✨ Enhance plasma loading features

.github/workflows/ci.yaml

@@ -37,7 +37,6 @@ jobs:
       - name: 🟨 Set up Pixi
         uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          pixi-version: v0.62.2 # NOTE: pin until https://github.com/prefix-dev/pixi/issues/5424 is resolved
           environments: ${{ matrix.environment }}
 
       - name: 🧪 Execute pytest

.github/workflows/docs.yml

@@ -25,7 +25,6 @@ jobs:
       - name: 🟨 Set up Pixi
         uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          pixi-version: v0.62.2 # NOTE: pin until https://github.com/prefix-dev/pixi/issues/5424 is resolved
           environments: docs
 
       - name: 📝 Build docs

.lefthook.yaml

@@ -17,7 +17,7 @@ output:
   - skips # Print "skip" (i.e. no files matched)
 
 pre-commit:
-  parallel: true
+  parallel: false
   jobs:
     - name: dprint
       glob: "*.{json,jsonc,md,yaml,yml}"
@@ -29,25 +29,21 @@ pre-commit:
       stage_fixed: true
       run: pixi {run} taplo {staged_files}
 
-    - name: ruff
+    - name: ruff check
       glob: "*.{py,pyi}"
-      group:
-        piped: true
-        jobs:
-          - name: ruff check
-            run: pixi {run} ruff check --fix {staged_files}
-            stage_fixed: true
-          - name: ruff format
-            run: pixi {run} ruff format {staged_files}
-            stage_fixed: true
+      stage_fixed: true
+      run: pixi {run} ruff check --fix {staged_files}
 
-    # - name: pyrefly
-    #   glob: "*.{py,pyi}"
-    #   run: pixi {run} pyrefly-check {staged_files}
+    - name: ruff format
+      glob: "*.{py,pyi}"
+      stage_fixed: true
+      skip:
+        - run: test ${CI} -eq 1
+      run: pixi {run} ruff format {staged_files}
 
-    # - name: mypy
-    #   glob: "*.{py,pyi}"
-    #   run: pixi {run} mypy {staged_files}
+    - name: pyrefly
+      glob: "*.{py,pyi}"
+      run: pixi {run} pyrefly-check {staged_files}
 
     - name: typos
       stage_fixed: true
@@ -69,3 +65,16 @@ pre-commit:
     - name: cython-lint
       glob: "*.{pyx,pxd}"
       run: pixi {run} cython-lint {staged_files}
+
+    - name: nbstripout clean
+      glob: "*.ipynb"
+      stage_fixed: true
+      skip:
+        - run: test ${CI} -eq 1
+      run: pixi {run} nbstripout {staged_files}
+
+    - name: nbstripout check
+      glob: "*.ipynb"
+      only:
+        - run: test ${CI} -eq 1
+      run: pixi {run} nbstripout --verify {staged_files}

CHANGELOG.md

@@ -11,10 +11,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Support Python 3.14
 - Add `visualize` function for bolometer camera geometry visualization using `plotly`
+- Add ion bundle splitting support in `load_plasma` for edge/core plasma loading
+- Add `solve_coronal_equilibrium` utility and corresponding fractional abundance notebook
+- Add dataset patching utility and update dataset registry/fetchers for JINTRAC workflows
+- Add new plasma data models (`SpeciesData`, `ProfileData`, `SpeciesComposition`, `VelocityData`) in common IDs utilities
 
 ### Changed
 
 - Change pixi environment to use Python 3.14 as default
+- Refactor core/edge profile loaders to use dataclass-driven species/profile handling
+- Refactor magnetic field and equilibrium loading paths and improve interpolator imports/types
+- Improve documentation notebooks and Sphinx configuration for plasma workflows
+- Update CI/quality tooling (`pyrefly`, pre-commit hooks, notebook stripping, pixi tasks)
 
 ## [0.3.0] - 2026-01-30
 

docs/notebooks/misc/fractional_abundances.ipynb

@@ -0,0 +1,165 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Fractional Abundances\n",
+    "\n",
+    "Here we compute the fractional abundances for Neon ions, assuming the coronal equilibrium model.\n",
+    "Let us plot the fractional abundances varying with the temperature for a fixed electron density.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import ultraplot as uplt\n",
+    "\n",
+    "from cherab.core.atomic.elements import neon\n",
+    "from cherab.imas.ids.common import solve_coronal_equilibrium\n",
+    "from cherab.openadas import OpenADAS\n",
+    "from cherab.openadas.install import install_adf11acd, install_adf11scd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "Download the necessary atomic data from OpenADAS if not already available.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "atomic_data = OpenADAS(permit_extrapolation=True, missing_rates_return_null=False)\n",
+    "try:\n",
+    "    atomic_data.ionisation_rate(neon, 1)\n",
+    "except RuntimeError:\n",
+    "    install_adf11acd(neon, \"adf11/acd96/acd96_ne.dat\", download=True)\n",
+    "    install_adf11scd(neon, \"adf11/scd96/scd96_ne.dat\", download=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "Set the electron density and the range of electron temperatures.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ELECTRON_DENSITY = 1e19\n",
+    "electron_temperatures = np.logspace(-0.2, 3.2, 100)"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "6",
+   "metadata": {
+    "raw_mimetype": "text/restructuredtext",
+    "vscode": {
+     "languageId": "raw"
+    }
+   },
+   "source": [
+    "The `.solve_coronal_equilibrium` function computes the fractional abundances by setting the total density to one."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "abundances = solve_coronal_equilibrium(\n",
+    "    neon,\n",
+    "    np.ones_like(electron_temperatures),\n",
+    "    np.full_like(electron_temperatures, ELECTRON_DENSITY),\n",
+    "    electron_temperatures,\n",
+    "    atomic_data=atomic_data,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
+   "source": [
+    "Plot the fractional abundances as a function of the electron temperature.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig, ax = uplt.subplots(refaspect=1.2, refwidth=4)\n",
+    "lines = ax.plot(\n",
+    "    electron_temperatures,\n",
+    "    abundances.T,\n",
+    "    cycle=\"tab20\",\n",
+    ")\n",
+    "ax.legend(\n",
+    "    lines,\n",
+    "    [f\"Ne {i}+\" for i in range(neon.atomic_number + 1)],\n",
+    "    ncols=1,\n",
+    "    loc=\"right\",\n",
+    "    frame=False,\n",
+    "    fontcolor=\"w\",\n",
+    ")\n",
+    "ax.format(\n",
+    "    style=\"dark_background\",\n",
+    "    xscale=\"log\",\n",
+    "    yformatter=(\"percent\", 1),\n",
+    "    tickminor=True,\n",
+    "    tickdir=\"in\",\n",
+    "    grid=True,\n",
+    "    gridalpha=0.3,\n",
+    "    xlabel=\"Electron Temperature [eV]\",\n",
+    "    title=r\"Fractional Abundances, $n_\\mathrm{e} = 10^{19}$ m$^{-3}$\",\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "docs",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.14.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}