Merge branch 'master' into dp/softmax

.github/workflows/benchmark.yml

@@ -1,10 +1,9 @@
 name: Benchmarks
 
 on:
-  pull_request:
+  pull_request_target:
     branches:
       - master
-  pull_request_target:
     types: [opened, synchronize]
   workflow_dispatch:
     inputs:

.github/workflows/changelog_update.yml

@@ -0,0 +1,35 @@
+name: Check changelog updated
+
+on:
+  pull_request:
+    branches:
+      - master
+    types: [opened, synchronize, labeled, unlabeled]
+
+jobs:
+  check_changelog_updated:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Filter changes
+        id: changes
+        uses: dorny/paths-filter@v3
+        with:
+          filters: |
+            has_changes:
+              - 'desc/**'
+              - 'requirements.txt'
+              - 'requirements_conda.yml'
+              - '.github/workflows/changelog_update.yml'
+
+      - name: Check for relevant changes
+        id: check_changes
+        run: echo "has_changes=${{ steps.changes.outputs.has_changes }}" >> $GITHUB_ENV
+
+      - uses: actions/checkout@v4
+
+      - if: ${{ !contains(github.event.pull_request.labels.*.name, 'skip_changelog') && env.has_changes == 'true'}}
+        uses: danieljimeneznz/ensure-files-changed@v4.1.0
+        with:
+          require-changes-to: |
+            CHANGELOG.md
+          token: ${{ secrets.GITHUB_TOKEN }}

desc/plotting.py

@@ -1354,6 +1354,8 @@ def plot_section(
         * ``phi``: float, int or array-like. Toroidal angles to plot. If an integer,
           plot that number equally spaced in [0,2pi/NFP). Default 1 for axisymmetry and
           6 for non-axisymmetry
+        * ``fill`` : bool,  Whether the contours are filled, i.e. whether to use
+          `contourf` or `contour`. Default to ``fill=True``
 
     Returns
     -------
@@ -1442,7 +1444,7 @@ def plot_section(
     R = coords["R"].reshape((nt, nr, nz), order="F")
     Z = coords["Z"].reshape((nt, nr, nz), order="F")
     data = data.reshape((nt, nr, nz), order="F")
-
+    op = "contour" + ("f" if kwargs.pop("fill", True) else "")
     contourf_kwargs = {}
     if log:
         data = np.abs(data)  # ensure data is positive for log plot
@@ -1474,7 +1476,9 @@ def plot_section(
     for i in range(nphi):
         divider = make_axes_locatable(ax[i])
 
-        cntr = ax[i].contourf(R[:, :, i], Z[:, :, i], data[:, :, i], **contourf_kwargs)
+        cntr = getattr(ax[i], op)(
+            R[:, :, i], Z[:, :, i], data[:, :, i], **contourf_kwargs
+        )
         cax = divider.append_axes("right", **cax_kwargs)
         cbar = fig.colorbar(cntr, cax=cax)
         cbar.update_ticks()

tests/conftest.py

@@ -284,13 +284,13 @@ def DummyMixedCoilSet(tmpdir_factory):
         vf_coil, displacement=[0, 0, 2], n=3, endpoint=True
     )
     xyz_coil = FourierXYZCoil(current=2)
-    phi = 2 * np.pi * np.linspace(0, 1, 20, endpoint=True) ** 2
+    phi = 2 * np.pi * np.linspace(0, 1, 20, endpoint=True)
     spline_coil = SplineXYZCoil(
         current=1,
         X=np.cos(phi),
         Y=np.sin(phi),
         Z=np.zeros_like(phi),
-        knots=np.linspace(0, 2 * np.pi, len(phi)),
+        knots=phi,
     )
     full_coilset = MixedCoilSet(
         (tf_coilset, vf_coilset, xyz_coil, spline_coil), check_intersection=False

tests/test_examples.py

@@ -1324,7 +1324,20 @@ def test_second_stage_optimization_CoilSet():
 
 @pytest.mark.slow
 @pytest.mark.unit
-def test_optimize_with_all_coil_types(DummyCoilSet, DummyMixedCoilSet):
+@pytest.mark.parametrize(
+    "coil_type",
+    [
+        "FourierPlanarCoil",
+        "FourierRZCoil",
+        "FourierXYZCoil",
+        "SplineXYZCoil",
+        "CoilSet sym",
+        "CoilSet asym",
+        "MixedCoilSet",
+        "nested CoilSet",
+    ],
+)
+def test_optimize_with_all_coil_types(DummyCoilSet, DummyMixedCoilSet, coil_type):
     """Test optimizing for every type of coil and dummy coil sets."""
     sym_coils = load(load_from=str(DummyCoilSet["output_path_sym"]), file_format="hdf5")
     asym_coils = load(
@@ -1340,66 +1353,63 @@ def test_optimize_with_all_coil_types(DummyCoilSet, DummyMixedCoilSet):
     quad_eval_grid = LinearGrid(M=2, sym=True)
     quad_field_grid = LinearGrid(N=2)
 
-    def test(c, method):
-        target = 11
-        rtol = 1e-3
-        # first just check that quad flux works for a couple iterations
-        # as this is an expensive objective to compute
-        obj = ObjectiveFunction(
-            QuadraticFlux(
-                eq=eq,
-                field=c,
-                vacuum=True,
-                weight=1e-4,
-                eval_grid=quad_eval_grid,
-                field_grid=quad_field_grid,
-            )
-        )
-        optimizer = Optimizer(method)
-        (c,), _ = optimizer.optimize(c, obj, maxiter=2, ftol=0, xtol=1e-15)
-
-        # now check with optimizing geometry and actually check result
-        objs = [
-            CoilLength(c, target=target),
-        ]
-        extra_msg = ""
-        if isinstance(c, MixedCoilSet):
-            # just to check they work without error
-            objs.extend(
-                [
-                    CoilCurvature(c, target=0.5, weight=1e-2),
-                    CoilTorsion(c, target=0, weight=1e-2),
-                ]
-            )
-            rtol = 3e-2
-            extra_msg = " with curvature and torsion obj"
-
-        obj = ObjectiveFunction(objs)
-
-        (c,), _ = optimizer.optimize(c, obj, maxiter=25, ftol=5e-3, xtol=1e-15)
-        flattened_coils = tree_leaves(
-            c, is_leaf=lambda x: isinstance(x, _Coil) and not isinstance(x, CoilSet)
-        )
-        lengths = [coil.compute("length")["length"] for coil in flattened_coils]
-        np.testing.assert_allclose(
-            lengths, target, rtol=rtol, err_msg=f"lengths {c}" + extra_msg
-        )
-
     spline_coil = mixed_coils.coils[-1].copy()
 
-    # single coil
-    test(FourierPlanarCoil(), "fmintr")
-    test(FourierRZCoil(), "fmintr")
-    test(FourierXYZCoil(), "fmintr")
-    test(spline_coil, "fmintr")
+    types = {
+        "FourierPlanarCoil": (FourierPlanarCoil(), "fmintr"),
+        "FourierRZCoil": (FourierRZCoil(), "fmintr"),
+        "FourierXYZCoil": (FourierXYZCoil(), "fmintr"),
+        "SplineXYZCoil": (spline_coil, "fmintr"),
+        "CoilSet sym": (sym_coils, "lsq-exact"),
+        "CoilSet asym": (asym_coils, "lsq-exact"),
+        "MixedCoilSet": (mixed_coils, "lsq-exact"),
+        "nested CoilSet": (nested_coils, "lsq-exact"),
+    }
+    c, method = types[coil_type]
+
+    target = 11
+    rtol = 1e-3
+    # first just check that quad flux works for a couple iterations
+    # as this is an expensive objective to compute
+    obj = ObjectiveFunction(
+        QuadraticFlux(
+            eq=eq,
+            field=c,
+            vacuum=True,
+            weight=1e-4,
+            eval_grid=quad_eval_grid,
+            field_grid=quad_field_grid,
+        )
+    )
+    optimizer = Optimizer(method)
+    (cc,), _ = optimizer.optimize(c, obj, maxiter=2, ftol=0, xtol=1e-8, copy=True)
+
+    # now check with optimizing geometry and actually check result
+    objs = [
+        CoilLength(c, target=target),
+    ]
+    extra_msg = ""
+    if isinstance(c, MixedCoilSet):
+        # just to check they work without error
+        objs.extend(
+            [
+                CoilCurvature(c, target=0.5, weight=1e-2),
+                CoilTorsion(c, target=0, weight=1e-2),
+            ]
+        )
+        rtol = 3e-2
+        extra_msg = " with curvature and torsion obj"
 
-    # CoilSet
-    test(sym_coils, "lsq-exact")
-    test(asym_coils, "lsq-exact")
+    obj = ObjectiveFunction(objs)
 
-    # MixedCoilSet
-    test(mixed_coils, "lsq-exact")
-    test(nested_coils, "lsq-exact")
+    (c,), _ = optimizer.optimize(c, obj, maxiter=25, ftol=5e-3, xtol=1e-8)
+    flattened_coils = tree_leaves(
+        c, is_leaf=lambda x: isinstance(x, _Coil) and not isinstance(x, CoilSet)
+    )
+    lengths = [coil.compute("length")["length"] for coil in flattened_coils]
+    np.testing.assert_allclose(
+        lengths, target, rtol=rtol, err_msg=f"lengths {c}" + extra_msg
+    )
 
 
 @pytest.mark.unit

tests/test_plotting.py

@@ -429,6 +429,14 @@ def test_section_J(self):
 
         return fig
 
+    @pytest.mark.unit
+    @pytest.mark.mpl_image_compare(remove_text=True, tolerance=tol_2d)
+    def test_section_chi_contour(self):
+        """Test plotting poincare section of poloidal flux, with fill=False."""
+        eq = get("DSHAPE_CURRENT")
+        fig, ax = plot_section(eq, "chi", fill=False, levels=20)
+        return fig
+
     @pytest.mark.unit
     @pytest.mark.mpl_image_compare(remove_text=True, tolerance=tol_2d)
     def test_section_F(self):