+    def __getitem__(self, key, /) -> npt.NDArray: ...
 
 
 class ArrayProxy(ArrayLike):

nibabel/dataobj_images.py

@@ -19,7 +19,7 @@
 from .filebasedimages import FileBasedHeader, FileBasedImage
 from .fileholders import FileMap
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
 
     from .filename_parser import FileSpec

nibabel/deprecated.py

@@ -8,7 +8,7 @@
 from .deprecator import Deprecator
 from .pkg_info import cmp_pkg_version
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     P = ty.ParamSpec('P')
 
 

nibabel/deprecator.py

@@ -9,7 +9,7 @@
 import warnings
 from textwrap import dedent
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     T = ty.TypeVar('T')
     P = ty.ParamSpec('P')
 

nibabel/filebasedimages.py

@@ -20,7 +20,7 @@
 from .filename_parser import TypesFilenamesError, _stringify_path, splitext_addext, types_filenames
 from .openers import ImageOpener
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from .filename_parser import ExtensionSpec, FileSpec
 
 FileSniff = ty.Tuple[bytes, str]
@@ -54,13 +54,13 @@ def from_header(klass: type[HdrT], header: FileBasedHeader | ty.Mapping | None =
 
     @classmethod
     def from_fileobj(klass: type[HdrT], fileobj: io.IOBase) -> HdrT:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def write_to(self, fileobj: io.IOBase) -> None:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def __eq__(self, other: object) -> bool:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def __ne__(self, other: object) -> bool:
         return not self == other
@@ -251,7 +251,7 @@ def from_filename(klass: type[ImgT], filename: FileSpec) -> ImgT:
 
     @classmethod
     def from_file_map(klass: type[ImgT], file_map: FileMap) -> ImgT:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def filespec_to_file_map(klass, filespec: FileSpec) -> FileMap:
@@ -308,7 +308,7 @@ def to_filename(self, filename: FileSpec, **kwargs) -> None:
         self.to_file_map(**kwargs)
 
     def to_file_map(self, file_map: FileMap | None = None, **kwargs) -> None:
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def make_file_map(klass, mapping: ty.Mapping[str, str | io.IOBase] | None = None) -> FileMap:
@@ -373,7 +373,7 @@ def from_image(klass: type[ImgT], img: FileBasedImage) -> ImgT:
         img : ``FileBasedImage`` instance
            Image, of our own class
         """
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     @classmethod
     def _sniff_meta_for(

nibabel/filename_parser.py

@@ -14,7 +14,7 @@
 import pathlib
 import typing as ty
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     FileSpec = str | os.PathLike[str]
     ExtensionSpec = tuple[str, str | None]
 

nibabel/loadsave.py

@@ -26,7 +26,7 @@
 _compressed_suffixes = ('.gz', '.bz2', '.zst')
 
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from .filebasedimages import FileBasedImage
     from .filename_parser import FileSpec
 

nibabel/onetime.py

@@ -137,12 +137,10 @@ def __init__(self, func: ty.Callable[[InstanceT], T]) -> None:
     @ty.overload
     def __get__(
         self, obj: None, objtype: type[InstanceT] | None = None
-    ) -> ty.Callable[[InstanceT], T]: ...  # pragma: no cover
+    ) -> ty.Callable[[InstanceT], T]: ...
 
     @ty.overload
-    def __get__(
-        self, obj: InstanceT, objtype: type[InstanceT] | None = None
-    ) -> T: ...  # pragma: no cover
+    def __get__(self, obj: InstanceT, objtype: type[InstanceT] | None = None) -> T: ...
 
     def __get__(
         self, obj: InstanceT | None, objtype: type[InstanceT] | None = None

nibabel/openers.py

@@ -18,7 +18,7 @@
 
 from ._compression import HAVE_INDEXED_GZIP, IndexedGzipFile, pyzstd
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from types import TracebackType
 
     from _typeshed import WriteableBuffer
@@ -36,9 +36,8 @@
 
 @ty.runtime_checkable
 class Fileish(ty.Protocol):
-    def read(self, size: int = -1, /) -> bytes: ...  # pragma: no cover
-
-    def write(self, b: bytes, /) -> int | None: ...  # pragma: no cover
+    def read(self, size: int = -1, /) -> bytes: ...
+    def write(self, b: bytes, /) -> int | None: ...
 
 
 class DeterministicGzipFile(gzip.GzipFile):

nibabel/pointset.py

@@ -30,7 +30,7 @@
 from nibabel.fileslice import strided_scalar
 from nibabel.spatialimages import SpatialImage
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     from typing_extensions import Self
 
     _DType = ty.TypeVar('_DType', bound=np.dtype[ty.Any])
@@ -41,12 +41,10 @@ class CoordinateArray(ty.Protocol):
     shape: tuple[int, int]
 
     @ty.overload
-    def __array__(
-        self, dtype: None = ..., /
-    ) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...  # pragma: no cover
+    def __array__(self, dtype: None = ..., /) -> np.ndarray[ty.Any, np.dtype[ty.Any]]: ...
 
     @ty.overload
-    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...  # pragma: no cover
+    def __array__(self, dtype: _DType, /) -> np.ndarray[ty.Any, _DType]: ...
 
 
 @dataclass

nibabel/spatialimages.py

@@ -154,26 +154,23 @@
 except ImportError:  # PY38
     from functools import lru_cache as cache
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
 
 SpatialImgT = ty.TypeVar('SpatialImgT', bound='SpatialImage')
 SpatialHdrT = ty.TypeVar('SpatialHdrT', bound='SpatialHeader')
 
 
 class HasDtype(ty.Protocol):
-    def get_data_dtype(self) -> np.dtype: ...  # pragma: no cover
-
-    def set_data_dtype(self, dtype: npt.DTypeLike) -> None: ...  # pragma: no cover
+    def get_data_dtype(self) -> np.dtype: ...
+    def set_data_dtype(self, dtype: npt.DTypeLike) -> None: ...
 
 
 @ty.runtime_checkable
 class SpatialProtocol(ty.Protocol):
-    def get_data_dtype(self) -> np.dtype: ...  # pragma: no cover
-
-    def get_data_shape(self) -> ty.Tuple[int, ...]: ...  # pragma: no cover
-
-    def get_zooms(self) -> ty.Tuple[float, ...]: ...  # pragma: no cover
+    def get_data_dtype(self) -> np.dtype: ...
+    def get_data_shape(self) -> ty.Tuple[int, ...]: ...
+    def get_zooms(self) -> ty.Tuple[float, ...]: ...
 
 
 class HeaderDataError(Exception):

nibabel/volumeutils.py

@@ -24,7 +24,7 @@
 from .casting import OK_FLOATS, shared_range
 from .externals.oset import OrderedSet
 
-if ty.TYPE_CHECKING:  # pragma: no cover
+if ty.TYPE_CHECKING:
     import numpy.typing as npt
 
     Scalar = np.number | float
@@ -1191,13 +1191,13 @@ def _ftype4scaled_finite(
 @ty.overload
 def finite_range(
     arr: npt.ArrayLike, check_nan: ty.Literal[False] = False
-) -> tuple[Scalar, Scalar]: ...  # pragma: no cover
+) -> tuple[Scalar, Scalar]: ...
 
 
 @ty.overload
 def finite_range(
     arr: npt.ArrayLike, check_nan: ty.Literal[True]
-) -> tuple[Scalar, Scalar, bool]: ...  # pragma: no cover
+) -> tuple[Scalar, Scalar, bool]: ...
 
 
 def finite_range(

nibabel/xmlutils.py

@@ -20,7 +20,7 @@ class XmlSerializable:
 
     def _to_xml_element(self) -> Element:
         """Output should be a xml.etree.ElementTree.Element"""
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def to_xml(self, enc='utf-8', **kwargs) -> bytes:
         r"""Generate an XML bytestring with a given encoding.
@@ -109,10 +109,10 @@ def parse(self, string=None, fname=None, fptr=None):
         parser.ParseFile(fptr)
 
     def StartElementHandler(self, name, attrs):
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def EndElementHandler(self, name):
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError
 
     def CharacterDataHandler(self, data):
-        raise NotImplementedError  # pragma: no cover
+        raise NotImplementedError

pyproject.toml

@@ -67,11 +67,12 @@ doc = [
   "tomli; python_version < '3.11'",
 ]
 test = [
-  "pytest<8.1",  # relax once pytest-doctestplus releases 1.2.0
+  "pytest",
   "pytest-doctestplus",
   "pytest-cov",
   "pytest-httpserver",
   "pytest-xdist",
+  "coverage>=7.2",
 ]
 # Remaining: Simpler to centralize in tox
 dev = ["tox"]