Release v0.6.0

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.github/workflows/ci.yaml

@@ -12,10 +12,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v7
 
       - name: 🟨 Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.9.4
+        uses: prefix-dev/setup-pixi@v0.10.1
         with:
           environments: lint
 
@@ -32,10 +32,10 @@ jobs:
 
     steps:
       - name: check out repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v7
 
       - name: 🟨 Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.9.4
+        uses: prefix-dev/setup-pixi@v0.10.1
         with:
           environments: ${{ matrix.environment }}
 
@@ -48,6 +48,6 @@ jobs:
         run: mv .coverage ".coverage.${{ matrix.environment }}.${{ matrix.os }}.xml"
 
       - name: 📤 Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/deploy-pypi.yml

@@ -29,10 +29,11 @@ jobs:
     steps:
       - name: Checkout LLVM on macOS
         if: runner.os == 'macOS'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           repository: llvm/llvm-project
-          ref: release/19.x
+          # Keep this pinned to a stable release for reproducible wheels.
+          ref: llvmorg-22.1.8
           path: llvm-project
 
       - name: Build OpenMP on macOS
@@ -49,21 +50,24 @@ jobs:
             -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
             -DCMAKE_C_COMPILER=clang \
             -DCMAKE_CXX_COMPILER=clang++ \
+            -DCMAKE_OSX_ARCHITECTURES="${{ matrix.arch }}" \
+            -DLIBOMP_ENABLE_SHARED=ON \
             -DLIBOMP_INSTALL_ALIASES=OFF \
             -S openmp \
             -B build
           cmake --build build --parallel
           cmake --install build
+          echo "REPAIR_LIBRARY_PATH=${PREFIX}/lib" >> "${GITHUB_ENV}"
 
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v7
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v9.0.0
 
       # For aarch64 support
       # https://cibuildwheel.pypa.io/en/stable/faq/#emulation
-      - uses: docker/setup-qemu-action@v3
+      - uses: docker/setup-qemu-action@v4
         with:
           platforms: all
         if: runner.os == 'Linux' && matrix.arch == 'aarch64'
@@ -76,27 +80,38 @@ jobs:
         # These needs to rotate every new Python release.
         if: github.event_name == 'pull_request'
         run: |
-          CIBW_SKIP="pp* *-musllinux* cp311-* cp313-* cp314-* cp314t-*"
+          CIBW_SKIP="pp* *-musllinux* cp311* cp313* cp314* cp315*"
           echo "CIBW_SKIP=${CIBW_SKIP}" >> "${GITHUB_ENV}"
           echo "Setting CIBW_SKIP=${CIBW_SKIP}"
 
       - name: Build wheels (at Pull Request)
         if: github.event_name == 'pull_request'
-        uses: pypa/cibuildwheel@v3.2.1
+        uses: pypa/cibuildwheel@v4.2
         env:
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=${{ matrix.macos }}
           CIBW_SKIP: ${{ env.CIBW_SKIP }}
 
       - name: Build wheels
         if: github.event_name != 'pull_request'
-        uses: pypa/cibuildwheel@v3.2.1
+        uses: pypa/cibuildwheel@v4.2
         env:
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=${{ matrix.macos }}
 
+      - name: Verify OpenMP is bundled on macOS
+        if: runner.os == 'macOS'
+        shell: bash
+        run: |
+          for wheel in wheelhouse/*.whl; do
+            if ! unzip -l "${wheel}" | grep -Eq 'libomp[^/]*\.dylib$'; then
+              echo "::error::libomp.dylib is not bundled in ${wheel}"
+              exit 1
+            fi
+          done
+
       - name: Upload wheels
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v7
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
@@ -105,12 +120,12 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
 
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v5
+      - uses: actions/upload-artifact@v7
         with:
           name: cibw-sdist
           path: dist/*.tar.gz
@@ -120,7 +135,7 @@ jobs:
     name: Show artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v6
+      - uses: actions/download-artifact@v8
         with:
           pattern: cibw-*
           path: ${{ github.workspace }}/dist
@@ -144,7 +159,7 @@ jobs:
     # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v8
         with:
           # unpacks all CIBW artifacts into dist/
           pattern: cibw-*

.github/workflows/docs.yml

@@ -20,18 +20,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v7
 
       - name: 🟨 Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.9.4
+        uses: prefix-dev/setup-pixi@v0.10.1
         with:
           environments: docs
 
       - name: 📝 Build docs
         run: pixi run -e docs doc-build
 
       - name: 📦 Upload artifact
-        uses: actions/upload-pages-artifact@v4
+        uses: actions/upload-pages-artifact@v5
         with:
           path: docs/build/html
 
@@ -45,4 +45,4 @@ jobs:
     steps:
       - name: 🚀 Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v7
 
       - name: Extract release notes
         id: notes
@@ -37,7 +37,7 @@ jobs:
           } >> "$GITHUB_OUTPUT"
 
       - name: Create GitHub release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           tag_name: ${{ github.ref_name }}
           name: ${{ github.ref_name }}

.lefthook.yaml

@@ -47,10 +47,6 @@ pre-commit:
         - run: test ${CI:-false} = true
       run: pixi {run} pyrefly-check {staged_files}
 
-    - name: typos
-      stage_fixed: true
-      run: pixi {run} typos {staged_files}
-
     - name: actionlint
       glob: ".github/workflows/*.{yaml,yml}"
       run: pixi {run} actionlint {staged_files}
@@ -80,3 +76,7 @@ pre-commit:
       only:
         - run: test ${CI:-false} = true
       run: pixi {run} nbstripout --verify {staged_files}
+
+    - name: typos
+      stage_fixed: true
+      run: pixi {run} typos {staged_files}

CHANGELOG.md

@@ -5,21 +5,57 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.5.1] - 2026-07-28
+## [0.6.0] - 2026-08-12
 
 ### Added
 
 - Add synthetic JINTRAC radiation values dataset support and related regression tests
 - Extend radiation emitter loading to support dual emissivity sources with improved validation
+- Add IDS path utility helpers and `get_entry_reference` for resolving entry references
+- Add unit tests for IDS path handling, grid loading via path references, and plasma utility entry-reference workflows
+- Add public `CellConnectivity`, `CellData`, and `VertexIndices` types and the `as_cell_data()`
+  validation helper for GGD meshes
+- Add validity-mask support for retaining the relationship between compacted 2D grids and their
+  source GGD face data
+- Add an optimized Cython implementation for calculating polygonal cell areas and area-weighted
+  centroids, with OpenMP support for large meshes
+- Add profile-shape inspection and plain-text/Rich summaries for species compositions
+- Add regression tests for 2D grid geometry, subset validity, molecular species, and core/edge
+  profile loading
+- Add a 2D radiation-emitter example notebook
 
 ### Changed
 
+- Select read mode automatically when CHERAB object loaders receive an IMAS URI or netCDF path;
+  explicit `"r"` arguments remain temporarily supported but are deprecated
+- Reject data-creating DBEntry modes in CHERAB object loader APIs
+- Update API docstrings, examples, demos, and notebooks to use mode-free loader calls
 - Improve radiation emitter loading checks for duplicate emissivity values and core-profile grid data
+- Refactor `load_grid` to support explicit `entry` selection and improve referenced-grid source resolution
+- Enhance plasma and emitter loading paths to use entry-reference aware grid resolution
+- **Breaking:** Change `load_grid(..., with_subsets=True)` and
+  `load_unstruct_grid_2d(..., with_subsets=True)` subset values from index arrays to
+  `(indices, valid_data_mask)` tuples
+- Extend `UnstructGrid2D` with source-data validity tracking so interpolation and plotting accept
+  either compacted cell data or source-sized data
+- Calculate cylindrical 2D cell volumes from area-weighted centroids over a full toroidal rotation
+- Filter edge and blended-plasma profile arrays consistently when invalid GGD faces are omitted
+- Classify neutral and charged molecular species consistently and retain molecular bundles in core
+  and edge species compositions
+- Promote `rich` from a test-only dependency to a runtime dependency
+- Summarize non-empty species groups with compact labels, conventional ionic charge notation, and
+  stable symbol-derived coloring in plain and `rich` tree output
+- Update the edge-plasma example to use the ITER-SOLPS sample dataset
 
 ### Fixed
 
 - Fix grid data loading checks for radiation core profiles
 - Improve error handling in radiation emitter loading workflows
+- Ignore missing, incomplete, and out-of-range GGD faces while preserving correct subset mappings
+- Fix triangle indexing, cylindrical cell-volume calculation, and volume preservation in 2D grid
+  subsets
+- Fix the Cython compile and link arguments on macOS
+- Preserve neutral and charged molecular species when loading core and edge compositions
 
 ## [0.5.0] - 2026-06-24
 

demos/ITER/core_plasma_plot_profiles.py

@@ -73,7 +73,7 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
 
 # Load and plot equilibrium
 path = iter_jintrac()
-equilibrium, psi_interpolator = load_equilibrium(path, "r", with_psi_interpolator=True)
+equilibrium, psi_interpolator = load_equilibrium(path, with_psi_interpolator=True)
 plot_equilibrium(equilibrium)
 plt.gcf().savefig(plots_path / "equilibrium.png", dpi=200)
 
@@ -95,7 +95,7 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
 fig.savefig(plots_path / "bz.png", dpi=200)
 
 # Load core plasma
-plasma = load_core_plasma(path, "r", equilibrium=equilibrium, psi_interpolator=psi_interpolator)
+plasma = load_core_plasma(path, equilibrium=equilibrium, psi_interpolator=psi_interpolator)
 
 # Sample and plot electron profiles
 ne_plasma = sample3d_grid(plasma.electron_distribution.density, xsamp, [0], zsamp)

demos/ITER/edge_plasma_plot_profiles.py

@@ -79,18 +79,22 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
 
 # Load and plot equilibrium
 try:
-    equilibrium = load_equilibrium(iter_jintrac(), "r")
+    equilibrium = load_equilibrium(iter_jintrac())
     plot_equilibrium(equilibrium)
     plt.gcf().savefig(plots_path / "equilibrium.png", dpi=200)
     b_field = equilibrium.b_field
 except RuntimeError:
     try:
-        b_field = load_magnetic_field(iter_jintrac(), "r")
+        b_field = load_magnetic_field(iter_jintrac())
     except RuntimeError:
         b_field = None
 
 # Sample and plot magnetic field
 plot_velocity = False
+b = None
+b_length = None
+radial_vector = None
+poloidal_vector = None
 if b_field is not None:
     try:
         xsamp, zsamp, b = samplevector2d(b_field, (xl, xu, nx), (zl, zu, nz))
@@ -116,7 +120,7 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
         )
 
 # Load edge plasma
-plasma = load_edge_plasma(iter_jintrac(), "r", b_field=b_field)
+plasma = load_edge_plasma(iter_jintrac(), b_field=b_field)
 
 # Sample and plot electron profiles
 xsamp, _, zsamp, ne_plasma = sample3d(
@@ -132,7 +136,7 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
 fig = plot_quantity(te_plasma, extent, title="Te [eV]", logscale=True)
 fig.savefig(plots_path / "edge_te.png", dpi=200)
 
-if plot_velocity:
+if plot_velocity and b is not None and b_length is not None:
     electron_velocity = samplevector3d_grid(
         plasma.electron_distribution.bulk_velocity, xsamp, [0], zsamp
     ).squeeze()
@@ -174,7 +178,13 @@ def plot_quantity(quantity, extent, title="", logscale=False, symmetric=False) -
             dpi=200,
         )
 
-        if plot_velocity:
+        if (
+            plot_velocity
+            and b is not None
+            and b_length is not None
+            and radial_vector is not None
+            and poloidal_vector is not None
+        ):
             velocity = samplevector3d_grid(
                 species.distribution.bulk_velocity, xsamp, [0], zsamp
             ).squeeze()