Add static type checking: use `mypy` to ensure that variable and
function calls are using the appropriate types.

Configure and run `mypy` checks in CI.

Take advantage of the commit to include running the spell checker in the
check matrix.

Documentation:
https://mypy.readthedocs.io/en/stable/index.html

Fix spelling mistakes detected by `codespell`.

Fixes:
```
./README.rst:77: difussion ==> diffusion
./src/nifreeze/testing/simulations.py:70: pricipal ==> principal
./src/nifreeze/registration/ants.py:392: initalizing ==> initializing
spellcheck: exit 65 (0.17 seconds) /home/runner/work/nifreeze/nifreeze> codespell . pid=1810
  spellcheck: FAIL code 65 (0.27=setup[0.11]+cmd[0.17] seconds)
  evaluation failed :( (0.34 seconds)
Error: Process completed with exit code 65.
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12435719520/job/34722102640?pr=28#step:8:21

Remove empty `latex_elements` section in documentation config file.

Fixes:
```
docs/conf.py:157: error:
 Need type annotation for "latex_elements" (hint: "latex_elements: dict[<type>, <type>] = ...")  [var-annotated]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:31

Fix arguments to the `unique` function in GP error analysis plot
script: get the unique values directly from the `pandas.Series`
instance and check the length of the returned values prior to getting
the first instance.

Fixes:
```
scripts/dwi_gp_estimation_error_analysis_plot.py:92: error:
 Argument 1 to "unique" has incompatible type
 "ExtensionArray | ndarray[Any, Any]"; expected "_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]]"  [arg-type]
scripts/dwi_gp_estimation_error_analysis_plot.py:93: error:
 Argument 1 to "unique" has incompatible type
 "ExtensionArray | ndarray[Any, Any]"; expected "_SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]]"  [arg-type]
scripts/dwi_gp_estimation_error_analysis_plot.py:94: error:
 Argument 1 to "unique" has incompatible type
```

raised for example in:

Convert list to array prior to computing mean and std dev using `NumPy`.

Fixes:
```
scripts/dwi_gp_estimation_error_analysis_plot.py:97: error:
 Argument 1 to "mean" has incompatible type
 "list[ExtensionArray | ndarray[Any, Any]]"; expected "_SupportsArray[dtype[bool_ | integer[Any] | floating[Any] | complexfloating[Any, Any]]] | _NestedSequence[_SupportsArray[dtype[bool_ | integer[Any] | floating[Any] | complexfloating[Any, Any]]]] | bool | int | float | complex | _NestedSequence[bool | int | float | complex] | _SupportsArray[dtype[object_]] | _NestedSequence[_SupportsArray[dtype[object_]]]"  [arg-type]
scripts/dwi_gp_estimation_error_analysis_plot.py:98: error:
 Argument 1 to "std" has incompatible type
 "list[ExtensionArray | ndarray[Any, Any]]"; expected "_SupportsArray[dtype[bool_ | integer[Any] | floating[Any] | complexfloating[Any, Any]]] | _NestedSequence[_SupportsArray[dtype[bool_ | integer[Any] | floating[Any] | complexfloating[Any, Any]]]] | bool | int | float | complex | _NestedSequence[bool | int | float | complex] | _SupportsArray[dtype[object_]] | _NestedSequence[_SupportsArray[dtype[object_]]]"  [arg-type]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:68

Use appropriate keyword argument names to instantiate
`SphericalKriging`: left behind in commit
nipreps/eddymotion@9e65c34

Fixes:
```
scripts/dwi_gp_estimation_simulated_signal.py:139: error:
 Unexpected keyword argument "a" for "SphericalKriging"  [call-arg]
src/nifreeze/model/gpr.py:365: note: "SphericalKriging" defined here
scripts/dwi_gp_estimation_simulated_signal.py:139: error:
 Unexpected keyword argument "lambda_s" for "SphericalKriging"  [call-arg]
src/nifreeze/model/gpr.py:365: note: "SphericalKriging" defined here
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:105

Select appropriate element in case the GPR prediction method returns a
tuple.

Fixes:
```
scripts/dwi_gp_estimation_simulated_signal.py:159: error:
 Item "tuple[ndarray[Any, Any], ...]" of
 "ndarray[Any, Any] | tuple[ndarray[Any, Any], ndarray[Any, Any], ndarray[Any, Any]] | tuple[ndarray[Any, Any], ndarray[Any, Any]]"
 has no attribute "T"  [union-attr]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:109

Group keyword arguments into a single dictionary.

Fixes:
```
scripts/optimize_registration.py:133: error:
 Argument "output_transform_prefix" to "generate_command" has incompatible type "str"; expected "dict[Any, Any]"  [arg-type]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:141

Use `str` instead of `Path` for `_parse_yaml_config` parameter since
`argparse` passes the argument as a string, not as a `Path`.

Fixes:
```
src/nifreeze/cli/parser.py:74: error:
 Argument "type" to "add_argument" of "_ActionsContainer" has incompatible type
 "Callable[[Path], dict[Any, Any]]"; expected "Callable[[str], Any] | FileType | str"  [arg-type]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:47

Use arrays in NumPy's `percentile` function arguments.

Fixes:
```
src/nifreeze/data/filtering.py:80: error:
 Argument 1 to "percentile" has incompatible type "ndarray[Any, dtype[number[Any] | bool_]] | ndarray[tuple[int, ...], dtype[number[Any] | bool_]]";
 expected "_SupportsArray[dtype[bool_ | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[bool_ | integer[Any] | floating[Any]]]] | bool | int | float | _NestedSequence[bool | int | float]"  [arg-type]
src/nifreeze/data/filtering.py:81: error:
 Argument 1 to "percentile" has incompatible type
 "ndarray[Any, dtype[number[Any] | bool_]] | ndarray[tuple[int, ...], dtype[number[Any] | bool_]]";
 expected "_SupportsArray[dtype[bool_ | integer[Any] | floating[Any]]] | _NestedSequence[_SupportsArray[dtype[bool_ | integer[Any] | floating[Any]]]] | bool | int | float | _NestedSequence[bool | int | float]"  [arg-type]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:130

List `sigma_sq` in the GP model slots.

Fixes:
```
src/nifreeze/model/_dipy.py:128: error:
 Trying to assign name "sigma_sq" that is not in "__slots__" of type "nifreeze.model._dipy.GaussianProcessModel"  [misc]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:102

Add the dimensionality to the `mask` ndarray parameter annotation.

Fixes:
```
src/nifreeze/model/_dipy.py:140: error:
 "ndarray" expects 2 type arguments, but 1 given  [type-arg]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:103

Fix type hint for `figsize` parameter: use `float` as values can be
floating point numbers.

Fixes:
```
src/nifreeze/viz/signals.py:40: error:
 Incompatible default for argument "figsize" (default has type "tuple[float, float]", argument has type "tuple[int, int]")  [assignment]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:49

Provide appropriate type hints to the `reg_target_type` parameter of the
`ants._run_registration` function. The expression is set to a tuple in
https://github.com/nipreps/nifreeze/blob/6b6ba707c47b2763c040f3d3a2ceabdcf450eefe/src/nifreeze/estimator.py#L103

Fixes:
```
src/nifreeze/registration/ants.py:459: error:
 Incompatible types in assignment (expression has type "tuple[str, str]", variable has type "str")  [assignment]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:133

Instantiate `namedtuple` using the correct syntax for `ImageFrid`:
`namedtuple` expects positional arguments for its fields, not keyword
argumentsi: define the `namedtuple` first and then instantiate it.

Fixes:
```
src/nifreeze/registration/ants.py:475: error:
 Unexpected keyword argument "shape" for "tuple"  [call-arg]
.tox/typecheck/lib/python3.12/site-packages/mypy/typeshed/stdlib/builtins.pyi:873:
 note: "tuple" defined here
src/nifreeze/registration/ants.py:475: error:
 Unexpected keyword argument "affine" for "tuple"  [call-arg]
.tox/typecheck/lib/python3.12/site-packages/mypy/typeshed/stdlib/builtins.pyi:873:
 note: "tuple" defined here
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:134

Remove type hint in overriden `diag` methods in kernel classes: it is
unsafe to override a method with a more specific argument type, as it
violates the Liskov substitution principle.

Fixes:
```
src/nifreeze/model/gpr.py:335: error:
 Argument 1 of "diag" is incompatible with supertype "Kernel";
 supertype defines the argument type as
 "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]"
  [override]
src/nifreeze/model/gpr.py:335: note: This violates the Liskov substitution principle
src/nifreeze/model/gpr.py:335: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides
src/nifreeze/model/gpr.py:445: error:
 Argument 1 of "diag" is incompatible with supertype "Kernel";
 supertype defines the argument type as
 "Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes]"
  [override]
src/nifreeze/model/gpr.py:445: note: This violates the Liskov substitution principle
src/nifreeze/model/gpr.py:335: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:93

Documentation:
https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides

Import `Bounds` from `scipy.optimize`.

Fixes:
```
src/nifreeze/model/gpr.py:32: error:
 Module "scipy.optimize._minimize" does not explicitly export attribute "Bounds"  [attr-defined]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:70

Avoid type checking for private function import statement.

Fixes:
```
src/nifreeze/model/gpr.py:215: error:
 Module "sklearn.utils.optimize" has no attribute "_check_optimize_result"  [attr-defined]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:73

Remove unused `namedtuple` definition in test.

Fixes:
```
test/test_gpr.py:31: error:
 First argument to namedtuple() should be "GradientTablePatch", not "gtab"  [name-match]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:129

Use `ClassVar` for type hinting the `GaussianProcessRegressor`
`_parameter_constraints` class variable in child class.

Fixes:
```
src/nifreeze/model/gpr.py:156: error:
 Cannot override class variable (previously declared on base class "GaussianProcessRegressor") with instance variable  [misc]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:71

Annotate the `optimizer` attribute type in the DiffusionGPR GPR child
class.

Fixes:
```
src/nifreeze/model/gpr.py:234: error:
 "DiffusionGPR" has no attribute "optimizer"  [attr-defined]
```

raised for example in:
https://github.com/nipreps/nifreeze/actions/runs/12437972140/job/34728973936#step:8:82