lint: Use same convention everywhere

Closes the-virtual-brain#60

.travis.yml

@@ -35,6 +35,6 @@ jobs:
       install: pip install flake8
       script:
         # stop the build if there are Python syntax errors or undefined names
-        - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        - flake8 . --show-source --statistics
         # exit-zero treats all errors as warnings
-        - flake8 . --exit-zero
+        - flake8 .

setup.py

@@ -50,14 +50,14 @@
 
 
 compiler_directives = {
-    'language_level': 3,
+    "language_level": 3,
 }
 
 # Disable assertions; one is failing geodesic_mesh.h:405
-define_macros = [('NDEBUG', 1)]
+define_macros = [("NDEBUG", 1)]
 
-if 'COVERAGE' in os.environ:
-    compiler_directives['linetrace'] = True
+if "COVERAGE" in os.environ:
+    compiler_directives["linetrace"] = True
     define_macros.append(("CYTHON_TRACE_NOGIL", "1"))
 
 GEODESIC_NAME = "gdist"
@@ -68,8 +68,8 @@
         sources=["gdist.pyx"],  # Filename of Cython source
         language="c++",  # Cython create C++ source
         define_macros=define_macros,
-        extra_compile_args=['--std=c++14'],
-        extra_link_args=['--std=c++14'],
+        extra_compile_args=["--std=c++14"],
+        extra_link_args=["--std=c++14"],
         include_dirs=[numpy.get_include(), "geodesic_library"],
     )
 ]
@@ -81,11 +81,12 @@
 
 TEAM = "Danil Kirsanov, Gaurav Malhotra and Stuart Knock"
 
-INSTALL_REQUIREMENTS = ['numpy', 'scipy', 'cython']
+INSTALL_REQUIREMENTS = ["numpy", "scipy", "cython"]
 
-with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as fd:
+with open(os.path.join(os.path.dirname(__file__), "README.rst")) as fd:
     DESCRIPTION = fd.read()
 
+
 class new_build_ext(build_ext):
     def finalize_options(self):
         self.distribution.ext_modules = cythonize(
@@ -100,18 +101,19 @@ def finalize_options(self):
         self.include_dirs.append(numpy.get_include())
         super().finalize_options()
 
+
 setuptools.setup(
     name="tvb-" + GEODESIC_NAME,
-    version='2.1.0',
+    version="2.1.0",
     ext_modules=GEODESIC_MODULE,
     include_dirs=INCLUDE_DIRS,
     cmdclass={"build_ext": new_build_ext},
     install_requires=INSTALL_REQUIREMENTS,
     description="Compute geodesic distances",
     long_description=DESCRIPTION,
-    license='GPL v3',
+    license="GPL v3",
     author=TEAM,
-    author_email='tvb.admin@thevirtualbrain.org',
-    url='https://github.com/the-virtual-brain/tvb-gdist',
-    keywords="gdist geodesic distance geo tvb"
+    author_email="tvb.admin@thevirtualbrain.org",
+    url="https://github.com/the-virtual-brain/tvb-gdist",
+    keywords="gdist geodesic distance geo tvb",
 )

tests/test_equality_with_stable.py

@@ -37,21 +37,19 @@
 
 
 def test_equality_with_stable():
-    surface_datas = ['inner_skull_642', 'outer_skull_642', 'scalp_1082']
+    surface_datas = ["inner_skull_642", "outer_skull_642", "scalp_1082"]
     for surface_data in surface_datas:
         expected = np.loadtxt(
-            f'data/surface_data/{surface_data}/gdist_matrix.txt')
+            f"data/surface_data/{surface_data}/gdist_matrix.txt"
+        )
         vertices = np.loadtxt(
-            f'data/surface_data/{surface_data}/vertices.txt',
-            dtype=np.float64,
+            f"data/surface_data/{surface_data}/vertices.txt", dtype=np.float64,
         )
         triangles = np.loadtxt(
-            f'data/surface_data/{surface_data}/triangles.txt',
-            dtype=np.int32,
+            f"data/surface_data/{surface_data}/triangles.txt", dtype=np.int32,
         )
         actual = gdist.local_gdist_matrix(
-            vertices=vertices,
-            triangles=triangles,
+            vertices=vertices, triangles=triangles,
         )
         actual = actual.toarray()
         np.testing.assert_array_almost_equal(actual, expected)

tests/test_gdist.py

@@ -38,36 +38,28 @@
 import gdist
 
 
-class TestComputeGdist():
+class TestComputeGdist:
     def test_flat_triangular_mesh(self):
         data = np.loadtxt("data/flat_triangular_mesh.txt", skiprows=1)
         vertices = data[0:121].astype(np.float64)
         triangles = data[121:].astype(np.int32)
         source = np.array([1], dtype=np.int32)
         target = np.array([2], dtype=np.int32)
         distance = gdist.compute_gdist(
-            vertices,
-            triangles,
-            source_indices=source,
-            target_indices=target
+            vertices, triangles, source_indices=source, target_indices=target
         )
         np.testing.assert_array_almost_equal(distance, [0.2])
 
     def test_flat_triangular_mesh_1_indexed(self):
         data = np.loadtxt(
-            "data/flat_triangular_mesh_1_indexed.txt",
-            skiprows=1,
+            "data/flat_triangular_mesh_1_indexed.txt", skiprows=1,
         )
         vertices = data[0:121].astype(np.float64)
         triangles = data[121:].astype(np.int32)
         source = np.array([2], dtype=np.int32)
         target = np.array([3], dtype=np.int32)
         distance = gdist.compute_gdist(
-            vertices,
-            triangles,
-            source,
-            target,
-            is_one_indexed=True,
+            vertices, triangles, source, target, is_one_indexed=True,
         )
         np.testing.assert_array_almost_equal(distance, [0.2])
 
@@ -77,12 +69,7 @@ def test_flat_triangular_mesh_no_target(self):
         triangles = data[121:].astype(np.int32)
         source = None
         target = None
-        distance = gdist.compute_gdist(
-            vertices,
-            triangles,
-            source,
-            target,
-        )
+        distance = gdist.compute_gdist(vertices, triangles, source, target,)
         expected = np.loadtxt("data/flat_triangular_mesh_no_target.txt")
         np.testing.assert_array_almost_equal(distance, expected)
 
@@ -93,10 +80,7 @@ def test_hedgehog_mesh(self):
         source = np.array([0], dtype=np.int32)
         target = np.array([1], dtype=np.int32)
         distance = gdist.compute_gdist(
-            vertices,
-            triangles,
-            source_indices=source,
-            target_indices=target
+            vertices, triangles, source_indices=source, target_indices=target
         )
         np.testing.assert_array_almost_equal(distance, [1.40522])
 
@@ -107,7 +91,7 @@ def test_flat_triangular_mesh(self):
         vertices = data[0:121].astype(np.float64)
         triangles = data[121:].astype(np.int32)
         distances = gdist.local_gdist_matrix(vertices, triangles)
-        epsilon = 1e-6 # the default value used in `assert_array_almost_equal`
+        epsilon = 1e-6  # the default value used in `assert_array_almost_equal`
         # test if the obtained matrix is symmetric
         assert (abs(distances - distances.T) > epsilon).nnz == 0
         np.testing.assert_array_almost_equal(distances.toarray()[1][0], 0.2)
@@ -119,15 +103,12 @@ def test_flat_triangular_mesh(self):
 
     def test_flat_triangular_mesh_1_indexed(self):
         data = np.loadtxt(
-            "data/flat_triangular_mesh_1_indexed.txt",
-            skiprows=1,
+            "data/flat_triangular_mesh_1_indexed.txt", skiprows=1,
         )
         vertices = data[0:121].astype(np.float64)
         triangles = data[121:].astype(np.int32)
         distances = gdist.local_gdist_matrix(
-            vertices,
-            triangles,
-            is_one_indexed=True
+            vertices, triangles, is_one_indexed=True
         )
         epsilon = 1e-6  # the default value used in `assert_array_almost_equal`
         # test if the obtained matrix is symmetric
@@ -144,7 +125,7 @@ def test_hedgehog_mesh(self):
         vertices = data[0:300].astype(np.float64)
         triangles = data[300:].astype(np.int32)
         distances = gdist.local_gdist_matrix(vertices, triangles)
-        epsilon = 1e-6 # the default value used in `assert_array_almost_equal`
+        epsilon = 1e-6  # the default value used in `assert_array_almost_equal`
         # test if the obtained matrix is symmetric
         assert (abs(distances - distances.T) > epsilon).nnz == 0
         np.testing.assert_array_almost_equal(
@@ -164,9 +145,7 @@ def test_flat_triangular_mesh(self):
         triangles = data[121:].astype(np.int32)
         points = np.array([2, 5, 10, 12, 14, 16], dtype=np.int32)
         distances = gdist.distance_matrix_of_selected_points(
-            vertices,
-            triangles,
-            points,
+            vertices, triangles, points,
         )
         epsilon = 1e-6
         expected = np.loadtxt("data/flat_triangular_mesh_pairwise_matrix.txt")