Bump mypy version and update ignores.

pymassspec_plot/__init__.py

@@ -29,17 +29,17 @@
 from typing import List, Mapping, Optional, Sequence, Tuple
 
 # 3rd party
-import matplotlib  # type: ignore[import]
-import matplotlib.pyplot as plt  # type: ignore[import]
-from matplotlib.axes import Axes  # type: ignore[import]
-from matplotlib.backend_bases import MouseEvent  # type: ignore[import]
-from matplotlib.container import BarContainer  # type: ignore[import]
-from matplotlib.figure import Figure  # type: ignore[import]
-from matplotlib.lines import Line2D  # type: ignore[import]
-from pyms import Peak  # type: ignore[import]
-from pyms.IonChromatogram import IonChromatogram  # type: ignore[import]
-from pyms.Peak.List.Function import is_peak_list  # type: ignore[import]
-from pyms.Spectrum import MassSpectrum, normalize_mass_spec  # type: ignore[import]
+import matplotlib  # type: ignore[import-untyped]
+import matplotlib.pyplot as plt  # type: ignore[import-untyped]
+from matplotlib.axes import Axes  # type: ignore[import-untyped]
+from matplotlib.backend_bases import MouseEvent  # type: ignore[import-untyped]
+from matplotlib.container import BarContainer  # type: ignore[import-untyped]
+from matplotlib.figure import Figure  # type: ignore[import-untyped]
+from matplotlib.lines import Line2D  # type: ignore[import-untyped]
+from pyms import Peak
+from pyms.IonChromatogram import IonChromatogram
+from pyms.Peak.List.Function import is_peak_list
+from pyms.Spectrum import MassSpectrum, normalize_mass_spec
 
 # this package
 from pymassspec_plot.utils import invert_mass_spec

pymassspec_plot/utils.py

@@ -26,7 +26,7 @@
 ################################################################################
 
 # 3rd party
-from pyms.Spectrum import MassSpectrum  # type: ignore[import]
+from pyms.Spectrum import MassSpectrum
 
 __all__ = ["invert_mass_spec"]
 

repo_helper.yml

@@ -16,6 +16,7 @@ min_coverage: 88
 use_whey: true
 sphinx_html_theme: furo
 python_deploy_version: 3.8
+mypy_version: "1.8.0"
 preserve_custom_theme: true
 
 conda_channels:

tests/conftest.py

@@ -6,15 +6,15 @@
 import numpy
 import pytest
 from domdf_python_tools.paths import PathPlus
-from pyms.BillerBiemann import BillerBiemann  # type: ignore[import]
-from pyms.GCMS.Class import GCMS_data  # type: ignore[import]
-from pyms.GCMS.IO.JCAMP import JCAMP_reader  # type: ignore[import]
-from pyms.IntensityMatrix import IntensityMatrix, build_intensity_matrix_i  # type: ignore[import]
-from pyms.IonChromatogram import IonChromatogram  # type: ignore[import]
-from pyms.Noise.SavitzkyGolay import savitzky_golay  # type: ignore[import]
-from pyms.Peak import Peak  # type: ignore[import]
-from pyms.Spectrum import MassSpectrum  # type: ignore[import]
-from pyms.TopHat import tophat  # type: ignore[import]
+from pyms.BillerBiemann import BillerBiemann
+from pyms.GCMS.Class import GCMS_data
+from pyms.GCMS.IO.JCAMP import JCAMP_reader
+from pyms.IntensityMatrix import IntensityMatrix, build_intensity_matrix_i
+from pyms.IonChromatogram import IonChromatogram
+from pyms.Noise.SavitzkyGolay import savitzky_golay
+from pyms.Peak import Peak
+from pyms.Spectrum import MassSpectrum
+from pyms.TopHat import tophat
 from pytest_regressions.data_regression import RegressionYamlDumper
 
 pytest_plugins = ("coincidence", )

tests/test_plot.py

@@ -6,15 +6,15 @@
 import pytest
 from coincidence.regressions import AdvancedFileRegressionFixture
 from domdf_python_tools.paths import PathPlus
-from matplotlib import pyplot as plt  # type: ignore[import]
-from matplotlib.backend_bases import MouseEvent  # type: ignore[import]
-from matplotlib.cbook import CallbackRegistry  # type: ignore[import]
-from matplotlib.figure import Figure  # type: ignore[import]
-from pyms.GCMS.Class import GCMS_data  # type: ignore[import]
-from pyms.IntensityMatrix import IntensityMatrix  # type: ignore[import]
-from pyms.IonChromatogram import IonChromatogram  # type: ignore[import]
-from pyms.Peak import Peak  # type: ignore[import]
-from pyms.Spectrum import MassSpectrum  # type: ignore[import]
+from matplotlib import pyplot as plt  # type: ignore[import-untyped]
+from matplotlib.backend_bases import MouseEvent  # type: ignore[import-untyped]
+from matplotlib.cbook import CallbackRegistry  # type: ignore[import-untyped]
+from matplotlib.figure import Figure  # type: ignore[import-untyped]
+from pyms.GCMS.Class import GCMS_data
+from pyms.IntensityMatrix import IntensityMatrix
+from pyms.IonChromatogram import IonChromatogram
+from pyms.Peak import Peak
+from pyms.Spectrum import MassSpectrum
 
 # this package
 from pymassspec_plot import ClickEventHandler, plot_head2tail, plot_ic, plot_mass_spec, plot_peaks
@@ -121,7 +121,7 @@ def test_plot_ic_errors(im_i: IntensityMatrix, data: GCMS_data, ms: MassSpectrum
 
 	for obj in [*test_sequences, test_string, *test_numbers, test_dict, im_i, data, ms]:
 		with pytest.raises(TypeError, match="'ic' must be an IonChromatogram"):
-			plot_ic(ax, obj)
+			plot_ic(ax, obj)  # type: ignore[arg-type]
 
 
 # Plotting tic with various Line2D options
@@ -185,7 +185,7 @@ def test_plot_tic_errors(im_i: IntensityMatrix, data: GCMS_data, ms: MassSpectru
 			ms,
 			]:
 		with pytest.raises(TypeError, match="'ic' must be an IonChromatogram"):
-			plot_ic(ax, obj)
+			plot_ic(ax, obj)  # type: ignore[arg-type]
 
 
 @check_images
@@ -250,7 +250,7 @@ def test_plot_mass_spec_errors(im_i: IntensityMatrix, data: GCMS_data, tic: IonC
 			tic,
 			]:
 		with pytest.raises(TypeError, match="'mass_spec' must be a MassSpectrum"):
-			plot_mass_spec(ax, obj)
+			plot_mass_spec(ax, obj)  # type: ignore[arg-type]
 
 
 @check_images
@@ -281,31 +281,41 @@ def test_plot_head2tail_errors(im_i: IntensityMatrix, data: GCMS_data):
 
 	for obj in [*test_sequences, test_string, *test_numbers, test_dict, im_i, data]:
 		with pytest.raises(TypeError, match="'top_mass_spec' must be a MassSpectrum"):
-			plot_head2tail(ax, obj, im_i.get_ms_at_index(150))
+			plot_head2tail(ax, obj, im_i.get_ms_at_index(150))  # type: ignore[arg-type]
 
 		with pytest.raises(TypeError, match="'bottom_mass_spec' must be a MassSpectrum"):
-			plot_head2tail(ax, im_i.get_ms_at_index(50), obj)
+			plot_head2tail(ax, im_i.get_ms_at_index(50), obj)  # type: ignore[arg-type]
 
 	for obj in [*test_sequences, test_string, *test_numbers, im_i.get_ms_at_index(250), im_i, data]:
 		with pytest.raises(
 				TypeError,
 				match="'top_spec_kwargs' must be a mapping of keyword arguments for the top mass spectrum."
 				):
-			plot_head2tail(ax, im_i.get_ms_at_index(50), im_i.get_ms_at_index(150), top_spec_kwargs=obj)
+			plot_head2tail(
+					ax,
+					im_i.get_ms_at_index(50),
+					im_i.get_ms_at_index(150),
+					top_spec_kwargs=obj,  # type: ignore[arg-type]
+					)
 
 		with pytest.raises(
 				TypeError,
 				match="'bottom_spec_kwargs' must be a mapping of keyword arguments for the bottom mass spectrum."
 				):
-			plot_head2tail(ax, im_i.get_ms_at_index(50), im_i.get_ms_at_index(150), bottom_spec_kwargs=obj)
+			plot_head2tail(
+					ax,
+					im_i.get_ms_at_index(50),
+					im_i.get_ms_at_index(150),
+					bottom_spec_kwargs=obj,  # type: ignore[arg-type]
+					)
 
 
 def test_plot_peaks(im_i: IntensityMatrix, data: GCMS_data, ms: MassSpectrum):
 	fig, ax = plt.subplots()
 
 	for obj in [*test_sequences, test_string, *test_numbers, test_dict, im_i, data, ms]:
 		with pytest.raises(TypeError, match="'peak_list' must be a list of Peak objects"):
-			plot_peaks(ax, obj)
+			plot_peaks(ax, obj)  # type: ignore[arg-type]
 
 
 @check_images

tests/test_utils.py

@@ -1,6 +1,6 @@
 # 3rd party
 from coincidence import AdvancedDataRegressionFixture
-from pyms.Spectrum import MassSpectrum  # type: ignore
+from pyms.Spectrum import MassSpectrum
 
 # this package
 from pymassspec_plot import invert_mass_spec

tox.ini

@@ -118,7 +118,7 @@ basepython = python3.8
 ignore_errors = True
 changedir = {toxinidir}
 deps =
-    mypy==0.971
+    mypy==1.8.0
     -r{toxinidir}/tests/requirements.txt
 commands = mypy pymassspec_plot tests {posargs}