hiddenSymmetries · mbkumar · Nov 1, 2023 · Oct 5, 2023 · Oct 27, 2023 · Oct 28, 2023
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -19,13 +19,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install python dependencies
-      run: |
-        pip install flake8
+    - name: Run ruff
+      uses: chartboost/ruff-action@v1
 
-    - name: Run linting tests
-      run: |
-        export EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
-        flake8  --ignore $EXCLUDE src/
-        flake8  --ignore $EXCLUDE tests/
-        flake8  --ignore $EXCLUDE examples/
diff --git a/examples/1_Simple/just_a_quadratic.py b/examples/1_Simple/just_a_quadratic.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 
-import logging
 from simsopt.objectives.functions import Identity
 from simsopt.objectives import LeastSquaresProblem
 from simsopt.solve import least_squares_serial_solve

diff --git a/examples/1_Simple/permanent_magnet_simple.py b/examples/1_Simple/permanent_magnet_simple.py
@@ -26,7 +26,6 @@
 from matplotlib import pyplot as plt
 from simsopt.field import DipoleField, ToroidalField
 from simsopt.geo import PermanentMagnetGrid, SurfaceRZFourier
-from simsopt.objectives import SquaredFlux
 from simsopt.solve import GPMO
 from simsopt.util.permanent_magnet_helper_functions import *
 

diff --git a/examples/1_Simple/stage_two_optimization_minimal.py b/examples/1_Simple/stage_two_optimization_minimal.py
@@ -135,7 +135,7 @@ def fun(dofs):
 """)
 res = minimize(fun, dofs, jac=True, method='L-BFGS-B',
                options={'maxiter': MAXITER, 'maxcor': 300, 'iprint': 5}, tol=1e-15)
-curves_to_vtk(curves, OUT_DIR + f"curves_opt", close=True)
+curves_to_vtk(curves, OUT_DIR + "curves_opt", close=True)
 pointData = {"B_N": np.sum(bs.B().reshape((nphi, ntheta, 3)) * s.unitnormal(), axis=2)[:, :, None]}
 s.to_vtk(OUT_DIR + "surf_opt", extra_data=pointData)
 

diff --git a/examples/1_Simple/tracing_fieldlines_QA.py b/examples/1_Simple/tracing_fieldlines_QA.py
@@ -17,7 +17,6 @@
 import time
 import os
 import logging
-import sys
 from pathlib import Path
 import numpy as np
 

diff --git a/examples/2_Intermediate/QSC.py b/examples/2_Intermediate/QSC.py
@@ -1,7 +1,5 @@
 #!/usr/bin/env python3
 
-import logging
-import numpy as np
 from qsc import Qsc
 
 from simsopt._core import Optimizable

diff --git a/examples/2_Intermediate/boozerQA.py b/examples/2_Intermediate/boozerQA.py
@@ -7,7 +7,7 @@
 from simsopt.configs import get_ncsx_data
 from simsopt.field import BiotSavart, coils_via_symmetries
 from simsopt.geo import SurfaceXYZTensorFourier, BoozerSurface, curves_to_vtk, boozer_surface_residual, \
-    ToroidalFlux, Volume, MajorRadius, CurveLength, CurveCurveDistance, NonQuasiSymmetricRatio, Iotas
+    Volume, MajorRadius, CurveLength, NonQuasiSymmetricRatio, Iotas
 from simsopt.objectives import QuadraticPenalty
 from simsopt.util import in_github_actions
 
@@ -83,7 +83,7 @@
 # sum the objectives together
 JF = J_nonQSRatio + J_iotas + J_major_radius + Jls
 
-curves_to_vtk(curves, OUT_DIR + f"curves_init")
+curves_to_vtk(curves, OUT_DIR + "curves_init")
 boozer_surface.surface.to_vtk(OUT_DIR + "surf_init")
 
 # let's fix the coil current
@@ -144,7 +144,7 @@ def fun(dofs):
 MAXITER = 50 if in_github_actions else 1e3
 
 res = minimize(fun, dofs, jac=True, method='BFGS', options={'maxiter': MAXITER}, tol=1e-15)
-curves_to_vtk(curves, OUT_DIR + f"curves_opt")
+curves_to_vtk(curves, OUT_DIR + "curves_opt")
 boozer_surface.surface.to_vtk(OUT_DIR + "surf_opt")
 
 print("End of 2_Intermediate/boozerQA.py")

diff --git a/examples/2_Intermediate/permanent_magnet_MUSE.py b/examples/2_Intermediate/permanent_magnet_MUSE.py
@@ -21,8 +21,6 @@
 https://github.com/akaptano/simsopt_permanent_magnet_advanced_scripts.git
 """
 
-import os
-import pickle
 import time
 from pathlib import Path
 
@@ -257,7 +255,6 @@
 # surface is at least 64 x 64 resolution.
 vmec_flag = False 
 if vmec_flag:
-    from mpi4py import MPI
     from simsopt.mhd.vmec import Vmec
     from simsopt.util.mpi import MpiPartition
     mpi = MpiPartition(ngroups=1)

diff --git a/examples/2_Intermediate/permanent_magnet_PM4Stell.py b/examples/2_Intermediate/permanent_magnet_PM4Stell.py
@@ -15,7 +15,6 @@
     Ken Hammond and the PM4Stell + MAGPIE teams. 
 '''
 
-import os
 from pathlib import Path
 import time
 

diff --git a/examples/2_Intermediate/permanent_magnet_QA.py b/examples/2_Intermediate/permanent_magnet_QA.py
@@ -31,12 +31,10 @@
 are available to OpenMP, e.g. through setting OMP_NUM_THREADS).
 """
 
-import os
 import time
 from pathlib import Path
 
 import numpy as np
-from matplotlib import pyplot as plt
 
 from simsopt.field import BiotSavart, DipoleField
 from simsopt.geo import PermanentMagnetGrid, SurfaceRZFourier
@@ -242,7 +240,6 @@
 # surface is at least 64 x 64 resolution.
 vmec_flag = False
 if vmec_flag:
-    from mpi4py import MPI
     from simsopt.mhd.vmec import Vmec
     from simsopt.util.mpi import MpiPartition
     mpi = MpiPartition(ngroups=1)

diff --git a/examples/2_Intermediate/stage_two_optimization.py b/examples/2_Intermediate/stage_two_optimization.py
@@ -166,7 +166,7 @@ def fun(dofs):
 ################################################################################
 """)
 res = minimize(fun, dofs, jac=True, method='L-BFGS-B', options={'maxiter': MAXITER, 'maxcor': 300}, tol=1e-15)
-curves_to_vtk(curves, OUT_DIR + f"curves_opt_short")
+curves_to_vtk(curves, OUT_DIR + "curves_opt_short")
 pointData = {"B_N": np.sum(bs.B().reshape((nphi, ntheta, 3)) * s.unitnormal(), axis=2)[:, :, None]}
 s.to_vtk(OUT_DIR + "surf_opt_short", extra_data=pointData)
 
@@ -177,7 +177,7 @@ def fun(dofs):
 dofs = res.x
 LENGTH_WEIGHT *= 0.1
 res = minimize(fun, dofs, jac=True, method='L-BFGS-B', options={'maxiter': MAXITER, 'maxcor': 300}, tol=1e-15)
-curves_to_vtk(curves, OUT_DIR + f"curves_opt_long")
+curves_to_vtk(curves, OUT_DIR + "curves_opt_long")
 pointData = {"B_N": np.sum(bs.B().reshape((nphi, ntheta, 3)) * s.unitnormal(), axis=2)[:, :, None]}
 s.to_vtk(OUT_DIR + "surf_opt_long", extra_data=pointData)
 

diff --git a/examples/2_Intermediate/stage_two_optimization_stochastic.py b/examples/2_Intermediate/stage_two_optimization_stochastic.py
@@ -163,10 +163,7 @@ def fun(dofs):
     JF.x = dofs
     J = JF.J()
     grad = JF.dJ()
-    cl_string = ", ".join([f"{J.J():.3f}" for J in Jls])
-    mean_AbsB = np.mean(bs.AbsB())
     jf = Jmpi.J()
-    BdotN = np.mean(np.abs(np.sum(bs.B().reshape((nphi, ntheta, 3)) * s.unitnormal(), axis=2)))
     outstr = f"J={J:.1e}, ⟨Jf⟩={jf:.1e}"
     cl_string = ", ".join([f"{J.J():.1f}" for J in Jls])
     kap_string = ", ".join(f"{np.max(c.kappa()):.1f}" for c in base_curves)

diff --git a/examples/3_Advanced/single_stage_optimization.py b/examples/3_Advanced/single_stage_optimization.py
@@ -8,7 +8,6 @@
 """
 import os
 import numpy as np
-from mpi4py import MPI
 from pathlib import Path
 from scipy.optimize import minimize
 from simsopt.util import MpiPartition, proc0_print, comm_world
@@ -57,7 +56,7 @@
 ARCLENGTH_WEIGHT = 1e-9  # Weight for the arclength variation penalty in the objective function
 ##########################################################################################
 ##########################################################################################
-directory = f'optimization_QH'
+directory = 'optimization_QH'
 vmec_verbose = False
 # Create output directories
 this_path = os.path.join(parent_path, directory)
@@ -109,7 +108,7 @@
 J_LENGTH_PENALTY = LENGTH_CON_WEIGHT * sum([QuadraticPenalty(Jls[i], LENGTH_THRESHOLD) for i in range(len(base_curves))])
 JF = Jf + J_CC + J_LENGTH + J_LENGTH_PENALTY + J_CURVATURE + J_MSC
 ##########################################################################################
-proc0_print(f'  Starting optimization')
+proc0_print('  Starting optimization')
 ##########################################################################################
 # Initial stage 2 optimization
 ##########################################################################################
@@ -229,7 +228,7 @@ def fun(dofs, prob_jacobian=None, info={'Nfeval': 0}):
     pointData = {"B_N": BdotN_surf[:, :, None]}
     surf.to_vtk(os.path.join(coils_results_path, "surf_opt"), extra_data=pointData)
 bs.save(os.path.join(coils_results_path, "biot_savart_opt.json"))
-vmec.write_input(os.path.join(this_path, f'input.final'))
+vmec.write_input(os.path.join(this_path, 'input.final'))
 proc0_print(f"Aspect ratio after optimization: {vmec.aspect()}")
 proc0_print(f"Mean iota after optimization: {vmec.mean_iota()}")
 proc0_print(f"Quasisymmetry objective after optimization: {qs.total()}")

diff --git a/examples/3_Advanced/single_stage_optimization_finite_beta.py b/examples/3_Advanced/single_stage_optimization_finite_beta.py
@@ -10,7 +10,6 @@
 """
 import os
 import numpy as np
-from mpi4py import MPI
 from math import isnan
 from pathlib import Path
 from scipy.optimize import minimize
@@ -62,7 +61,7 @@
 ARCLENGTH_WEIGHT = 1e-9  # Weight for the arclength variation penalty in the objective function
 ##########################################################################################
 ##########################################################################################
-directory = f'optimization_QH_finitebeta'
+directory = 'optimization_QH_finitebeta'
 vmec_verbose = False
 # Create output directories
 this_path = os.path.join(parent_path, directory)
@@ -122,7 +121,7 @@
 JF = Jf + J_CC + J_LENGTH + J_LENGTH_PENALTY + J_CURVATURE + J_MSC
 
 ##########################################################################################
-proc0_print(f'  Starting optimization')
+proc0_print('  Starting optimization')
 ##########################################################################################
 # Initial stage 2 optimization
 ##########################################################################################
@@ -169,7 +168,7 @@ def fun_J(prob, coils_prob):
         try:
             vc = VirtualCasing.from_vmec(vmec, src_nphi=vc_src_nphi, trgt_nphi=nphi_VMEC, trgt_ntheta=ntheta_VMEC, filename=None)
             Jf.target = vc.B_external_normal
-        except ObjectiveFailure as e:
+        except ObjectiveFailure:
             pass
 
     bs.set_points(surf.gamma().reshape((-1, 3)))
@@ -265,7 +264,7 @@ def fun(dofss, prob_jacobian, info={'Nfeval': 0}):
     pointData = {"B_N": BdotN_surf[:, :, None]}
     surf.to_vtk(os.path.join(coils_results_path, "surf_opt"), extra_data=pointData)
 bs.save(os.path.join(coils_results_path, "biot_savart_opt.json"))
-vmec.write_input(os.path.join(this_path, f'input.final'))
+vmec.write_input(os.path.join(this_path, 'input.final'))
 proc0_print(f"Aspect ratio after optimization: {vmec.aspect()}")
 proc0_print(f"Mean iota after optimization: {vmec.mean_iota()}")
 proc0_print(f"Quasisymmetry objective after optimization: {qs.total()}")

diff --git a/examples/stellarator_benchmarks/1DOF_circularCrossSection_varyAxis_targetIota.py b/examples/stellarator_benchmarks/1DOF_circularCrossSection_varyAxis_targetIota.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 
 import os
-from mpi4py import MPI
 import numpy as np
 
 from simsopt.mhd import Vmec

diff --git a/examples/stellarator_benchmarks/1DOF_circularCrossSection_varyR0_targetVolume.py b/examples/stellarator_benchmarks/1DOF_circularCrossSection_varyR0_targetVolume.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 
 import numpy as np
-from mpi4py import MPI
 
 from simsopt.objectives import LeastSquaresProblem
 from simsopt.mhd import Vmec

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,3 +3,18 @@ requires = ["setuptools>=45", "wheel", "oldest-supported-numpy", "cmake", "ninja
 build-backend = "setuptools.build_meta"
 
 [tools.setuptools_scm]
+
+[tool.ruff]
+src = ["src/simsopt"] 
+ignore = ["E226","E265","E266","E4","E501","E701","E702","E712","E722","E731","E741","F403","F405","F406","W5"]
+extend-exclude = ["thirdparty"]
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402","F401"]
+"src/simsopt/field/magneticfieldclasses.py" = ["E743"]
+"src/simsopt/mhd/bootstrap.py" = ["F841"]
+"src/simsopt/mhd/vmec_diagnostics.py" = ["F841"]
+"tests/verify_MPI_not_initialized.py" = ["F401"]
+"tests/geo/test_plot.py" = ["F401"]
+"tests/geo/test_curve.py" = ["F401"]
+"tests/geo/test_surface.py" = ["F401"]
+"tests/mhd/test_virtual_casing.py" = ["F841"]
diff --git a/run_autopep b/run_autopep
@@ -2,7 +2,8 @@
 # https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
 set -ex
 
-EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
+# EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
+EXCLUDE="E226,E265,E266,E4,E501,E722,F403,F405,F406,W5"
 flake8  --ignore $EXCLUDE src/ || (exit 0)
 flake8  --ignore $EXCLUDE tests/ || (exit 0)
 flake8  --ignore $EXCLUDE examples/ || (exit 0)

diff --git a/run_ruff b/run_ruff
@@ -0,0 +1,7 @@
+#!/bin/bash
+# https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
+set -ex
+
+ruff check . || (exit 0)
+ruff check --fix .
+ruff check .
diff --git a/src/simsopt/_core/optimizable.py b/src/simsopt/_core/optimizable.py
@@ -1289,7 +1289,6 @@ def upper_bounds(self) -> RealArray:
         Upper bounds of the free DOFs associated with the current
         Optimizable object and those of its ancestors
         """
-        opts = self.ancestors + [self]
         return np.concatenate([opt._dofs.free_upper_bounds for opt in self.unique_dof_lineage])
 
     @upper_bounds.setter

diff --git a/src/simsopt/field/coil.py b/src/simsopt/field/coil.py
@@ -4,7 +4,7 @@
 from simsopt._core.optimizable import Optimizable
 from simsopt._core.derivative import Derivative
 from simsopt.geo.curvexyzfourier import CurveXYZFourier
-from simsopt.geo.curve import RotatedCurve, Curve
+from simsopt.geo.curve import RotatedCurve
 import simsoptpp as sopp
 
 

diff --git a/src/simsopt/field/magneticfield.py b/src/simsopt/field/magneticfield.py
@@ -118,9 +118,6 @@ def to_mgrid(self, filename, nr=10, nphi=4, nz=12, rmin=1.0, rmax=2.0, zmin=-0.5
         zs = np.linspace(zmin, zmax, nz, endpoint=True)
 
         Phi, Z, R = np.meshgrid(phis, zs, rs, indexing='ij')
-        X = R * np.cos(Phi)
-        Y = R * np.sin(Phi)
-        Z = Z
 
         RPhiZ = np.zeros((R.size, 3))
         RPhiZ[:, 0] = R.flatten()

diff --git a/src/simsopt/field/magneticfieldclasses.py b/src/simsopt/field/magneticfieldclasses.py
@@ -46,7 +46,6 @@ def _B_impl(self, B):
 
     def _dB_by_dX_impl(self, dB):
         points = self.get_points_cart_ref()
-        phi = np.arctan2(points[:, 1], points[:, 0])
         R = np.sqrt(np.square(points[:, 0]) + np.square(points[:, 1]))
 
         x = points[:, 0]
@@ -66,8 +65,6 @@ def _dB_by_dX_impl(self, dB):
 
     def _d2B_by_dXdX_impl(self, ddB):
         points = self.get_points_cart_ref()
-        x = points[:, 0]
-        y = points[:, 1]
         ddB[:] = 2*self.B0*self.R0*np.multiply(
             1/(points[:, 0]**2+points[:, 1]**2)**3, np.array([
                 [[3*points[:, 0]**2+points[:, 1]**3, points[:, 0]**3-3*points[:, 0]*points[:, 1]**2, np.zeros((len(points)))], [
@@ -397,7 +394,6 @@ def _B_impl(self, B):
         k = np.sqrt(1-np.divide(np.square(alpha), np.square(beta)))
         ellipek2 = ellipe(k**2)
         ellipkk2 = ellipk(k**2)
-        gamma = np.square(points[:, 0]) - np.square(points[:, 1])
         B[:] = np.dot(self.rotMatrix, np.array(
             [self.Inorm*points[:, 0]*points[:, 2]/(2*alpha**2*beta*rho**2+1e-31)*((self.r0**2+r**2)*ellipek2-alpha**2*ellipkk2),
              self.Inorm*points[:, 1]*points[:, 2]/(2*alpha**2*beta*rho**2+1e-31)*((self.r0**2+r**2)*ellipek2-alpha**2*ellipkk2),
@@ -666,7 +662,6 @@ def _toVTK(self, vtkname):
         mx = np.ascontiguousarray(self.m_vec[:, 0])
         my = np.ascontiguousarray(self.m_vec[:, 1])
         mz = np.ascontiguousarray(self.m_vec[:, 2])
-        mmag = np.sqrt(mx ** 2 + my ** 2 + mz ** 2)
         mx_normalized = np.ascontiguousarray(mx / self.m_maxima)
         my_normalized = np.ascontiguousarray(my / self.m_maxima)
         mz_normalized = np.ascontiguousarray(mz / self.m_maxima)
@@ -680,11 +675,12 @@ def _toVTK(self, vtkname):
         mtheta_normalized = np.ascontiguousarray(mtheta / self.m_maxima)
 
         # Save all the data to a vtk file which can be visualized nicely with ParaView
-        data = {"m": (mx, my, mz), "m_normalized": (mx_normalized, my_normalized, mz_normalized), "m_rphiz": (mr, mphi, mz), "m_rphiz_normalized": (mr_normalized, mphi_normalized, mz_normalized), "m_rphitheta": (mrminor, mphi, mtheta), "m_rphitheta_normalized": (mrminor_normalized, mphi_normalized, mtheta_normalized)}
+        data = {"m": (mx, my, mz), "m_normalized": (mx_normalized, my_normalized, mz_normalized),
+                "m_rphiz": (mr, mphi, mz), "m_rphiz_normalized": (mr_normalized, mphi_normalized, mz_normalized),
+                "m_rphitheta": (mrminor, mphi, mtheta),
+                "m_rphitheta_normalized": (mrminor_normalized, mphi_normalized, mtheta_normalized)}
         from pyevtk.hl import pointsToVTK
-        pointsToVTK(
-            str(vtkname), ox, oy, oz, data=data
-        )
+        pointsToVTK(str(vtkname), ox, oy, oz, data=data)
 
 
 class Dommaschk(MagneticField):

diff --git a/src/simsopt/field/mgrid.py b/src/simsopt/field/mgrid.py
@@ -1,4 +1,3 @@
-import sys
 import numpy as np
 from scipy.io import netcdf_file
 

diff --git a/src/simsopt/field/tracing.py b/src/simsopt/field/tracing.py
@@ -475,7 +475,6 @@ def compute_resonances(res_tys, res_phi_hits, ma=None, delta=1e-2):
             theta0 = res_tys[ip][0, 2]
             zeta0 = res_tys[ip][0, 3]
             theta0_mod = theta0 % (2*np.pi)
-            zeta0_mod = zeta0 % (2*np.pi)
             x0 = s0 * np.cos(theta0)
             y0 = s0 * np.sin(theta0)
         else:
@@ -550,10 +549,10 @@ def compute_resonances(res_tys, res_phi_hits, ma=None, delta=1e-2):
                             logger.debug(f'(R,Z)r = {np.sqrt(res_tys[ip][indexr,1]**2 + res_tys[ip][indexr,2]**2),res_tys[ip][indexr,3]}')
 
                         mpol = np.amax([mpoll, mpolm, mpolr])
-                        index_mpol = np.argmax([mpoll, mpolm, mpolr])
+                        # index_mpol = np.argmax([mpoll, mpolm, mpolr])
                         ntor = np.amax([ntorl, ntorm, ntorr])
-                        index_ntor = np.argmax([ntorl, ntorm, ntorr])
-                        index = np.amax([index_mpol, index_ntor])
+                        # index_ntor = np.argmax([ntorl, ntorm, ntorr])
+                        # index = np.amax([index_mpol, index_ntor])
                         resonances.append(np.asarray([R0, Z0, phi0, vpar0, t, mpol, ntor]))
     return resonances