Merge branch 'master' into yge/writing-inputfiles

Author: YigitElma

.github/workflows/benchmark.yml

@@ -21,6 +21,10 @@ jobs:
   benchmark:
     if: ${{ contains(github.event.pull_request.labels.*.name, 'run_benchmarks') || github.event_name == 'workflow_dispatch' }}
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write  # allows posting the benchmark comment on the PR
+      contents: read        # allows checkout; prevents the token from pushing code or modifying workflows if exfiltrated by fork code
+      actions: read         # allows `gh cache list`; all other scopes default to none
     env:
       GH_TOKEN: ${{ github.token }}
     strategy:
@@ -38,6 +42,7 @@ jobs:
       - uses: actions/checkout@v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
+          allow-unsafe-pr-checkout: true
 
       - name: Filter changes
         id: changes
@@ -50,6 +55,7 @@ jobs:
               - 'tests/benchmarks/compare_bench_results.py'
               - 'setup.cfg'
               - '.github/workflows/benchmark.yml'
+              - 'requirements.txt'
 
       - name: Check for relevant changes
         id: check_changes
@@ -119,6 +125,38 @@ jobs:
         if: env.has_changes == 'true'
         run: git checkout ${{ github.event.pull_request.head.sha }} -- tests/benchmarks
 
+      - name: Remove PR virtual environment before master setup
+        if: env.has_changes == 'true'
+        run: rm -rf .venv-${{ env.version }}
+
+      - name: Restore Python environment cache
+        if: env.has_changes == 'true'
+        id: restore-env2
+        uses: actions/cache/restore@v5
+        with:
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env2.outputs.cache-hit != 'true' && env.has_changes == 'true'
+        run: |
+          gh cache list
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
+          python -m pip install --upgrade pip
+          pip install -r devtools/dev-requirements.txt
+          pip install matplotlib==3.10.8
+
+      - name: Action Details
+        if: env.has_changes == 'true'
+        run: |
+          source .venv-${{ env.version }}/bin/activate
+          which python
+          python --version
+          pwd
+          lscpu
+          pip list
+
       - name: Benchmark with pytest-benchmark (MASTER)
         if: env.has_changes == 'true'
         run: |

.github/workflows/memory_benchmark.yml

@@ -10,6 +10,10 @@ on:
 jobs:
   memory-benchmark:
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write  # allows posting the benchmark comment on the PR
+      contents: read        # allows checkout; prevents the token from pushing code or modifying workflows if exfiltrated by fork code
+      actions: read         # allows `gh cache list`; all other scopes default to none
     env:
       GH_TOKEN: ${{ github.token }}
     strategy:
@@ -20,6 +24,7 @@ jobs:
       - uses: actions/checkout@v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
+          allow-unsafe-pr-checkout: true
 
       - name: Filter changes
         id: changes
@@ -32,7 +37,7 @@ jobs:
               - 'requirements.txt'
               - 'devtools/dev-requirements.txt'
               - 'setup.cfg'
-              - '.github/workflows/memory_benchmarks.yml'
+              - '.github/workflows/memory_benchmark.yml'
 
       - name: Check for relevant changes
         id: check_changes
@@ -103,6 +108,38 @@ jobs:
         if: env.has_changes == 'true'
         run: git checkout ${{ github.event.pull_request.head.sha }} -- tests/benchmarks
 
+      - name: Remove PR virtual environment before master setup
+        if: env.has_changes == 'true'
+        run: rm -rf .venv-${{ env.version }}
+
+      - name: Restore Python environment cache
+        if: env.has_changes == 'true'
+        id: restore-env2
+        uses: actions/cache/restore@v5
+        with:
+          path: .venv-${{ env.version }}
+          key: ${{ runner.os }}-venv-${{ env.version }}-${{ hashFiles('devtools/dev-requirements.txt', 'requirements.txt') }}
+
+      - name: Set up virtual environment if not restored from cache
+        if: steps.restore-env2.outputs.cache-hit != 'true' && env.has_changes == 'true'
+        run: |
+          gh cache list
+          python -m venv .venv-${{ env.version }}
+          source .venv-${{ env.version }}/bin/activate
+          python -m pip install --upgrade pip
+          pip install -r devtools/dev-requirements.txt
+          pip install matplotlib==3.10.8
+
+      - name: Action Details
+        if: env.has_changes == 'true'
+        run: |
+          source .venv-${{ env.version }}/bin/activate
+          which python
+          python --version
+          pwd
+          lscpu
+          pip list
+
       - name: Benchmark with pytest-benchmark (MASTER)
         if: env.has_changes == 'true'
         run: |

CHANGELOG.md

@@ -8,6 +8,8 @@ Performance Improvements
 Bug Fixes
 
 - Fixes bug that was always setting NFP=1 in ``to_FourierRZ`` methods.
+- Fixes ``VMECIO.save`` metadata for current-density variables and corrects the
+  asymmetric ``currvmns`` magnetic-axis extrapolation.
 
 
 v0.17.2

desc/vmec.py

@@ -53,10 +53,11 @@ def load(
         boundary is loaded and the DESC Equilibrium R,Z are constrained to
         match the given VMEC boundary.
 
-        NOTE: This is only a fit, so the DESC Equilibrium returned is not
-        expected to be in force balance. It is recommended to solve the
-        Equilibrium once loaded before using the Equilibrium for any
-        analysis.
+        NOTE: This is only a fit of the VMEC R, Z and lambda, so the DESC
+        Equilibrium returned is not expected to be in force balance. It is
+        recommended to solve the Equilibrium once loaded before using the
+        Equilibrium for any analysis or computing any derived quantities in
+        DESC (e.g. anything that is not just R, Z or lambda).
 
         Parameters
         ----------
@@ -734,7 +735,7 @@ def save(  # noqa: C901
         jcuru[0] = 0
 
         jcurv = file.createVariable("jcurv", np.float64, ("radius",))
-        jcuru.long_name = "flux surface average of sqrt(g)*J^zeta, on full mesh"
+        jcurv.long_name = "flux surface average of sqrt(g)*J^zeta, on full mesh"
         jcurv.units = "A/m^3"
         jcurv[:] = surface_averages(
             grid_full,
@@ -1331,7 +1332,7 @@ def fullfit(x):
         # TODO (#1379): evaluate current at rho=0 nodes instead of extrapolation
         if not eq.sym:
             currvmns[:, :] = -s
-            currumns[0, :] = -(
+            currvmns[0, :] = -(
                 s[1, :] - (s[2, :] - s[1, :]) / (s_full[2] - s_full[1]) * s_full[1]
             )
         timer.stop("J^zeta*sqrt(g)")

tests/test_vmec.py

@@ -1027,6 +1027,25 @@ def test_vmec_save_asym(VMEC_save_asym):
     np.testing.assert_allclose(
         vmec.variables["jcurv"][20:100], desc.variables["jcurv"][20:100], rtol=2
     )
+    assert desc.variables["jcuru"].long_name == (
+        "flux surface average of sqrt(g)*J^theta, on full mesh"
+    )
+    assert desc.variables["jcurv"].long_name == (
+        "flux surface average of sqrt(g)*J^zeta, on full mesh"
+    )
+    s_full = np.linspace(0, 1, desc.dimensions["radius"].size)
+    expected_currumns_axis = desc.variables["currumns"][1, :] - (
+        (desc.variables["currumns"][2, :] - desc.variables["currumns"][1, :])
+        / (s_full[2] - s_full[1])
+        * s_full[1]
+    )
+    expected_currvmns_axis = desc.variables["currvmns"][1, :] - (
+        (desc.variables["currvmns"][2, :] - desc.variables["currvmns"][1, :])
+        / (s_full[2] - s_full[1])
+        * s_full[1]
+    )
+    np.testing.assert_allclose(desc.variables["currumns"][0, :], expected_currumns_axis)
+    np.testing.assert_allclose(desc.variables["currvmns"][0, :], expected_currvmns_axis)
     np.testing.assert_allclose(
         vmec.variables["DShear"][20:100], desc.variables["DShear"][20:100], rtol=6e-2
     )