Merge pull request #5 from boutproject/cleanup

Cleanup some dead code as well as add GHA for linting

.github/workflows/black-fix.yml

@@ -0,0 +1,39 @@
+name: linting
+
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        ref: ${{ github.head_ref }}
+
+    - name: Install black
+      run: |
+        sudo apt update -y
+        sudo apt -y install python3-pip python3-setuptools python3-wheel
+        pip3 install black isort
+
+    - name: Version
+      run: |
+        python3 --version
+        $HOME/.local/bin/black --version
+        $HOME/.local/bin/isort --version
+
+    - name: Run black
+      run: |
+        pwd
+        ls
+        $HOME/.local/bin/black zoidberg
+        $HOME/.local/bin/isort zoidberg
+
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: "[skip ci] Apply black/isort changes"

zoidberg/__init__.py

@@ -1,9 +1,6 @@
 import zoidberg
-from . import grid
-from . import field
-from . import fieldtracer
-from . import plot
 
+from . import field, fieldtracer, grid, plot
 from .zoidberg import make_maps, write_maps
 
 __all__ = [

zoidberg/field.py

@@ -317,22 +317,8 @@ def Rfunc(self, x, z, phi):
 
 
 try:
-    from sympy import (
-        Symbol,
-        atan2,
-        cos,
-        sin,
-        log,
-        pi,
-        sqrt,
-        lambdify,
-        Piecewise,
-        Sum,
-        gamma,
-        And,
-        factorial,
-        diff,
-    )
+    from sympy import (And, Piecewise, Sum, Symbol, atan2, cos, diff,
+                       factorial, gamma, lambdify, log, pi, sin, sqrt)
 
     class StraightStellarator(MagneticField):
         """A "rotating ellipse" stellarator without curvature
@@ -1124,7 +1110,7 @@ def read_vmec_file(self, vmec_file, ntheta=None, nzeta=None):
 
     def __init__(self, vmec_file, ntheta=None, nzeta=None, nr=32, nz=32):
         # Only needed here
-        from scipy.interpolate import griddata, RegularGridInterpolator
+        from scipy.interpolate import RegularGridInterpolator, griddata
 
         self.read_vmec_file(vmec_file, ntheta, nzeta)
 
@@ -1433,8 +1419,8 @@ def __init__(
             While the description are at:
             http://svvmec1.ipp-hgw.mpg.de:8080/vmecrest/v1/Coil_currents_1_AA_T_0011.pdf
         """
-        from scipy.interpolate import RegularGridInterpolator
         import numpy as np
+        from scipy.interpolate import RegularGridInterpolator
 
         ## create 1D arrays of cylindrical coordinates
         r = np.linspace(x_range[0], x_range[-1], nx)
@@ -1497,13 +1483,14 @@ def field_values(r, phi, z, configuration=0, plot_poincare=False):
         Contact [email protected] for questions
 
         """
-        from osa import Client
         import os.path
-        import xarray as xr
         import pickle
-        import matplotlib.pyplot as plt
         from time import sleep
 
+        import matplotlib.pyplot as plt
+        import xarray as xr
+        from osa import Client
+
         tracer = Client("http://esb.ipp-hgw.mpg.de:8280/services/FieldLineProxy?wsdl")
 
         nx = r.shape[0]
@@ -1684,10 +1671,11 @@ def plasma_field(r, phi, z, wout_file="wout.nc"):
         Contact [email protected] for questions
 
         """
-        from osa import Client
         import os.path
         import pickle
 
+        from osa import Client
+
         cl = Client("http://esb.ipp-hgw.mpg.de:8280/services/Extender?wsdl")
 
         vmecURL = "http://svvmec1.ipp-hgw.mpg.de:8080/vmecrest/v1/w7x_ref_1/wout.nc"
@@ -1826,8 +1814,8 @@ def __init__(
         phi_range=[0, 2 * np.pi],
         vmec_id="w7x_ref_171",
     ):
-        from scipy.interpolate import RegularGridInterpolator
         import numpy as np
+        from scipy.interpolate import RegularGridInterpolator
 
         ## create 1D arrays of cylindrical coordinates
         r = np.linspace(x_range[0], x_range[-1], nx)

zoidberg/grid.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import numpy as np
 
 # Import classes representing poloidal grids

zoidberg/plot.py

@@ -1,8 +1,8 @@
-from . import fieldtracer
+import warnings
 
 import numpy as np
 
-import warnings
+from . import fieldtracer
 
 try:
     import matplotlib.animation as anim

zoidberg/poloidal_grid.py

@@ -18,13 +18,13 @@
 
 """
 
+import warnings
+
 import numpy as np
-from numpy import pi, linspace, zeros
+from numpy import linspace, pi, zeros
 from scipy.interpolate import RectBivariateSpline
 from scipy.spatial import cKDTree as KDTree
 
-import warnings
-
 try:
     import matplotlib.pyplot as plt
 

zoidberg/rzline.py

@@ -3,13 +3,12 @@
 
 """
 
-import numpy as np
+import warnings
 
-from numpy import pi, linspace, sqrt, cos, sin, append, argmin
-from scipy.interpolate import splrep, splev, interp1d
+import numpy as np
+from numpy import append, argmin, cos, linspace, pi, sin, sqrt
 from scipy.integrate import cumtrapz
-
-import warnings
+from scipy.interpolate import interp1d, splev, splrep
 
 try:
     import matplotlib.pyplot as plt
@@ -518,7 +517,6 @@ def line_from_points(rarray, zarray, show=False):
 
     #############################################################################
     # Define the magnetic field
-
     # Length in y after which the coils return to their starting (R,Z) locations
     yperiod = 10.0
 

zoidberg/test_field.py

@@ -1,5 +1,6 @@
 import numpy as np
-from .field import Slab, CurvedSlab
+
+from .field import CurvedSlab, Slab
 
 
 def test_slab():

zoidberg/test_fieldtracer.py

@@ -1,7 +1,6 @@
 import numpy as np
 
-from . import fieldtracer
-from . import field
+from . import field, fieldtracer
 
 
 def test_slab():

zoidberg/test_grid.py

@@ -1,6 +1,7 @@
-from .grid import rectangular_grid
 import numpy as np
 
+from .grid import rectangular_grid
+
 
 def test_getPoloidalGrid():
     # Create a simple non-periodic grid

zoidberg/test_poloidal_grid.py

@@ -1,7 +1,6 @@
 import numpy as np
 
-from . import rzline
-from . import poloidal_grid
+from . import poloidal_grid, rzline
 
 
 def test_out_of_domain():

zoidberg/test_rzline.py

@@ -1,7 +1,7 @@
-from . import rzline
-
 import numpy as np
 
+from . import rzline
+
 
 def test_circular_boundaries():
     inner = rzline.circle(R0=1.0, r=1.0, n=20)
@@ -37,7 +37,6 @@ def test_distance():
 def test_order_by_distance():
     # Check the RZline.equallySpaced function
     inner = rzline.circle(R0=1.0, r=1.0, n=20)
-    outer = rzline.circle(R0=1.0, r=2.0, n=20)
 
     new_inner = inner.equallySpaced(n=10)
 

zoidberg/test_zoidberg.py

@@ -1,6 +1,8 @@
 from itertools import chain, product
+
 import numpy as np
-from . import zoidberg, grid, field
+
+from . import field, grid, zoidberg
 
 
 def test_make_maps_slab():

zoidberg/zoidberg.py

@@ -1,9 +1,8 @@
-from __future__ import division
+from collections import namedtuple
+from itertools import chain
 
 import numpy as np
 from boututils import datafile as bdata
-from collections import namedtuple
-from itertools import chain
 
 from . import fieldtracer
 from .progress import update_progress
@@ -483,8 +482,8 @@ def upscale(field, maps, upscale_factor=4, quiet=True):
 
     """
 
-    from scipy.ndimage.interpolation import map_coordinates
     from scipy.interpolate import griddata
+    from scipy.ndimage.interpolation import map_coordinates
 
     xt_prime = maps["forward_xt_prime"]
     zt_prime = maps["forward_zt_prime"]