🎉 Release: merge develop into master

.codecov.yml

@@ -0,0 +1,26 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecov-yaml
+
+github_checks:
+  annotations: true
+
+comment:
+  layout: 'reach, diff, flags, files'
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        # Make project coverage informational (won't block PR)
+        informational: true
+    patch:
+      default:
+        target: auto
+        # Require patch coverage but with threshold
+        threshold: 1%

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.11.3
+_commit: v0.12.0
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/coverage.yml

@@ -63,32 +63,8 @@ jobs:
           files: ./coverage-unit.xml
           token: ${{ secrets.CODECOV_TOKEN }}
 
-  # Job 2: Run integration tests with coverage and upload to Codecov
-  integration-tests-coverage:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check-out repository
-        uses: actions/checkout@v6
-
-      - name: Set up pixi
-        uses: ./.github/actions/setup-pixi
-
-      - name: Run integration tests with coverage
-        run:
-          pixi run integration-tests-coverage --cov-report=xml:coverage-integration.xml
-
-      - name: Upload integration tests coverage to Codecov
-        if: ${{ !cancelled() }}
-        uses: ./.github/actions/upload-codecov
-        with:
-          name: integration-tests-job
-          flags: integration
-          files: ./coverage-integration.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
-    needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs
+    needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
     uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/dashboard.yml

@@ -32,9 +32,13 @@ jobs:
       - name: Set up pixi
         uses: ./.github/actions/setup-pixi
 
+      # Install badgery into the active Pixi environment without modifying
+      # pixi.toml/pixi.lock. Using `pixi add` here re-solves the whole project
+      # and rebuilds the local editable package, which can cause intermittent
+      # Linux CI failures (`Text file busy`, os error 26).
       - name: Install badgery
         shell: bash
-        run: pixi add --pypi --git https://github.com/enhantica/badgery badgery
+        run: pixi run python -m pip install git+https://github.com/enhantica/badgery
 
       - name: Run docstring coverage and code complexity/maintainability checks
         run: |

.prettierignore

@@ -25,6 +25,9 @@ docs/docs/assets/
 # Node
 node_modules
 
+# Tox
+.tox
+
 # Misc
 .benchmarks
 .cache

docs/docs/assets/stylesheets/extra.css

@@ -200,7 +200,14 @@ label.md-nav__title[for="__drawer"] {
 
 /* Change the overall width of the page */
 .md-grid {
-  max-width: 1280px;
+  max-width: 116em;
+}
+
+/* Keep prose line length stable when sidebars are hidden at narrower widths */
+.md-main .md-content > .md-content__inner {
+  width: min(100%, 40.5em);
+  margin-left: auto !important;
+  margin-right: auto !important;
 }
 
 /* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */

docs/docs/tutorials/analysis1d.ipynb

@@ -81,15 +81,15 @@
     ")\n",
     "\n",
     "fit_result = my_analysis.fit()\n",
-    "my_analysis.plot_data_and_model()"
+    "my_analysis.plot_data_and_model(plot_residuals=True)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (Pixi)",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "pixi-kernel-python3"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -101,7 +101,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.14.5"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/components.ipynb

@@ -192,7 +192,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.5"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/delta_lorentz.ipynb

@@ -0,0 +1,118 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Delta Lorentz\n",
+    "Model of Delta function and Lorentzian with intensities given by the Debye-Waller factor:\n",
+    "\n",
+    "$ I\n",
+    "= K \\exp \\left( \\frac{-\\langle u^2 \\rangle Q^2}{3} \\right)[A_0 \\delta(E) + A_1 L(E, \\Gamma)]\n",
+    "$,\n",
+    "\n",
+    "where $K$ is the scale factor, $\\langle u^2 \\rangle$ is the mean square displacement, $Q$ is\n",
+    "the scattering vector, $A_0$ and $A_1$ are the relative amplitudes of the delta function and\n",
+    "Lorentzian, respectively, with the constraint that $A_0+A_1=1$, and $L(E, \\Gamma)$ is the\n",
+    "Lorentzian function with width $\\Gamma$. $A_0$, $A_1$ and the width of the Lorentzian can be\n",
+    "the same at all $Q$ or be allowed to vary with $Q$.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
+    "from easydynamics.sample_model.diffusion_model.delta_lorentz import DeltaLorentz\n",
+    "\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6d6e1984",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Q = np.linspace(0.5, 2, 7)\n",
+    "energy = np.linspace(-2, 2, 501)\n",
+    "scale = 1.0\n",
+    "mean_u_squared = 0.5\n",
+    "A_0 = 0.2\n",
+    "lorentzian_width = 0.2\n",
+    "\n",
+    "diffusion_model = DeltaLorentz(\n",
+    "    scale=scale,\n",
+    "    mean_u_squared=mean_u_squared,\n",
+    "    A_0=A_0,\n",
+    "    lorentzian_width=lorentzian_width,\n",
+    "    allow_Q_variation={'A_0': True, 'lorentzian_width': True},\n",
+    "    Q=Q,\n",
+    "    lorentzian_name='Lorentzian',\n",
+    "    delta_name='Delta function',\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "389aa3cd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "component_collections = diffusion_model.get_component_collections()\n",
+    "cmap = plt.cm.jet\n",
+    "nQ = len(component_collections)\n",
+    "plt.figure()\n",
+    "for Q_index in range(len(component_collections)):\n",
+    "    color = cmap(Q_index / (nQ - 1))\n",
+    "    y = component_collections[Q_index].evaluate(energy)\n",
+    "    plt.plot(energy, y, label=f'Q={Q[Q_index]} Å^-1', color=color)\n",
+    "\n",
+    "plt.legend()\n",
+    "plt.show()\n",
+    "plt.xlabel('Energy (meV)')\n",
+    "plt.ylabel('Intensity (arb. units)')\n",
+    "plt.title('Delta-Lorentz Model')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bf360b45",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "diffusion_model.get_all_variables()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.14.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/docs/tutorials/diffusion_model.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "# Diffusion Model\n",
-    "We support several standard models of diffusion. Here we show an example of Browniand Translational Diffusion, where the scattering is a Lorentzian with width ($\\Gamma$) given by $\\Gamma = D Q^2$, where $D$ is the diffusion coefficient (in m$^2$/s) and $Q$ is the momentum transfer."
+    "We support several standard models of diffusion. Here we show an example of Brownian Translational Diffusion, where the scattering is a Lorentzian with width ($\\Gamma$) given by $\\Gamma = D Q^2$, where $D$ is the diffusion coefficient (in m$^2$/s) and $Q$ is the momentum transfer."
    ]
   },
   {
@@ -41,12 +41,10 @@
     "diffusion_coefficient = 2.4e-9  # m^2/s\n",
     "\n",
     "diffusion_model = BrownianTranslationalDiffusion(\n",
-    "    display_name='DiffusionModel',\n",
-    "    scale=scale,\n",
-    "    diffusion_coefficient=diffusion_coefficient,\n",
+    "    display_name='DiffusionModel', scale=scale, diffusion_coefficient=diffusion_coefficient, Q=Q\n",
     ")\n",
     "\n",
-    "component_collections = diffusion_model.create_component_collections(Q)\n",
+    "component_collections = diffusion_model.get_component_collections()\n",
     "\n",
     "\n",
     "cmap = plt.cm.jet\n",
@@ -87,7 +85,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easydynamics_newbase",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -101,7 +99,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.14.4"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/index.md

@@ -50,6 +50,9 @@ tutorials.
   balancing.
 - [Diffusion model](diffusion_model.ipynb) – Learn how to create and use
   a model of diffusion.
+- [DeltaLorentz](delta_lorentz.ipynb) – Learn how to create and use a
+  model with a Delta function and a Lorentzian that have a shared
+  Debye-Waller-like Q-dependence.
 - [Sample model](sample_model.ipynb) – Learn how to create a model of
   the scattering from your sample including model components and
   diffusion models.

docs/docs/tutorials/sample_model.ipynb

@@ -148,7 +148,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.5"
   }
  },
  "nbformat": 4,