Release: merge develop into master

.copier-answers.yml

@@ -1,16 +1,16 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.0
+_commit: v0.10.1-2-gd05af4f
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
-app_doi: 10.5281/zenodo.18163581
+app_doi: 10.5281/zenodo.18877180
 app_package_name: easydynamics_app
 app_python: '3.12'
 app_repo_name: dynamics-app
 home_page_url: https://easyscience.github.io/dynamics
 home_repo_name: dynamics
 lib_docs_url: https://easyscience.github.io/dynamics-lib
-lib_doi: 10.5281/zenodo.18163581
+lib_doi: 10.5281/zenodo.18877180
 lib_package_name: easydynamics
 lib_python_max: '3.12'
 lib_python_min: '3.11'

docs/docs/assets/javascripts/extra.js

@@ -1,6 +1,5 @@
-(function() {
-
-  "use strict"
+;(function () {
+  'use strict'
 
   // Variables
   const header = document.getElementsByTagName('header')[0]
@@ -10,20 +9,19 @@
   // Hide-show header shadow
   function toggleHeaderShadow() {
     if (window.pageYOffset <= 0) {
-      header.classList.remove("md-header--shadow")
+      header.classList.remove('md-header--shadow')
     } else {
-      header.classList.add("md-header--shadow")
+      header.classList.add('md-header--shadow')
     }
   }
 
   // Onload
-  window.onload = function() {
+  window.onload = function () {
     toggleHeaderShadow()
   }
 
   // Onscroll
-  window.onscroll = function() {
+  window.onscroll = function () {
     toggleHeaderShadow()
   }
-
 })()

docs/docs/assets/javascripts/mathjax.js

@@ -3,21 +3,27 @@ window.MathJax = {
     //inlineMath: [['\\(', '\\)']],
     //displayMath: [['\\[', '\\]']],
     // Add support for $...$ and \(...\) delimiters
-    inlineMath: [['$', '$'], ['\\(', '\\)']],
+    inlineMath: [
+      ['$', '$'],
+      ['\\(', '\\)'],
+    ],
     // Add support for $$...$$ and \[...]\ delimiters
-    displayMath: [['$$', '$$'], ['\\[', '\\]']],
+    displayMath: [
+      ['$$', '$$'],
+      ['\\[', '\\]'],
+    ],
     processEscapes: true,
-    processEnvironments: true
+    processEnvironments: true,
   },
   options: {
     //ignoreHtmlClass: ".*|",
     //processHtmlClass: "arithmatex"
     // Skip code blocks only
-    skipHtmlTags: ['script','noscript','style','textarea','pre','code'],
+    skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre', 'code'],
     // Only ignore explicit opt-out
     ignoreHtmlClass: 'no-mathjax|tex2jax_ignore',
-  }
-};
+  },
+}
 
 document$.subscribe(() => {
   MathJax.startup.output.clearCache()

docs/docs/installation-and-setup/index.md

@@ -225,49 +225,32 @@ Google Colab.
 
 If you decide to run the tutorials locally, you need to download them
 first. This can be done individually via the :material-download:
-**Download Notebook** button available on each tutorial page, or all at
-once using the command line, as shown below.
+**Download Notebook** button available on each tutorial page.
 
 ### Run Tutorials Locally with Pixi <small>recommended</small> { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" }
 
 - Navigate to your existing Pixi project, created as described in the
   [Installing with Pixi](#installing-with-pixi) section.
-- Add JupyterLab and the Pixi kernel for Jupyter:
+- Launch the Jupyter Lab server:
   ```txt
-  pixi add --pypi jupyterlab pixi-kernel
-  ```
-- Download all the EasyDynamics tutorials to the `tutorials/` directory:
-  ```txt
-  pixi run easydynamics download-all-tutorials
-  ```
-- Start JupyterLab in the `tutorials/` directory to access the
-  notebooks:
-  ```txt
-  pixi run jupyter lab tutorials/
+  pixi run jupyter lab
   ```
 - Your web browser should open automatically. Click on one of the
-  `*.ipynb` files and select the `Python (Pixi)` kernel to get started.
+  `*.ipynb` files downloaded previously and select the `Python (Pixi)`
+  kernel to get started.
 
 ### Classical Run Tutorials Locally
 
-- Install Jupyter Notebook and IPython kernel:
-  ```txt
-  pip install notebook ipykernel
-  ```
 - Add the virtual environment as a Jupyter kernel:
   ```txt
   python -m ipykernel install --user --name=venv --display-name "EasyDynamics Python kernel"
   ```
-- Download all the EasyDynamics tutorials to the `tutorials/` directory:
-  ```txt
-  python -m easydynamics download-all-tutorials
-  ```
-- Launch the Jupyter Notebook server (opens browser automatically at
-  `http://localhost:8888/`):
+- Launch the Jupyter Notebook server:
   ```txt
-  jupyter notebook tutorials/
+  jupyter notebook
   ```
-- Open one of the `*.ipynb` files and select the
+- Your web browser should open automatically. Click on one of the
+  `*.ipynb` files downloaded previously and select the
   `EasyDynamics Python kernel` to get started.
 
 ### Run Tutorials via Google Colab

docs/docs/introduction/index.md

@@ -45,7 +45,7 @@ Zenodo, each with a version-specific Digital Object Identifier (DOI).
 
 Citation details in various styles (e.g., APA, MLA) and formats (e.g.,
 BibTeX, JSON) are available on the
-[Zenodo archive page](https://doi.org/10.5281/zenodo.18163581).
+[Zenodo archive page](https://doi.org/10.5281/zenodo.18877180).
 
 ## Contributing
 

docs/docs/tutorials/analysis.ipynb

@@ -21,6 +21,8 @@
    "outputs": [],
    "source": [
     "# Imports\n",
+    "import pooch\n",
+    "\n",
     "from easydynamics.analysis.analysis import Analysis\n",
     "from easydynamics.experiment import Experiment\n",
     "from easydynamics.sample_model import BrownianTranslationalDiffusion\n",
@@ -46,7 +48,12 @@
    "source": [
     "# Load the vanadium data\n",
     "vanadium_experiment = Experiment('Vanadium')\n",
-    "vanadium_experiment.load_hdf5(filename='vanadium_data_example.h5')"
+    "file_path = pooch.retrieve(\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/docs/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
+    "    known_hash='16cc1b327c303feeb88fb9dda5390dc4880b62396b1793f98c6fef0b27c7b873',\n",
+    ")\n",
+    "\n",
+    "vanadium_experiment.load_hdf5(filename=file_path)"
    ]
   },
   {
@@ -164,7 +171,12 @@
     "# Now it's time to look at the data we want to fit. We first load the\n",
     "# data\n",
     "diffusion_experiment = Experiment('Diffusion')\n",
-    "diffusion_experiment.load_hdf5(filename='diffusion_data_example.h5')"
+    "\n",
+    "file_path = pooch.retrieve(\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/docs/docs/docs/tutorials/data/diffusion_data_example.h5',\n",
+    ")\n",
+    "\n",
+    "diffusion_experiment.load_hdf5(filename=file_path)"
    ]
   },
   {
@@ -330,9 +342,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easydynamics_newbase",
+   "display_name": "Python (Pixi)",
    "language": "python",
-   "name": "python3"
+   "name": "pixi-kernel-python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -344,7 +356,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/analysis1d.ipynb

@@ -11,11 +11,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "bca91d3c",
    "metadata": {},
    "outputs": [],
    "source": [
+    "import pooch\n",
+    "\n",
     "from easydynamics.analysis.analysis1d import Analysis1d\n",
     "from easydynamics.experiment import Experiment\n",
     "from easydynamics.sample_model import DeltaFunction\n",
@@ -31,18 +33,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "8deca9b6",
    "metadata": {},
    "outputs": [],
    "source": [
     "vanadium_experiment = Experiment('Vanadium')\n",
-    "vanadium_experiment.load_hdf5(filename='vanadium_data_example.h5')"
+    "\n",
+    "file_path = pooch.retrieve(\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/docs/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
+    "    known_hash='16cc1b327c303feeb88fb9dda5390dc4880b62396b1793f98c6fef0b27c7b873',\n",
+    ")\n",
+    "\n",
+    "\n",
+    "vanadium_experiment.load_hdf5(filename=file_path)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "41f842f0",
    "metadata": {},
    "outputs": [],
@@ -73,15 +82,16 @@
     ")\n",
     "\n",
     "fit_result = my_analysis.fit()\n",
-    "fig = my_analysis.plot_data_and_model()"
+    "fig = my_analysis.plot_data_and_model()\n",
+    "fig"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easydynamics_newbase",
+   "display_name": "Python (Pixi)",
    "language": "python",
-   "name": "python3"
+   "name": "pixi-kernel-python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -93,7 +103,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/experiment.ipynb

@@ -16,6 +16,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import pooch\n",
+    "\n",
     "from easydynamics.experiment import Experiment\n",
     "\n",
     "%matplotlib widget"
@@ -29,8 +31,15 @@
    "outputs": [],
    "source": [
     "# Load and plot example vanadium data\n",
+    "# Load the vanadium data\n",
     "vanadium_experiment = Experiment('Vanadium')\n",
-    "vanadium_experiment.load_hdf5(filename='vanadium_data_example.h5')\n",
+    "\n",
+    "file_path = pooch.retrieve(\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/docs/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
+    "    known_hash='16cc1b327c303feeb88fb9dda5390dc4880b62396b1793f98c6fef0b27c7b873',\n",
+    ")\n",
+    "\n",
+    "vanadium_experiment.load_hdf5(filename=file_path)\n",
     "\n",
     "vanadium_experiment.plot_data()"
    ]
@@ -61,9 +70,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easydynamics_newbase",
+   "display_name": "Python (Pixi)",
    "language": "python",
-   "name": "python3"
+   "name": "pixi-kernel-python3"
   },
   "language_info": {
    "codemirror_mode": {

docs/docs/tutorials/index.md

@@ -17,20 +17,34 @@ The tutorials are organized into the following categories:
 
 ## Getting Started
 
-- [Component collection](component_collection.ipynb) – Learn how to
-  create a collectin of components for fitting.
+We are working on expanding the list of tutorials to include advanced
+concept such as interpolating `Parameter`s, sharing `Parameter`s at
+multiple `Q` and analysing complex inelastic data.
+
+- [Tutorial 1: Brownian Diffusion](tutorial1_brownian.ipynb) - Learn how
+  to analyse QENS data with elastic incoherent background and Brownian
+  diffusion.
+
+## Classes and Methods
+
+Here we go into more detail with each class that is used in the
+tutorials.
+
 - [Components](components.ipynb) – Learn how to use the EasyDynamics
-  components.
+  model components, which are the basic building blocks of your model.
+- [Component collection](component_collection.ipynb) – Learn how to
+  create a collection of components for fitting.
 - [Convolution](convolution.ipynb) – Learn how to calculate the
   convolution of your resolution function with your model.
-- [Detailed balance](detailed_balance.ipynb) – Learn how to apply
-  detailed balancing to your model.
+- [Detailed balance](detailed_balance.ipynb) – Learn about detailed
+  balancing.
 - [Diffusion model](diffusion_model.ipynb) – Learn how to create and use
   a model of diffusion.
 - [Sample model](sample_model.ipynb) – Learn how to create a model of
-  the scattering from your sample.
+  the scattering from your sample including model components and
+  diffusion models.
 - [Instrument model](instrument_model.ipynb) – Learn how to create a.
-  model of your instrument.
+  model of your instrument including resolution and background.
 - [Experiment](experiment.ipynb) - Learn how to load and bin your data.
 - [Analysis](analysis.ipynb) - Learn how to fit a model to your data.
 - [Analysis 1D](analysis1d.ipynb) - Learn how to fit a model to your