fix various lint and mypy checks

jcreinhold · Mar 14, 2022 · 4481b52 · 4481b52
1 parent 4bbf273
commit 4481b52
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Showing 3 changed files with 60 additions and 59 deletions.
diff --git a/intensity_normalization/normalize/fcm.py b/intensity_normalization/normalize/fcm.py
@@ -195,7 +195,9 @@ def from_argparse_args(cls, args: argparse.Namespace, /) -> FCMNormalize:
         tt = intnormt.TissueTypes.from_string(args.tissue_type)
         return cls(norm_value=args.norm_value, tissue_type=tt)
 
-    def call_from_argparse_args(self, args: argparse.Namespace, /) -> None:
+    def call_from_argparse_args(
+        self, args: argparse.Namespace, /, **kwargs: typing.Any
+    ) -> None:
         if args.mask is not None:
             if args.modality is not None:
                 if args.modality.lower() != "t1":

diff --git a/intensity_normalization/normalize/whitestripe.py b/intensity_normalization/normalize/whitestripe.py
@@ -10,7 +10,6 @@
 import argparse
 import builtins
 import typing
-import warnings
 
 import numpy as np
 import numpy.typing as npt

diff --git a/setup.cfg b/setup.cfg
@@ -1,8 +1,3 @@
-[bumpversion]
-current_version = 2.2.1
-commit = True
-tag = False
-
 [metadata]
 name = intensity_normalization
 version = attr: intensity_normalization.__version__
@@ -14,71 +9,76 @@ author = Jacob Reinhold
 author_email = jcreinhold@gmail.com
 license = Apache Software License 2.0
 license_file = LICENSE
-classifiers = 
-	Development Status :: 5 - Production/Stable
-	Intended Audience :: Developers
-	License :: OSI Approved :: Apache Software License
-	Natural Language :: English
-	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3 :: Only
-	Programming Language :: Python :: 3.9
-	Programming Language :: Python :: Implementation :: CPython
-	Typing :: Typed
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Intended Audience :: Developers
+    License :: OSI Approved :: Apache Software License
+    Natural Language :: English
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: Implementation :: CPython
+    Typing :: Typed
 keywords = intensity, normalization, mri
-project_urls = 
-	Bug Tracker = https://github.com/jcreinhold/intensity-normalization/issues
-	Documentation = https://intensity-normalization.readthedocs.io/
+project_urls =
+    Bug Tracker = https://github.com/jcreinhold/intensity-normalization/issues
+    Documentation = https://intensity-normalization.readthedocs.io/
 
 [options]
 packages = find:
-install_requires = 
-	SimpleITK>=2.1.0,<3
-	nibabel>=3,<4
-	numpy>=1.22,<2
-	pillow>=9.0.0
-	pydicom>=2.2.2,<3
-	pymedio>=0.2.8,<1
-	scikit-fuzzy>=0.4.2,<1
-	scikit-image>=0.17,<1
-	scikit-learn>=0.24,<2
-	scipy>=1.5,<2
-	statsmodels>=0.12,<1
+install_requires =
+    SimpleITK>=2.1.0,<3
+    nibabel>=3,<4
+    numpy>=1.22,<2
+    pillow>=9.0.0
+    pydicom>=2.2.2,<3
+    pymedio>=0.2.8,<1
+    scikit-fuzzy>=0.4.2,<1
+    scikit-image>=0.17,<1
+    scikit-learn>=0.24,<2
+    scipy>=1.5,<2
+    statsmodels>=0.12,<1
 python_requires = >=3.9, !=3.10.*, !=3.11.*
 include_package_data = True
 test_suite = tests
 zip_safe = False
 
 [options.packages.find]
-exclude = 
-	tests
-	docs
-include = 
-	intensity_normalization
-	intensity_normalization.*
+exclude =
+    tests
+    docs
+include =
+    intensity_normalization
+    intensity_normalization.*
 
 [options.entry_points]
-console_scripts = 
-	fcm-normalize = intensity_normalization.cli.fcm:fcm_main
-	kde-normalize = intensity_normalization.cli.kde:kde_main
-	lsq-normalize = intensity_normalization.cli.lsq:lsq_main
-	nyul-normalize = intensity_normalization.cli.nyul:nyul_main
-	ws-normalize = intensity_normalization.cli.whitestripe:whitestripe_main
-	zscore-normalize = intensity_normalization.cli.zscore:zscore_main
-	plot-histograms = intensity_normalization.cli.histogram:histogram_main [plot]
-	tissue-membership = intensity_normalization.cli.tissue_membership:tissue_membership_main
-	ravel-normalize = intensity_normalization.cli.ravel:ravel_main [ants]
-	preprocess = intensity_normalization.cli.preprocess:preprocess_main [ants]
-	coregister = intensity_normalization.cli.coregister:coregister_main [ants]
+console_scripts =
+    fcm-normalize = intensity_normalization.cli.fcm:fcm_main
+    kde-normalize = intensity_normalization.cli.kde:kde_main
+    lsq-normalize = intensity_normalization.cli.lsq:lsq_main
+    nyul-normalize = intensity_normalization.cli.nyul:nyul_main
+    ws-normalize = intensity_normalization.cli.whitestripe:whitestripe_main
+    zscore-normalize = intensity_normalization.cli.zscore:zscore_main
+    plot-histograms = intensity_normalization.cli.histogram:histogram_main [plot]
+    tissue-membership = intensity_normalization.cli.tissue_membership:tissue_membership_main
+    ravel-normalize = intensity_normalization.cli.ravel:ravel_main [ants]
+    preprocess = intensity_normalization.cli.preprocess:preprocess_main [ants]
+    coregister = intensity_normalization.cli.coregister:coregister_main [ants]
 
 [options.extras_require]
-ants = 
-	antspyx>=0.2.7
-plot = 
-	matplotlib>=3,<4
+ants =
+    antspyx>=0.2.7
+plot =
+    matplotlib>=3,<4
 
 [options.package_data]
 intensity_normalization = py.typed
 
+[bumpversion]
+current_version = 2.2.1
+commit = True
+tag = False
+
 [bumpversion:file:intensity_normalization/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
@@ -88,8 +88,8 @@ count = True
 doctests = True
 exclude = docs
 extend-ignore = E203
-per-file-ignores = 
-	__init__.py: F401
+per-file-ignores =
+    __init__.py: F401
 max-line-length = 88
 statistics = True
 
@@ -99,6 +99,6 @@ test = pytest
 [tool:pytest]
 addopts = --doctest-modules --ignore=setup.py
 doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL NUMBER
-testpaths = 
-	intensity_normalization
-	tests
+testpaths =
+    intensity_normalization
+    tests