Merge branch 'master' into ruff2

.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

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:

src/simsopt/field/tracing.py

@@ -798,7 +798,8 @@ class IterationStoppingCriterion(sopp.IterationStoppingCriterion):
     pass
 
 
-def plot_poincare_data(fieldlines_phi_hits, phis, filename, mark_lost=False, aspect='equal', dpi=300, xlims=None, ylims=None, surf=None):
+def plot_poincare_data(fieldlines_phi_hits, phis, filename, mark_lost=False, aspect='equal', dpi=300, xlims=None, 
+                       ylims=None, surf=None, s=2, marker='o'):
     """
     Create a poincare plot. Usage:
 
@@ -845,7 +846,7 @@ def plot_poincare_data(fieldlines_phi_hits, phis, filename, mark_lost=False, asp
             if data_this_phi.size == 0:
                 continue
             r = np.sqrt(data_this_phi[:, 2]**2+data_this_phi[:, 3]**2)
-            axs[row, col].scatter(r, data_this_phi[:, 4], marker='o', s=2, linewidths=0, c=color)
+            axs[row, col].scatter(r, data_this_phi[:, 4], marker=marker, s=s, linewidths=0, c=color)
 
         plt.rc('axes', axisbelow=True)
         axs[row, col].grid(True, linewidth=0.5)

src/simsopt/mhd/vmec.py

@@ -308,7 +308,7 @@ def __init__(self,
                 raise RuntimeError(
                     "Running VMEC from simsopt requires VMEC python extension. "
                     "Install the VMEC python extension from "
-                    "https://https://github.com/hiddenSymmetries/VMEC2000")
+                    "https://github.com/hiddenSymmetries/VMEC2000")
 
             comm = self.mpi.comm_groups
             self.fcomm = comm.py2f()

tests/field/test_biotsavart.py

@@ -33,33 +33,22 @@ def test_biotsavart_both_interfaces_give_same_result(self):
         assert np.allclose(B1, B2)
 
     def test_biotsavart_exponential_convergence(self):
-        coil = BiotSavart([Coil(get_curve(), Current(1e4))])
-        from time import time
-        # points = np.asarray(17 * [[-1.41513202e-03,  8.99999382e-01, -3.14473221e-04 ]])
+        BiotSavart([Coil(get_curve(), Current(1e4))])
         points = np.asarray(10 * [[-1.41513202e-03, 8.99999382e-01, -3.14473221e-04]])
-        tic = time()
         btrue = BiotSavart([Coil(get_curve(1000), Current(1e4))]).set_points(points).B()
-        # print(btrue)
         bcoarse = BiotSavart([Coil(get_curve(10), Current(1e4))]).set_points(points).B()
         bfine = BiotSavart([Coil(get_curve(20), Current(1e4))]).set_points(points).B()
         assert np.linalg.norm(btrue-bfine) < 1e-4 * np.linalg.norm(bcoarse-bfine)
-        # print(time()-tic)
 
-        tic = time()
         dbtrue = BiotSavart([Coil(get_curve(1000), Current(1e4))]).set_points(points).dB_by_dX()
-        # print(dbtrue)
         dbcoarse = BiotSavart([Coil(get_curve(10), Current(1e4))]).set_points(points).dB_by_dX()
         dbfine = BiotSavart([Coil(get_curve(20), Current(1e4))]).set_points(points).dB_by_dX()
-        assert np.linalg.norm(btrue-bfine) < 1e-4 * np.linalg.norm(bcoarse-bfine)
-        # print(time()-tic)
+        assert np.linalg.norm(dbtrue-dbfine) < 1e-4 * np.linalg.norm(dbcoarse-dbfine)
 
-        tic = time()
         dbtrue = BiotSavart([Coil(get_curve(1000), Current(1e4))]).set_points(points).d2B_by_dXdX()
-        # print("dbtrue", dbtrue)
         dbcoarse = BiotSavart([Coil(get_curve(10), Current(1e4))]).set_points(points).d2B_by_dXdX()
         dbfine = BiotSavart([Coil(get_curve(20), Current(1e4))]).set_points(points).d2B_by_dXdX()
-        assert np.linalg.norm(btrue-bfine) < 1e-4 * np.linalg.norm(bcoarse-bfine)
-        # print(time()-tic)
+        assert np.linalg.norm(dbtrue-dbfine) < 1e-4 * np.linalg.norm(dbcoarse-dbfine)
 
     def test_dB_by_dcoilcoeff_reverse_taylortest(self):
         np.random.seed(1)
@@ -180,7 +169,7 @@ def subtest_biotsavart_d2B_by_dXdX_taylortest(self, idx):
         bs = BiotSavart([coil])
         points = np.asarray(17 * [[-1.41513202e-03, 8.99999382e-01, -3.14473221e-04]])
         bs.set_points(points)
-        dB_by_dX, d2B_by_dXdX = bs.dB_by_dX(), bs.d2B_by_dXdX()
+        d2B_by_dXdX = bs.d2B_by_dXdX()
         for d1 in range(3):
             for d2 in range(3):
                 second_deriv = d2B_by_dXdX[idx, d1, d2]
@@ -255,7 +244,7 @@ def subtest_biotsavart_d2A_by_dXdX_taylortest(self, idx):
         bs = BiotSavart([coil])
         points = np.asarray(17 * [[-1.41513202e-03, 8.99999382e-01, -3.14473221e-04]])
         bs.set_points(points)
-        dA_by_dX, d2A_by_dXdX = bs.dA_by_dX(), bs.d2A_by_dXdX()
+        d2A_by_dXdX = bs.d2A_by_dXdX()
         for d1 in range(3):
             for d2 in range(3):
                 second_deriv = d2A_by_dXdX[idx, d1, d2]