Merge branch 'planar' of https://github.com/AlexWiedman/simsopt into …

…planar

.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/

.readthedocs.yaml

@@ -1,6 +1,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/source/conf.py
@@ -11,9 +16,7 @@ sphinx:
 # formats:
 #   - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.8
    install:
    - requirements: docs/requirements.txt
    - requirements: requirements.txt

CMakeLists.txt

@@ -58,6 +58,8 @@ else()
     	set(CMAKE_CXX_FLAGS "-O3 -ffp-contract=fast")
     endif()
 endif()
+# Ensure all code used from Eigen does not have LGPL license:
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DEIGEN_MPL2_ONLY")
 message(STATUS "CMAKE_CXX_FLAGS are ${CMAKE_CXX_FLAGS}")
 
 if(DEFINED ENV{CONDA_PREFIX})

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Simsopt contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

conda.recipe/meta.yaml

@@ -51,8 +51,8 @@ requirements:
 about:
   home: {{ data.get('url') }}
   summary: simplified framework for stellarator optimization
-  license: LGPL
-  license_file: ["COPYING", "COPYING.LESSER"]
+  license: MIT
+  license_file: "LICENSE"
   description:
   doc_url: https://simsopt.readthedocs.io/
   dev_url: {{ data.get('url') }}

docs/source/installation.rst

@@ -25,16 +25,19 @@ Optional Packages
 -----------------
 
 Several other optional packages are needed for certain aspects of
-simsopt, such as visualization/graphics and building the documentation.  These
-requirements can be found in the ``[options.extras_require]`` section
-of
-`setup.cfg <https://github.com/hiddenSymmetries/simsopt/blob/master/setup.cfg>`_.
+simsopt, such as running SPEC or VMEC, visualization/graphics, and building the
+documentation.  These requirements can be found in the
+``[options.extras_require]`` section of `setup.cfg
+<https://github.com/hiddenSymmetries/simsopt/blob/master/setup.cfg>`_.
 Also,
 
 - For MPI support:
     * mpi4py
 - For VMEC support:
-    * https://github.com/hiddenSymmetries/vmec2000
+    * https://github.com/hiddenSymmetries/vmec2000 Note that the
+      python extension in this repository is required to run VMEC or
+      optimize VMEC configurations, but is not needed for computing
+      properties of existing ``wout`` output files.
 - For computing Boozer coordinates:
     * `booz_xform <https://hiddensymmetries.github.io/booz_xform/>`_
 - For SPEC support:

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

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 *
 

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)
 

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
 

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

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")

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)

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
 

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)