Upgrading to Jupyter 2

.readthedocs.yml

@@ -1,22 +1,24 @@
 version: 2
 
+# conda:
+#   environment: environment.yml
+
 build:
   os: ubuntu-22.04
   tools:
     python: "miniconda-latest"
+    nodejs: "20"
   apt_packages:
     - libglx-mesa0
     - libgl1
     - xvfb
-  jobs:
-    pre_build:
-      # Generate the Sphinx configuration for this Jupyter Book so it builds.
-      - "jupyter-book config sphinx book/"
-
-conda:
-  environment: environment.yml
-
-sphinx:
-  builder: html
-  fail_on_warning: true
-  configuration: book/_config.yml
+  commands:
+    - npm install -g mystmd
+    # - pip install "jupyter-book>=2.0.0a0"
+    - conda env create --name festim-workshop-jupyter2 --file environment.yml
+    - mkdir -p $READTHEDOCS_OUTPUT/site
+    - ls
+    - export HOST=127.0.0.1
+    - export BASE_URL=.
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && jupyter book build --html"
+    - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build

book/content/species_reactions/reactions.ipynb

@@ -28,9 +28,9 @@
     "\n",
     "We'll start with a simple reaction between species A and B forming species C at a rate $k$ and assume there is no backward reaction.\n",
     "\n",
-    "```{math}\n",
+    "<!-- ```{math}\n",
     "\\ce{A + B ->[k] C}\n",
-    "```"
+    "``` -->"
    ]
   },
   {
@@ -224,9 +224,6 @@
     "\n",
     "The previous example can be very easily extended to a two-way reaction:\n",
     "\n",
-    "```{math}\n",
-    "\\ce{A + B <-->[k][p] C}\n",
-    "```\n",
     "\n",
     "The governing equations for this problem are:\n",
     "\n",
@@ -350,13 +347,9 @@
     "Here we consider a reaction scheme where mobile species A and B react to form species C (immobile).\n",
     "Species C then reacts *on its own* to form species D.\n",
     "\n",
-    "```{math}\n",
-    "\\ce{A + B <-->[k_1][p_1] C}\n",
-    "```\n",
-    "\n",
-    "```{math}\n",
+    "<!-- ```{math}\n",
     "\\ce{C ->[k_2] D}\n",
-    "```\n",
+    "``` -->\n",
     "\n",
     "The governing equations of this system are:\n",
     "\n",
@@ -500,10 +493,7 @@
     "\n",
     "\n",
     "Hydrogen trapping can be represented as a reaction too. Here we consider mobile hydrogen ($\\mathrm{H}$) reacting with an empty trap ($[\\ ]$) to form trapped hydrogen ($\\mathrm{[H]}$):\n",
-    "\n",
-    "```{math}\n",
-    "\\ce{H + [ ] <-->[k][p] [H]}\n",
-    "```\n"
+    "\n"
    ]
   },
   {
@@ -884,18 +874,6 @@
     "\n",
     "Let's consider a trap with 3 occupancy levels. We have the following reaction scheme:\n",
     "\n",
-    "```{math}\n",
-    "\\ce{H + [ ] <-->[k][p] [1H]}\n",
-    "```\n",
-    "\n",
-    "```{math}\n",
-    "\\ce{H + [1H] <-->[k][p] [2H]}\n",
-    "```\n",
-    "\n",
-    "```{math}\n",
-    "\\ce{H + [2H] <-->[k][p] [3H]}\n",
-    "```\n",
-    "\n",
     "The underlying governing equations are:\n",
     "\n",
     "\\begin{align}\n",
@@ -1040,13 +1018,6 @@
     "\n",
     "Now we consider a unique trapping site that can react with two different mobile species H and D:\n",
     "\n",
-    "```{math}\n",
-    "\\ce{H + [\\ ] <-->[k][p] [H]}\n",
-    "```\n",
-    "\n",
-    "```{math}\n",
-    "\\ce{D + [\\ ] <-->[k][p] [D]}\n",
-    "```\n",
     "\n",
     "The governing equations for this problem are:\n",
     "\n",
@@ -1203,9 +1174,7 @@
     "\n",
     "``Reaction`` objects can have multiple products. This is useful to simulate things like isotope swapping where a mobile species reacts with a trapped species, and swap their positions:\n",
     "\n",
-    "```{math}\n",
-    "\\ce{H + [T] <-->[k_\\mathrm{swap}][k_\\mathrm{swap}] T + [H]}\n",
-    "```\n",
+    "\n",
     "\n",
     "In this example we consider the above reaction, with an initial condition for the trapped T concentration and mobile H diffusing in the domain, slowly swapping trapped T.\n",
     "\n",
@@ -1352,11 +1321,7 @@
    "cell_type": "markdown",
    "id": "e238c83e",
    "metadata": {},
-   "source": [
-    "```{math}\n",
-    "\\ce{A ->[\\lambda] \\emptyset}\n",
-    "```"
-   ]
+   "source": []
   },
   {
    "cell_type": "markdown",
@@ -1468,9 +1433,7 @@
     "\n",
     "Another use case of this type of reaction is metal interstitial atoms recombining with vacancies (both forming a Frenkel pair) and annihilate.\n",
     "\n",
-    "```{math}\n",
-    "\\ce{I + V ->[k] \\emptyset}\n",
-    "```\n",
+    "\n",
     "\n",
     "In this example, we define two mobile species I and V, both diffusing from one side of the 1D domain and annihilating."
    ]

book/intro.md

@@ -1,3 +1,25 @@
-# The FESTIM tutorial
+# FESTIM-workshop
 
-Welcome to the FESTIM tutorial!
+The FESTIM workshop is a tutorial covering many aspects of the hydrogen transport code FESTIM.
+Check out the [website](https://festim-workshop.readthedocs.io).
+
+## Launch in Binder
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/festim-dev/FESTIM-workshop/main)
+
+[Run this workshop](https://mybinder.org/v2/gh/festim-dev/FESTIM-workshop/main) in BinderHub
+
+## Local install
+
+1. Clone this repo
+
+```
+git clone https://github.com/festim-dev/FESTIM-workshop
+```
+2. Create Conda environment (requires conda)
+
+```
+conda env create -f environment.yml
+```
+
+3. You should then be able to execute the notebooks with the ``festim-workshop`` environment

book/myst.yml

@@ -0,0 +1,49 @@
+version: 1
+project:
+  title: FESTIM workshop
+  authors:
+    - name: The FESTIM community
+  github: festim-dev/FESTIM-workshop
+  thebe:
+    binder:
+      repo: festim-dev/FESTIM-workshop
+      provider: github
+      url: https://mybinder.org
+      ref: festim2
+  toc:
+    - file: intro.md
+    - title: Getting started
+      children:
+        - file: content/applications/task01.ipynb
+    - title: Meshing
+      children:
+        - file: content/meshes/mesh_festim.ipynb
+        - file: content/meshes/mesh_fenics.ipynb
+        - file: content/meshes/mesh_gmsh.ipynb
+        - file: content/meshes/mesh_salome.ipynb
+    - title: Materials
+      children:
+        - file: content/material/material_basics.md
+        - file: content/material/material_htm.md
+        - file: content/material/material_advanced.md
+    - title: Species & Reactions
+      children:
+        - file: content/species_reactions/species.ipynb
+        - file: content/species_reactions/reactions.ipynb
+        - file: content/species_reactions/surface_reactions.ipynb
+    - title: Applications
+      children:
+        - file: content/applications/task02.ipynb
+        - file: content/applications/task03.ipynb
+        - file: content/applications/task04.ipynb
+        - file: content/applications/task07.ipynb
+        - file: content/applications/task08.ipynb
+        - file: content/applications/task06.ipynb
+        - file: content/applications/task10.ipynb
+        - file: content/applications/microstructure.md
+site:
+  options:
+    logo: images/logo_light.png
+    logo_dark: images/logo_dark.svg
+    folders: true
+  template: "https://github.com/myst-templates/book-theme/archive/de4c1e9c09c6cd12fc529c1f22e8abf8e7f35381.zip"

environment.yml

@@ -1,11 +1,11 @@
-name: festim-workshop
+name: festim-workshop-jupyter2
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - jupyter-book
   - jupytext # necessary to open MyST files using BinderHub https://jupyterbook.org/en/stable/interactive/launchbuttons.html#launchbuttons-binder
   - sphinx-tags
+  - nodejs
   - matplotlib
   - meshio[all]
   - pip>=20.1
@@ -17,6 +17,8 @@ dependencies:
   - shapely
   - scipy
   - pip:
+    - "jupyter-book>=2.0.0a0"
+    - "--pre"
     - pyparsing
     - h-transport-materials==0.16
     - pyvista[all,trame]  # trame cannot be installed on conda