Minor changes

book/_config.yml

@@ -68,6 +68,7 @@ sphinx:
     - "sphinx.ext.autodoc"
     - "sphinx.ext.intersphinx"
     - "sphinx_codeautolink"
+    # - "sphinx_design"
 
 parse:
   myst_enable_extensions:

book/_toc.yml

@@ -77,4 +77,5 @@ parts:
     - file: content/applications/task08
     - file: content/applications/task06
     - file: content/applications/task10
-    - file: content/applications/microstructure
+    - file: content/applications/microstructure
+    - file: content/applications/ml

book/content/applications/ml.md

@@ -0,0 +1,17 @@
+---
+jupytext:
+  formats: ipynb,md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.18.1
+kernelspec:
+  display_name: festim-workshop
+  language: python
+  name: python3
+---
+
+# Training a FESTIM surrogate model
+
+Coming soon!

book/content/applications/task02.ipynb

@@ -142,7 +142,7 @@
                 "\n",
                 "where $\\varphi =2.5 \\times 10^{19} \\text{m}^{-2}\\text{s}^{-1}$ and $f(x)$ is a Gaussian spatial distribution with a mean value of $4.5 \\: \\text{nm}$ and a width of $2.5 \\: \\text{nm}$.\n",
                 "\n",
-                "FESTIM has a special class for this case: `ImplantationFlux`.\n",
+                "FESTIM has a special class for this case: {py:class}`ParticleSource<festim.source.ParticleSource>`.\n",
                 "\n",
                 "The ion flux is temporally defined using a Sympy Piecewise expression, to be active for the `implantation_time`.\n",
                 "\n",
@@ -186,7 +186,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "Boundary conditions (BCs) can be of several types in FESTIM, the most simple of them being the `FixedConcentrationBC` where an analytical expression is given in the argument: `value`. The argument `subdomain` is the subdomain on which the BC is applied. If no BC is applied on a surface, it will be considered as a non flux surface (ie $\\frac{\\partial c}{\\partial\\textbf{n}} = 0$).\n",
+                "Boundary conditions (BCs) can be of several types in FESTIM, the most simple of them being the {py:class}`FixedConcentrationBC<festim.boundary_conditions.FixedConcentrationBC>` where an analytical expression is given in the argument: `value`. The argument `subdomain` is the subdomain on which the BC is applied. If no BC is applied on a surface, it will be considered as a non flux surface (ie $\\frac{\\partial c}{\\partial\\textbf{n}} = 0$).\n",
                 "\n",
                 "In this case, the solute concentration is set to zero on the left and right surface."
             ]
@@ -273,7 +273,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The `Stepsize` object defines the simulation stepsize.\n",
+                "The {py:class}`Stepsize<festim.stepsize.Stepsize>` object defines the simulation stepsize.\n",
                 "\n",
                 "The argument `initial_value` is the initial stepsize is expressed in $\\text{s}$.\n",
                 "\n",
@@ -294,7 +294,7 @@
                 "To do so, we'll use 'derived quantities' objects.\n",
                 "There is a wide range of derived quantities available in FESTIM.\n",
                 "\n",
-                "Here, we'll use `TotalVolume` (volume integration) and `HydrogenFlux`."
+                "Here, we'll use {py:class}`TotalVolume<festim.exports.TotalVolume>` (volume integration) and {py:class}`SurfaceFlux<festim.exports.SurfaceFlux>`."
             ]
         },
         {
@@ -556,7 +556,7 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.13.5"
+            "version": "3.13.12"
         },
         "orig_nbformat": 4
     },

book/content/applications/task03.ipynb

@@ -24,7 +24,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "The first step is to create a model using a `Simulation` object."
+                "The first step is to create a model using a {py:class}`HydrogenTransportProblem<festim.hydrogen_transport_problem.HydrogenTransportProblem>` object."
             ]
         },
         {

book/content/applications/task04.ipynb

@@ -17,7 +17,7 @@
          "cell_type": "markdown",
          "metadata": {},
          "source": [
-            "## 1) Model with barrier\n",
+            "## Model with barrier\n",
             "\n",
             "Let's first create a model where tungsten is coated with 1 micron of barrier material on both sides."
          ]
@@ -328,7 +328,7 @@
          "cell_type": "markdown",
          "metadata": {},
          "source": [
-            "## 2) Model without barrier\n",
+            "## Model without barrier\n",
             "\n",
             "We can also run the equivalent model without permeation barriers with bare tungsten.\n",
             "Let's make a few modifications:"
@@ -387,7 +387,7 @@
          "cell_type": "markdown",
          "metadata": {},
          "source": [
-            "## 3) Calculate the PRF"
+            "## Calculate the PRF"
          ]
       },
       {
@@ -516,7 +516,7 @@
          "name": "python",
          "nbconvert_exporter": "python",
          "pygments_lexer": "ipython3",
-         "version": "3.13.5"
+         "version": "3.13.12"
       },
       "orig_nbformat": 4
    },

book/content/boundary_conditions/bc_intro.md

@@ -8,7 +8,7 @@ jupytext:
     jupytext_version: 1.19.1
 ---
 
-# Fixed value and flux boundary condition mathematics
+# Backgrounc
 
 This section discusses the math behind fixed temperature/concentration and flux boundary conditions (BCs).
 

book/content/meshes/index.md

@@ -12,4 +12,5 @@ kernelspec:
   name: python3
 ---
 
+(meshes)=
 # Meshes

book/content/meshes/mesh_festim.ipynb

@@ -20,7 +20,7 @@
     "\n",
     "## Uniform 1D meshes\n",
     "\n",
-    "The `Mesh1D` class in FESTIM allows you to define 1D meshes by simply specifying the coordinates of the mesh vertices. This makes it easy to construct uniform or structured meshes over a given interval.\n",
+    "The {py:class}`Mesh1D<festim.mesh.Mesh1D>` class in FESTIM allows you to define 1D meshes by simply specifying the coordinates of the mesh vertices. This makes it easy to construct uniform or structured meshes over a given interval.\n",
     "\n",
     "A **uniform mesh** is one where the spacing between points is constant. This type of mesh is ideal for problems where the physical properties or expected solution gradients are evenly distributed across the domain.\n",
     "\n",

book/content/misc/dolfinx_steady.md

@@ -76,7 +76,7 @@ from dolfinx import fem
 import basix
 ```
 
-We then create a mesh using `create_unit_square()`
+We then create a mesh using {py:func}`create_unit_square<dolfinx.mesh.create_unit_square>`
 
 ```{code-cell} ipython3
 nx = ny = 96

book/content/species_reactions/index.md

@@ -12,4 +12,4 @@ kernelspec:
   name: python3
 ---
 
-# Meshes
+# Species and reactions

book/intro.md

@@ -1,3 +1,48 @@
+---
+jupytext:
+  formats: ipynb,md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.18.1
+kernelspec:
+  display_name: festim-workshop
+  language: python
+  name: python3
+---
+
+
 # The FESTIM tutorial
 
-Welcome to the FESTIM tutorial!
+Welcome to the FESTIM tutorial! 🎉
+
+Here you can learn to run FESTIM simulations from complete application cases and from the fundamental building blocks of the code!
+
+Comments and corrections to this webpage should be submitted to the issue tracker by going to the relevant page in the tutorial, then click the {fab}`github` repository symbol in the top right corner and either {fas}`lightbulb` “open issue” or {fas}`pencil` "suggest edit".
+
+## Interactive tutorials
+
+You don't have to install FESTIM locally to be able to run these examples yourself. 
+
+Press the {fas}`rocket` button on the toolbar, then the {fas}`play` button to edit and run the code.
+
+```{note}
+This might take a while to load after new releases of the book.
+```
+
+```{code-cell} ipython3
+import festim as F
+
+print(F.__version__)
+```
+
+## Clickable API links
+
+You can directly click modules, functions, and classes to have access to their API documentation.
+
+```{code-cell} ipython3
+from festim import Mesh1D  # click Mesh1D
+import matplotlib  # click matplotlib
+from dolfinx import fem  # click fem
+```