Merge branch 'master' into yge/tr_direct

.github/dependabot.yml

@@ -0,0 +1,44 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    groups:
+      # group similar dependencies together into fewer PRs
+      docs:
+        patterns:
+          - "sphinx"
+      linting:
+        patterns:
+          - "flake8"
+          - "black"
+          - "pre-commit"
+      testing:
+        patterns:
+          - "pytest"
+          - "qic"
+          - "qsc"
+          - "shapely"
+      minor_packages:
+        patterns:
+          - "colorama"
+          - "nvgpu"
+          - "psutil"
+          - "pylatexenc"
+          - "termcolor"
+      jax:
+        patterns:
+          - "jax"
+          - "diffrax"
+          - "interpax"
+          - "orthax"
+          - "quadax"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/benchmark.yml

@@ -82,6 +82,7 @@ jobs:
           source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
+          pip list
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='Latest_Commit' \
@@ -108,6 +109,7 @@ jobs:
           source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
+          pip list
           cd tests/benchmarks
           python -m pytest benchmark_cpu_small.py -vv \
             --benchmark-save='master' \
@@ -149,12 +151,12 @@ jobs:
 
       - name: Comment PR with the results
         if: env.has_changes == 'true'
-        uses: thollander/actions-comment-pull-request@v2
+        uses: thollander/actions-comment-pull-request@v3
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
         with:
-          filePath: tests/benchmarks/commit_msg.txt
-          comment_tag: benchmark
+          file-path: tests/benchmarks/commit_msg.txt
+          comment-tag: benchmark
 
       - name: Upload benchmark data
         if: always() && env.has_changes == 'true'

.github/workflows/jax_tests.yml

@@ -44,6 +44,7 @@ jobs:
         run: |
           pwd
           lscpu
+          pip list
           python -m pytest -m unit \
             --durations=0 \
             --mpl \

.github/workflows/mpl_tests.yml

@@ -72,4 +72,5 @@ jobs:
         run: |
           pwd
           lscpu
+          pip list
           python -m pytest tests/test_plotting.py --durations=0 --mpl --maxfail=1

.github/workflows/notebook_tests.yml

@@ -75,6 +75,7 @@ jobs:
           source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
+          pip list
           export PYTHONPATH=$(pwd)
           pytest -v --nbmake "./docs/notebooks" \
             --nbmake-timeout=2000 \

.github/workflows/regression_tests.yml

@@ -80,6 +80,7 @@ jobs:
           source .venv-${{ matrix.python-version }}/bin/activate
           pwd
           lscpu
+          pip list
           python -m pytest -v -m regression\
             --durations=0 \
             --cov-report xml:cov.xml \
@@ -106,14 +107,9 @@ jobs:
       - name: Upload coverage
         if: env.has_changes == 'true'
         id : codecov
-        uses: Wandalen/wretry.action@v3.5.0
+        uses: codecov/codecov-action@v5
         with:
-          action: codecov/codecov-action@v4
-          with: |
-            token: ${{ secrets.CODECOV_TOKEN }}
-            name: codecov-umbrella
-            files: ./cov.xml
-            fail_ci_if_error: true
-            verbose: true
-          attempt_limit: 10
-          attempt_delay: 60000 # ms, 1 min
+          name: codecov-umbrella
+          files: ./cov.xml
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/release.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Build package
         run: python -m build --sdist --wheel
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/unit_tests.yml

@@ -86,6 +86,7 @@ jobs:
           source .venv-${{ matrix.combos.python_version }}/bin/activate
           pwd
           lscpu
+          pip list
           python -m pytest -v -m unit \
             --durations=0 \
             --cov-report xml:cov.xml \
@@ -112,14 +113,9 @@ jobs:
       - name: Upload coverage
         if: env.has_changes == 'true'
         id : codecov
-        uses: Wandalen/wretry.action@v3.5.0
+        uses: codecov/codecov-action@v5
         with:
-          action: codecov/codecov-action@v4
-          with: |
-            token: ${{ secrets.CODECOV_TOKEN }}
-            name: codecov-umbrella
-            files: ./cov.xml
-            fail_ci_if_error: true
-            verbose: true
-          attempt_limit: 10
-          attempt_delay: 60000 # ms, 1 min
+          name: codecov-umbrella
+          files: ./cov.xml
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/update_notebook_examples.yml

@@ -0,0 +1,75 @@
+name: Update Notebooks and Examples
+on:
+  schedule:
+    # runs on the first of every month at noon
+    - cron: '00 12 1 * *'
+
+jobs:
+  create_issue:
+    name: Create issues to update notebooks and examples
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Create issue to update notebooks
+        run: |
+          if [[ $CLOSE_PREVIOUS == true ]]; then
+            previous_issue_number=$(gh issue list \
+              --label "$LABELS" \
+              --json number \
+              --jq '.[0].number')
+            if [[ -n $previous_issue_number ]]; then
+              gh issue close "$previous_issue_number"
+              gh issue unpin "$previous_issue_number"
+            fi
+          fi
+          new_issue_url=$(gh issue create \
+            --title "$TITLE" \
+            --assignee "$ASSIGNEES" \
+            --label "$LABELS" \
+            --body "$BODY")
+          if [[ $PINNED == true ]]; then
+            gh issue pin "$new_issue_url"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          TITLE: Update Notebooks
+          ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
+          LABELS: monthly_update_notebooks
+          BODY: |
+            Reminder to check that notebooks evaluate correctly, and to update
+            if necessary.
+          PINNED: false
+          CLOSE_PREVIOUS: true
+      - name: Create issue to update notebooks
+        run: |
+            if [[ $CLOSE_PREVIOUS == true ]]; then
+                previous_issue_number=$(gh issue list \
+                --label "$LABELS" \
+                --json number \
+                --jq '.[0].number')
+                if [[ -n $previous_issue_number ]]; then
+                gh issue close "$previous_issue_number"
+                gh issue unpin "$previous_issue_number"
+                fi
+            fi
+            new_issue_url=$(gh issue create \
+                --title "$TITLE" \
+                --assignee "$ASSIGNEES" \
+                --label "$LABELS" \
+                --body "$BODY")
+            if [[ $PINNED == true ]]; then
+                gh issue pin "$new_issue_url"
+            fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          TITLE: Update Examples
+          ASSIGNEES: f0uriest, dpanici, ddudt, rahulgaur104, kianorr, YigitElma
+          LABELS: monthly_update_examples
+          BODY: |
+              Reminder to check that examples run correctly, and to update
+              if necessary.
+          PINNED: false
+          CLOSE_PREVIOUS: true

.github/workflows/weekly_tests.yml

@@ -35,6 +35,7 @@ jobs:
         run: |
           pwd
           lscpu
+          pip list
           python -m pytest -v -m unit \
             --durations=0 \
             --splits 4 \

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         log_file: devtools/pre-commit.log
@@ -22,20 +22,20 @@ repos:
       - id: no-commit-to-branch
         log_file: devtools/pre-commit.log
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/PyCQA/flake8
-    rev: "5.0.4"
+    rev: "7.1.1"
     hooks:
       - id: flake8
         additional_dependencies: ["flake8-docstrings", "flake8-eradicate", "flake8-isort"]
         log_file: devtools/pre-commit.log
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.0
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         log_file: devtools/pre-commit.log

CHANGELOG.md

@@ -5,6 +5,10 @@ New Feature
 
 - Adds a new profile class ``PowerProfile`` for raising profiles to a power.
 
+Bug Fixes
+
+- Small bug fix to use the correct normalization length ``a`` in the BallooningStability objective
+
 v0.13.0
 -------
 
@@ -27,6 +31,7 @@ New Features
 - Adds ``eq_fixed`` flag to ``ToroidalFlux`` to allow for the equilibrium/QFM surface to vary during optimization, useful for single-stage optimizations.
 - Adds tutorial notebook showcasing QFM surface capability.
 - Adds ``rotate_zeta`` function to ``desc.compat`` to rotate an ``Equilibrium`` around Z axis.
+- Adds an option ``scaled_termination`` (defaults to True) to all of the desc optimizers to measure the norms for ``xtol`` and ``gtol`` in the scaled norm provided by ``x_scale`` (which defaults to using an adaptive scaling based on the Jacobian or Hessian). This should make things more robust when optimizing parameters with widely different magnitudes. The old behavior can be recovered by passing ``options={"scaled_termination": False}``.
 
 Bug Fixes
 

desc/__main__.py

@@ -37,7 +37,7 @@ def main(cl_args=sys.argv[1:]):
         and (inputs[-1]["pres_ratio"] is None)
         and (inputs[-1]["bdry_ratio"] is None)
     ):
-        eq = Equilibrium(**inputs[-1], check_kwargs=False)
+        eq = Equilibrium(**inputs[-1], check_kwargs=False, ensure_nested=False)
         equil_fam = EquilibriaFamily.solve_continuation_automatic(
             eq,
             objective=inputs[-1]["objective"],

desc/backend.py

@@ -73,7 +73,7 @@
     from jax.lax import cond, fori_loop, scan, switch, while_loop
     from jax.nn import softmax as softargmax
     from jax.numpy import bincount, flatnonzero, repeat, take
-    from jax.numpy.fft import irfft, rfft, rfft2
+    from jax.numpy.fft import ifft, irfft, irfft2, rfft, rfft2
     from jax.scipy.fft import dct, idct
     from jax.scipy.linalg import block_diag, cho_factor, cho_solve, qr, solve_triangular
     from jax.scipy.special import gammaln
@@ -434,7 +434,7 @@ def tangent_solve(g, y):
     jit = lambda func, *args, **kwargs: func
     execute_on_cpu = lambda func: func
     import scipy.optimize
-    from numpy.fft import irfft, rfft, rfft2  # noqa: F401
+    from numpy.fft import ifft, irfft, irfft2, rfft, rfft2  # noqa: F401
     from scipy.fft import dct, idct  # noqa: F401
     from scipy.integrate import odeint  # noqa: F401
     from scipy.linalg import (  # noqa: F401

desc/compute/__init__.py

@@ -35,6 +35,7 @@
     _field,
     _geometry,
     _metric,
+    _neoclassical,
     _omnigenity,
     _profiles,
     _stability,