pass black

.github/workflows/blacktest.yml

@@ -25,7 +25,8 @@ jobs:
         python -m pip install --upgrade pip
         # pip install black
         # pip install black==21.10b0  # specify version 21.10b0 exactly
-        pip install black==22.3.0
+        # pip install black==22.3.0
+        pip install black
         pip install flake8
     - name: Test with Black
       run: |

cli/io/example/README.md

@@ -7,11 +7,19 @@ Given a comma separated values (`.csv`) file, plot columns with `xyfigure`
 
 ## Getting Started
 
+Create a virtual environment:
+
+```sh
+cd ~/sibl
+python -m venv .venv
+```
+
 Activate the virtual environment:
 
 ```sh
-cd ~/sibl/cli
 source ~/sibl/.venv/bin/activate
+cd ~/sibl/cli
+pip install -e .
 ```
 
 ## Example 1

cli/process/exodus/visualization.py

@@ -8,7 +8,6 @@
     > python visualization.py
 """
 
-
 import os
 
 import numpy as np

cli/process/tpav/test_three_points_angular_velocity.py

@@ -267,7 +267,6 @@ def test_t0_t1(self):
 
     @unittest.expectedFailure
     def test_t0_insufficient_rank_omega_perpendicular(self):
-
         """
         This function tests a single time step input with a rank-insufficient
         configuration space (rOR gets set to rOQ, which fails to span R3).
@@ -353,7 +352,6 @@ def test_t0_insufficient_rank_omega_perpendicular(self):
 
     @unittest.expectedFailure
     def test_t0_insufficient_rank_omega_parallel(self):
-
         """
         This function tests a single time step input with a rank-insufficient
         configuration space (rOR gets set to rOQ, which fails to span R3).

cli/pyproject.toml

@@ -29,7 +29,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "black==22.6.0", "flake8", "matplotlib", "pytest", "pytest-cov", "pyyaml", "scipy"
+    "black", "flake8", "matplotlib", "pytest", "pytest-cov", "pyyaml", "scipy"
 ]
 
 # Entry Points

cli/src/xyfigure/xymodel.py

@@ -438,7 +438,9 @@ def __init__(self, guid, **kwargs):
                                         ]
                                     ),
                                 )
-                            except IndexError:  # handle 2D input files, append 0.0 as z coordinate
+                            except (
+                                IndexError
+                            ):  # handle 2D input files, append 0.0 as z coordinate
                                 new_nodes = (
                                     tuple(
                                         [

cli/src/xyfigure/xytypes.py

@@ -8,6 +8,7 @@
 
 class Kwargs(NamedTuple):
     """The keyword arguments, kwargs, forwarded to Matplotlib."""
+
     alpha: float = 0.5
     color: str = "blue"
     label: str = "label"
@@ -17,6 +18,7 @@ class Kwargs(NamedTuple):
 
 class Model(NamedTuple):
     """The basic ingredients to create a single (x, y) trace."""
+
     folder: Path
     file: Path
     plot_kwargs: Kwargs
@@ -26,13 +28,15 @@ class Model(NamedTuple):
 
 class RhsAxis(NamedTuple):
     """The constituents of a right hand side vertical axis."""
+
     scale: float
     label: str
     yticks: list[float] | None
 
 
 class View(NamedTuple):
     """The plot on which the models are placed."""
+
     folder: Path
     file: Path
     size: list[float]

cli/tests/img_same_diff/image_diff.py

@@ -3,6 +3,7 @@
     Typical use case:
     $ python image_diff.py image_a image_b
 """
+
 # https://www.python.org/dev/peps/pep-0008/#imports
 # standard library imports
 import sys

cli/tests/img_same_diff/test_image_diff.py

@@ -7,6 +7,7 @@
 $ python -m unittest -v test_image_diff.py  # for higher verbosity
 
 """
+
 # https://www.python.org/dev/peps/pep-0008/#imports
 # standard library imports
 from unittest import TestCase, main

cli/tests/service/xyfigure_deprecatedtest.py

@@ -18,6 +18,7 @@
 # e.g., to test the test_same() method
 $ python -m unittest xyfigure_test.TestImageDiff.test_same
 """
+
 # https://www.python.org/dev/peps/pep-0008/#imports
 # standard library imports
 import os

cli/tests/tpav/test_three_points_angular_velocity.py

@@ -267,7 +267,6 @@ def test_t0_t1(self):
 
     @unittest.expectedFailure
     def test_t0_insufficient_rank_omega_perpendicular(self):
-
         """
         This function tests a single time step input with a rank-insufficient
         configuration space (rOR gets set to rOQ, which fails to span R3).
@@ -353,7 +352,6 @@ def test_t0_insufficient_rank_omega_perpendicular(self):
 
     @unittest.expectedFailure
     def test_t0_insufficient_rank_omega_parallel(self):
-
         """
         This function tests a single time step input with a rank-insufficient
         configuration space (rOR gets set to rOQ, which fails to span R3).

geo/doc/dual/lesson_21_deprecated.py

@@ -9,6 +9,7 @@
 # update lesson_21.py as needed
 > python lesson_21.py
 """
+
 import math
 from pathlib import Path
 from typing import Final

geo/doc/plot_voronoi.py

@@ -6,6 +6,7 @@
 > conda activate siblenv
 > python plot_voronoi.py
 """
+
 # import argparse
 import numpy as np
 import matplotlib.pyplot as plt

geo/doc/snakes_baseline.py

@@ -11,6 +11,7 @@
 
 1. Snakes: Active contour models. Kass, M.; Witkin, A.; Terzopoulos, D. International Journal of Computer Vision 1 (4): 321 (1988). DOI:10.1007/BF00133570
 """
+
 from pathlib import Path
 
 import numpy as np

geo/examples/bspline_surface_Bezier_recovery.py

@@ -6,6 +6,7 @@
 > conda activate siblenv
 > python bspline_surface_Bezier_recovery.py
 """
+
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib import rc

geo/examples/quadtree_example.py

@@ -5,6 +5,7 @@
 > cd ~/sibl/geo/examples
 > python quadtree_example.py
 """
+
 from pathlib import Path
 
 import matplotlib.pyplot as plt

geo/src/post/benchmark.py

@@ -9,6 +9,7 @@
 # update benchmark.py as needed
 > python benchmark.py
 """
+
 # from itertools import repeat
 import math
 from pathlib import Path

geo/src/ptg/bspline_basis_manual.py

@@ -110,7 +110,7 @@ def bspline_basis_manual(
             print(f"f(t) = {f_of_t}")
 
     if p == 1:
-        for (eix, te) in enumerate(t):  # e for evaluations, ix for index
+        for eix, te in enumerate(t):  # e for evaluations, ix for index
             if te >= knot_vector_t[knot_i] and te < knot_vector_t[knot_i + 1]:
                 f_of_t[eix] = (te - knot_vector_t[knot_i]) / (
                     knot_vector_t[knot_i + 1] - knot_vector_t[knot_i]
@@ -121,7 +121,7 @@ def bspline_basis_manual(
                 )
 
     if p == 2:
-        for (eix, te) in enumerate(t):  # e for evaluations, ix for index
+        for eix, te in enumerate(t):  # e for evaluations, ix for index
             if te >= knot_vector_t[knot_i] and te < knot_vector_t[knot_i + 1]:
 
                 a_1 = (te - knot_vector_t[knot_i]) / (

geo/src/ptg/copyright.py

@@ -22,7 +22,9 @@
 
 
 def text_block() -> str:
-    copyright_text: Final = "# Copyright 2020 National Technology and Engineering Solutions of Sandia, LLC (NTESS).\n# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains\n# certain rights in this software.\n"
+    copyright_text: Final = (
+        "# Copyright 2020 National Technology and Engineering Solutions of Sandia, LLC (NTESS).\n# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains\n# certain rights in this software.\n"
+    )
     return copyright_text
 
 

geo/src/ptg/domain_merge.py

@@ -195,18 +195,22 @@ def domain_merge(
     # renumber faces to global numbering scheme
     faces0 = tuple(
         tuple(
-            domain0.mesh.connectivity[i][j] + nnp0
-            if domain0.mesh.connectivity[i][j] < 0
-            else domain0.mesh.connectivity[i][j]
+            (
+                domain0.mesh.connectivity[i][j] + nnp0
+                if domain0.mesh.connectivity[i][j] < 0
+                else domain0.mesh.connectivity[i][j]
+            )
             for j in range(0, nen0)
         )
         for i in range(0, n_faces0)
     )
     faces1 = tuple(
         tuple(
-            domain1.mesh.connectivity[i][j] + nnp1 + nnp0
-            if domain1.mesh.connectivity[i][j] < 0
-            else domain1.mesh.connectivity[i][j] + nnp0
+            (
+                domain1.mesh.connectivity[i][j] + nnp1 + nnp0
+                if domain1.mesh.connectivity[i][j] < 0
+                else domain1.mesh.connectivity[i][j] + nnp0
+            )
             for j in range(0, nen1)
         )
         for i in range(0, n_faces1)
@@ -215,18 +219,22 @@ def domain_merge(
     # renumber boundaries to global numbering scheme
     bounds0 = tuple(
         tuple(
-            domain0.boundaries[i][j] + nnp0
-            if domain0.boundaries[i][j] < 0
-            else domain0.boundaries[i][j]
+            (
+                domain0.boundaries[i][j] + nnp0
+                if domain0.boundaries[i][j] < 0
+                else domain0.boundaries[i][j]
+            )
             for j in range(0, n_pts_per_bound0[i])
         )
         for i in range(0, n_bound0)
     )
     bounds1 = tuple(
         tuple(
-            domain1.boundaries[i][j] + nnp1 + nnp0
-            if domain1.boundaries[i][j] < 0
-            else domain1.boundaries[i][j] + nnp0
+            (
+                domain1.boundaries[i][j] + nnp1 + nnp0
+                if domain1.boundaries[i][j] < 0
+                else domain1.boundaries[i][j] + nnp0
+            )
             for j in range(0, n_pts_per_bound1[i])
         )
         for i in range(0, n_bound1)

geo/src/ptg/modified_bezier.py

@@ -168,9 +168,7 @@ def modified_bezier(
         N0 = np.array(tuple(map(lambda t: 0.5 * (1.0 - t) ** 2, t)))  # $\hat{N}_0$
         N1 = np.array(
             tuple(
-                map(
-                    lambda t: 0.5 * (1.0 - t) ** 2 + 2 * (1.0 - t) * t + 0.5 * t**2, t
-                )
+                map(lambda t: 0.5 * (1.0 - t) ** 2 + 2 * (1.0 - t) * t + 0.5 * t**2, t)
             )
         )  # $\hat{N}_1$
         N2 = np.array(tuple(map(lambda t: 0.5 * t**2, t)))  # $\hat{N}_2$

geo/src/ptg/quadtree.py

@@ -687,9 +687,11 @@ def _domain_dual(
             n_subquads_per_quad: Final = 4  # given transition from level -> level + 1
             quad_levels_recursive_parent = tuple(
                 (
-                    (level + 1,)
-                    if x == 1
-                    else tuple(repeat((level + 2,), n_subquads_per_quad))
+                    (
+                        (level + 1,)
+                        if x == 1
+                        else tuple(repeat((level + 2,), n_subquads_per_quad))
+                    )
                     for x in n_parent_quads
                 )
             )

geo/tests/test_bspline.py

@@ -5,6 +5,7 @@
 $ cd ~/sibl
 $ pytest geo/tests/test_bspline.py -v
 """
+
 from unittest import TestCase, main
 import pytest
 import numpy as np

geo/tests/test_mesh.py

@@ -18,6 +18,7 @@
 For flake8:
 flake8 --ignore E203,E501,W503 geo/tests/test_mesh.py --statistics
 """
+
 from math import isinf, isnan
 from pathlib import Path
 

geo/tests/test_mesh_morph.py

@@ -17,6 +17,7 @@
 For flake8:
 flake8 --ignore E203,E501,W503 geo/tests/test_mesh_morph.py --statistics
 """
+
 import numpy as np
 
 import ptg.mesh_morph as morph

geo/tests/test_translator.py

@@ -17,6 +17,7 @@
 For flake8:
 flake8 --ignore E203,E501,W503 geo/tests/test_translator.py --statistics
 """
+
 from pathlib import Path
 
 import pytest
@@ -38,7 +39,7 @@ def test_string_to_vertex():
         translator.MeshFileVertex(x=-0.51, y=-0.87, z=-0.08, face_id=42),
         translator.MeshFileVertex(x=-0.55, y=-0.88, z=-0.09, face_id=12),
     )
-    for (x, y) in zip(xs, ys):
+    for x, y in zip(xs, ys):
         fx = translator.string_to_vertex(vertex_string=x)
         assert y == fx
 
@@ -95,7 +96,7 @@ def test_string_to_hexahedron():
         translator.MeshFileHexahedron(nodes=(2, 3, 6, 5, 11, 12, 15, 14), vol_id=1),
         translator.MeshFileHexahedron(nodes=(4, 5, 8, 7, 13, 14, 17, 16), vol_id=1),
     )
-    for (x, y) in zip(xs, ys):
+    for x, y in zip(xs, ys):
         fx = translator.string_to_hexahedron(hex_string=x)
         assert y == fx
 

geo/tests/test_view_bernstein_surface.py

@@ -8,6 +8,7 @@
 $ pytest geo/tests/test_view_bernstein_surface.py -v
 $ pytest geo/tests/test_view_bernstein_surface.py -v --cov=geo/src/ptg --cov-report term-missing
 """
+
 from unittest import TestCase, main
 
 import ptg.view_bernstein_surface as bsurf

geo/tests/test_view_bezier.py

@@ -8,6 +8,7 @@
 $ pytest geo/tests/test_view_bezier.py -v
 $ pytest geo/tests/test_view_bezier.py -v --cov=geo/src/ptg --cov-report term-missing
 """
+
 # import runpy
 # import sys
 from pathlib import Path  # stop using os.path, use pathlib instead

geo/tests/test_view_bspline.py

@@ -8,6 +8,7 @@
 $ pytest geo/tests/test_view_bspline.py -v
 $ pytest geo/tests/test_view_bspline.py -v --cov=geo/src/ptg --cov-report term-missing
 """
+
 # import runpy
 # import sys
 from pathlib import Path  # stop using os.path, use pathlib instead