Formatting and linting

.pre-commit-config.yaml

@@ -1,9 +1,4 @@
 repos:
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.1
-    hooks:
-    - id: flake8
-
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:

01-freeboundary.py

@@ -8,39 +8,45 @@
 
 tokamak = freegs4e.machine.TestTokamak()
 
-eq = freegs4e.Equilibrium(tokamak=tokamak,
-                        Rmin=0.1, Rmax=2.0,    # Radial domain
-                        Zmin=-1.0, Zmax=1.0,   # Height range
-                        nx=65, ny=65,          # Number of grid points
-                        boundary=freegs4e.boundary.freeBoundaryHagenow)  # Boundary condition
+eq = freegs4e.Equilibrium(
+    tokamak=tokamak,
+    Rmin=0.1,
+    Rmax=2.0,  # Radial domain
+    Zmin=-1.0,
+    Zmax=1.0,  # Height range
+    nx=65,
+    ny=65,  # Number of grid points
+    boundary=freegs4e.boundary.freeBoundaryHagenow,
+)  # Boundary condition
 
 
 #########################################
 # Plasma profiles
 
-profiles = freegs4e.jtor.ConstrainPaxisIp(1e3, # Plasma pressure on axis [Pascals]
-                                        2e5, # Plasma current [Amps]
-                                        2.0) # Vacuum f=R*Bt
+profiles = freegs4e.jtor.ConstrainPaxisIp(
+    1e3, 2e5, 2.0  # Plasma pressure on axis [Pascals]  # Plasma current [Amps]
+)  # Vacuum f=R*Bt
 
 #########################################
 # Coil current constraints
 #
 # Specify locations of the X-points
 # to use to constrain coil currents
 
-xpoints = [(1.1, -0.6),   # (R,Z) locations of X-points
-           (1.1, 0.8)]
+xpoints = [(1.1, -0.6), (1.1, 0.8)]  # (R,Z) locations of X-points
 
-isoflux = [(1.1,-0.6, 1.1,0.6)] # (R1,Z1, R2,Z2) pair of locations
+isoflux = [(1.1, -0.6, 1.1, 0.6)]  # (R1,Z1, R2,Z2) pair of locations
 
 constrain = freegs4e.control.constrain(xpoints=xpoints, isoflux=isoflux)
 
 #########################################
 # Nonlinear solve
 
-freegs4e.solve(eq,          # The equilibrium to adjust
-             profiles,    # The toroidal current profile function
-             constrain)   # Constraint function to set coil currents
+freegs4e.solve(
+    eq,  # The equilibrium to adjust
+    profiles,  # The toroidal current profile function
+    constrain,
+)  # Constraint function to set coil currents
 
 # eq now contains the solution
 
@@ -78,6 +84,7 @@
 # Safety factor
 
 import matplotlib.pyplot as plt
+
 plt.plot(*eq.q())
 plt.xlabel(r"Normalised $\psi$")
 plt.ylabel("Safety factor")

02-read-geqdsk.py

@@ -1,11 +1,10 @@
-from freegs4e import geqdsk
-from freegs4e import machine
+from freegs4e import geqdsk, machine
 from freegs4e.plotting import plotEquilibrium
 
-#tokamak = machine.MAST_sym()
+# tokamak = machine.MAST_sym()
 tokamak = machine.TestTokamak()
 
-#with open("g014220.00200") as f:
+# with open("g014220.00200") as f:
 with open("lsn.geqdsk") as f:
     eq = geqdsk.read(f, tokamak, show=True)
 

03-mast.py

@@ -8,44 +8,53 @@
 
 tokamak = freegs4e.machine.MAST()
 
-eq = freegs4e.Equilibrium(tokamak=tokamak,
-                        Rmin=0.1, Rmax=2.0,    # Radial domain
-                        Zmin=-2.0, Zmax=2.0,   # Height range
-                        nx=65, ny=65)          # Number of grid points
+eq = freegs4e.Equilibrium(
+    tokamak=tokamak,
+    Rmin=0.1,
+    Rmax=2.0,  # Radial domain
+    Zmin=-2.0,
+    Zmax=2.0,  # Height range
+    nx=65,
+    ny=65,
+)  # Number of grid points
 
 #########################################
 # Plasma profiles
 
-profiles = freegs4e.jtor.ConstrainPaxisIp(3e3, # Plasma pressure on axis [Pascals]
-                                        7e5, # Plasma current [Amps]
-                                        0.4) # vacuum f = R*Bt
+profiles = freegs4e.jtor.ConstrainPaxisIp(
+    3e3, 7e5, 0.4  # Plasma pressure on axis [Pascals]  # Plasma current [Amps]
+)  # vacuum f = R*Bt
 
 #########################################
 # Coil current constraints
 #
 # Specify locations of the X-points
 # to use to constrain coil currents
 
-xpoints = [(0.7, -1.1),   # (R,Z) locations of X-points
-           (0.7, 1.1)]
+xpoints = [(0.7, -1.1), (0.7, 1.1)]  # (R,Z) locations of X-points
 
-isoflux = [(0.7,-1.1, 1.45, 0.0)   # Outboard midplane, lower X-point
-           ,(0.7,1.1, 1.45, 0.0)   # Outboard midplane, upper X-point
-#           ,(0.7,-1.1, 1.5,-1.9)  # Lower X-point, lower outer leg
-#           ,(0.7,1.1,  1.5, 1.9)  # Upper X-point, upper outer leg
-           ]
+isoflux = [
+    (0.7, -1.1, 1.45, 0.0),  # Outboard midplane, lower X-point
+    (0.7, 1.1, 1.45, 0.0),  # Outboard midplane, upper X-point
+    #           ,(0.7,-1.1, 1.5,-1.9)  # Lower X-point, lower outer leg
+    #           ,(0.7,1.1,  1.5, 1.9)  # Upper X-point, upper outer leg
+]
 
-constrain = freegs4e.control.constrain(xpoints=xpoints, gamma=1e-12, isoflux=isoflux)
+constrain = freegs4e.control.constrain(
+    xpoints=xpoints, gamma=1e-12, isoflux=isoflux
+)
 
 constrain(eq)
 
 #########################################
 # Nonlinear solve
 
-freegs4e.solve(eq,          # The equilibrium to adjust
-             profiles,    # The plasma profiles
-             constrain,   # Plasma control constraints
-             show=True)   # Shows results at each nonlinear iteration
+freegs4e.solve(
+    eq,  # The equilibrium to adjust
+    profiles,  # The plasma profiles
+    constrain,  # Plasma control constraints
+    show=True,
+)  # Shows results at each nonlinear iteration
 
 # eq now contains the solution
 
@@ -68,4 +77,5 @@
 
 # Call matplotlib show so plot pauses
 import matplotlib.pyplot as plt
+
 plt.show()

04-read-mast-geqdsk.py

@@ -1,13 +1,11 @@
-from freegs4e import geqdsk
-from freegs4e import machine
+from freegs4e import geqdsk, machine
 from freegs4e.plotting import plotEquilibrium
 
 # Reading MAST equilibrium, up-down symmetric coils
 tokamak = machine.MAST()
 
-#with open("g014220.00200") as f:
+# with open("g014220.00200") as f:
 with open("mast.geqdsk") as f:
-  eq = geqdsk.read(f, tokamak, show=True)
+    eq = geqdsk.read(f, tokamak, show=True)
 
 plotEquilibrium(eq)
-

05-fixed-boundary.py

@@ -10,18 +10,24 @@
 # Boundary conditions
 import freegs4e.boundary as boundary
 
-profiles = freegs4e.jtor.ConstrainPaxisIp(1e3, # Plasma pressure on axis [Pascals]
-                                        1e5, # Plasma current [Amps]
-                                        1.0) # fvac = R*Bt
-
-eq = freegs4e.Equilibrium(Rmin=0.1, Rmax=2.0,
-                        Zmin=-1.0, Zmax=1.0,
-                        nx=65, ny=65,
-                        boundary=boundary.fixedBoundary)
+profiles = freegs4e.jtor.ConstrainPaxisIp(
+    1e3, 1e5, 1.0  # Plasma pressure on axis [Pascals]  # Plasma current [Amps]
+)  # fvac = R*Bt
+
+eq = freegs4e.Equilibrium(
+    Rmin=0.1,
+    Rmax=2.0,
+    Zmin=-1.0,
+    Zmax=1.0,
+    nx=65,
+    ny=65,
+    boundary=boundary.fixedBoundary,
+)
 
 # Nonlinear solver for Grad-Shafranov equation
-freegs4e.solve(eq,           # The equilibrium to adjust
-             profiles)     # The toroidal current profile function
+freegs4e.solve(
+    eq, profiles  # The equilibrium to adjust
+)  # The toroidal current profile function
 
 print("Done!")
 
@@ -31,6 +37,5 @@
 
 # Plot equilibrium
 from freegs4e.plotting import plotEquilibrium
-plotEquilibrium(eq)
-
 
+plotEquilibrium(eq)

06-xpoints.py

@@ -2,23 +2,22 @@
 #
 # Example demonstrating functions for creating and finding X-points
 
+import matplotlib.pyplot as plt
+
 import freegs4e
 
 # Plotting routines
-from freegs4e.plotting import plotEquilibrium, plotCoils, plotConstraints
-
-import matplotlib.pyplot as plt
+from freegs4e.plotting import plotCoils, plotConstraints, plotEquilibrium
 
 tokamak = freegs4e.machine.TestTokamak()
-eq = freegs4e.Equilibrium(tokamak=tokamak, nx=256,ny=256)
+eq = freegs4e.Equilibrium(tokamak=tokamak, nx=256, ny=256)
 
 ##########################################################
 # Calculate currents in coils to create X-points
 # in specified locations
-# 
+#
 
-xpoints = [(1.1, -0.8),   # (R,Z) locations of X-points
-           (1.1, 0.8)]
+xpoints = [(1.1, -0.8), (1.1, 0.8)]  # (R,Z) locations of X-points
 
 control = freegs4e.control.constrain(xpoints=xpoints)
 control(eq)  # Apply control to Equilibrium eq
@@ -34,27 +33,28 @@
 
 ##########################################################
 # Find critical points (O- and X-points)
-# 
-# 
+#
+#
 
 import freegs4e.critical as critical
+
 opt, xpt = critical.find_critical(eq.R, eq.Z, psi)
 
 print("=> Found O- and X-points")
 
 ax = plotEquilibrium(eq, show=False, oxpoints=False)
-for r,z,_ in xpt:
-    ax.plot(r,z,'ro')
-for r,z,_ in opt:
-    ax.plot(r,z,'go')
+for r, z, _ in xpt:
+    ax.plot(r, z, "ro")
+for r, z, _ in opt:
+    ax.plot(r, z, "go")
 psi_bndry = xpt[0][2]
-sep_contour=ax.contour(eq.R, eq.Z,psi, levels=[psi_bndry], colors='r')
+sep_contour = ax.contour(eq.R, eq.Z, psi, levels=[psi_bndry], colors="r")
 plt.show()
 
 ##########################################################
 # Create a mask array, 1 in the core and 0 outside
-# 
-# 
+#
+#
 
 mask = critical.core_mask(eq.R, eq.Z, psi, opt, xpt)
 

07-increase-resolution.py

@@ -1,4 +1,3 @@
-
 import freegs4e
 from freegs4e import geqdsk
 from freegs4e.equilibrium import refine
@@ -7,9 +6,9 @@
 # Reading MAST equilibrium, up-down symmetric coils
 tokamak = freegs4e.machine.MAST()
 
-#with open("g014220.00200") as f:
+# with open("g014220.00200") as f:
 with open("mast.geqdsk") as f:
-  eq = geqdsk.read(f, tokamak, show=True)
+    eq = geqdsk.read(f, tokamak, show=True)
 
 # Increase resolution by a factor of 2
 eq2 = refine(eq)
@@ -19,7 +18,6 @@
 
 # Save to G-EQDSK
 with open("mast-highres.geqdsk", "w") as f:
-  geqdsk.write(eq2, f)
+    geqdsk.write(eq2, f)
 
 plotEquilibrium(eq2)
-