lint

Author: kjfisch

README.rst

@@ -6,14 +6,14 @@ Scatterkit
 .. inclusion-readme-intro-start
 
 **Scatterkit** is an object-oriented python toolkit for analysing scattering of
-fluids from molecular simulations. Combined with MDAnalysis_, 
-Scatterkit can be used to extract X-ray scattering data from trajectory files, 
+fluids from molecular simulations. Combined with MDAnalysis_,
+Scatterkit can be used to extract X-ray scattering data from trajectory files,
 including LAMMPS, GROMACS, CHARMM or NAMD data. Scatterkit is open source and is
 released under the GNU general public license v3.0.
 
 Scatterkit is a tool for beginners of molecular simulations with no prior Python experience.
 For these users Scatterkit provides a descriptive command line interface. Also experienced
-users can use the Python API for their day to day analysis. 
+users can use the Python API for their day to day analysis.
 
 Scatterkit is maintained by the MAICoS developer team.
 Keep up to date with Scatterkit news by following us on Twitter_. If you find an issue, you

setup.py

@@ -19,9 +19,8 @@
 from pathlib import Path
 
 import numpy as np
-from setuptools import Extension, setup
-
 import versioneer
+from setuptools import Extension, setup
 
 VERSION = versioneer.get_version()
 

src/scatterkit/__init__.py

@@ -1,19 +1,15 @@
-"""scatterkit: SAXS analysis of MD trajectories"""
+"""scatterkit: SAXS analysis of MD trajectories."""
 
 __authors__ = "MAICoS Developer Team"
 
-import warnings
-
 from ._version import get_versions
+from .saxs import Saxs
 
-__authors__ = "MAICoS Developer Team"
-#: Version information for MAICoS, following :pep:`440`
+#: Version information for Scatterkit, following :pep:`440`
 #: and `semantic versioning <http://semver.org/>`_.
 __version__ = get_versions()["version"]
 del get_versions
 
-from .saxs import Saxs
-
 __all__ = [
     "Saxs",
 ]

src/scatterkit/lib/math.py

@@ -49,7 +49,8 @@ def atomic_form_factor(q: float, element: str) -> float:
         The magnitude of the scattering vector in reciprocal angstroms (1/Å).
     element : str
         The element for which the atomic form factor is calculated. Known elements are
-        listed in the :attr:`scatterkit.lib.tables.elements` set. United-atom models such as
+        listed in the :attr:`scatterkit.lib.tables.elements` set.
+        United-atom models such as
         ``"CH1"``, ``"CH2"``, ``"CH3"``, ``"CH4"``, ``"NH1"``, ``"NH2"``, and ``"NH3"``
         are also supported.
 
@@ -99,6 +100,7 @@ def atomic_form_factor(q: float, element: str) -> float:
 
     return form_factor.reshape(q2.shape)
 
+
 def rdf_structure_factor(
     rdf: np.ndarray, r: np.ndarray, density: float
 ) -> tuple[np.ndarray, np.ndarray]:

src/scatterkit/lib/util.py

@@ -9,8 +9,6 @@
 
 import re
 from collections.abc import Callable
-from pathlib import Path
-import sys
 
 DOC_REGEX_PATTERN = re.compile(r"\$\{([^\}]+)\}")
 
@@ -158,5 +156,3 @@ def scatterkit_banner(version: str = "", frame_char: str = "-") -> str:
 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 """
     return banner.replace("@", frame_char)
-
-

src/scatterkit/saxs.py

@@ -11,8 +11,8 @@
 
 import MDAnalysis as mda
 import numpy as np
-
 from maicos.core import AnalysisBase
+
 from .lib.math import atomic_form_factor, structure_factor
 from .lib.util import render_docs
 

tests/data/__init__.py

@@ -28,5 +28,3 @@
 # An SPC/E water molecule pointing in z-direction
 SPCE_ITP = DIR_PATH / "spce.itp"
 SPCE_GRO = DIR_PATH / "spce.gro"
-
-

tests/lib/test_math.py

@@ -13,13 +13,13 @@
 import MDAnalysis as mda
 import numpy as np
 import pytest
-from numpy.testing import assert_allclose, assert_equal
+from numpy.testing import assert_allclose
 
 import scatterkit.lib.math
 import scatterkit.lib.util
 
 sys.path.append(str(Path(__file__).parents[1]))
-from data import SPCE_GRO, SPCE_ITP, WATER_GRO_NPT, WATER_TPR_NPT  # noqa: E402
+from data import WATER_GRO_NPT, WATER_TPR_NPT  # noqa: E402
 
 
 class Test_sfactor:

tests/lib/test_util.py

@@ -7,15 +7,16 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 """Tests for the utilities."""
 
-import pytest
-from numpy.testing import assert_allclose, assert_equal
 import sys
 from pathlib import Path
 
+import pytest
+
 import scatterkit.lib.util
 
 sys.path.append(str(Path(__file__).parents[1]))
 
+
 def test_banner():
     """Test banner string by checking some necesarry features.
 
@@ -31,7 +32,9 @@ def test_banner():
     assert scatterkit.lib.util.scatterkit_banner().endswith("\n")
     # Check for correct length of lines (80 characters excluding top and bottom)
     # Also add in a long version string to check that it doesn't overflow
-    for line in scatterkit.lib.util.scatterkit_banner(version="v1.10.11").split("\n")[1:-1]:
+    for line in scatterkit.lib.util.scatterkit_banner(version="v1.10.11").split("\n")[
+        1:-1
+    ]:
         assert len(line) == 80
     # Check that the version is correctly inserted
     assert "v0.0.1" in scatterkit.lib.util.scatterkit_banner(version="v0.0.1")

tox.ini

@@ -12,7 +12,7 @@ envlist =
 lint_folders =
     "{toxinidir}/setup.py" \
     "{toxinidir}/src" \
-    "{toxinidir}/tests" \
+    "{toxinidir}/tests" 
 
 # configures which environments run with each python version
 [testenv]