From bbbef6558a03d494174431a10bdcbcb9527b2ad2 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 2 Oct 2025 17:07:55 -0400
Subject: [PATCH 01/38] upgraded to jupyter 2, made myst.yml instead of toc and
 conf

---
 book/myst.yml   | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 environment.yml |  2 +-
 2 files changed, 49 insertions(+), 1 deletion(-)
 create mode 100644 book/myst.yml

diff --git a/book/myst.yml b/book/myst.yml
new file mode 100644
index 0000000..6f3e4a1
--- /dev/null
+++ b/book/myst.yml
@@ -0,0 +1,48 @@
+version: 1
+project:
+  title: FESTIM tutorial
+  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
+    folders: true
+  template: book-theme
diff --git a/environment.yml b/environment.yml
index 155b7b8..90498a9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - jupyter-book
+  - jupyter-book==2.*
   - jupytext # necessary to open MyST files using BinderHub https://jupyterbook.org/en/stable/interactive/launchbuttons.html#launchbuttons-binder
   - sphinx-tags
   - matplotlib

From b35cd29c95b6b1f304e30a512f3332fc5a35f018 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 2 Oct 2025 17:10:32 -0400
Subject: [PATCH 02/38] removed old .yml files

---
 book/_config.yml | 48 ------------------------------------------------
 book/_toc.yml    | 39 ---------------------------------------
 2 files changed, 87 deletions(-)
 delete mode 100644 book/_config.yml
 delete mode 100644 book/_toc.yml

diff --git a/book/_config.yml b/book/_config.yml
deleted file mode 100644
index 3224c33..0000000
--- a/book/_config.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-# Book settings
-# Learn more at https://jupyterbook.org/customize/config.html
-
-title: FESTIM tutorial
-author: The FESTIM community
-
-# Information about where the book exists on the web
-repository:
-  url: https://github.com/festim-dev/FESTIM-workshop  # Online location of your book
-  path_to_book: book  # Optional path to your book, relative to the repository root
-  branch: festim2  # Which branch of the repository should be used when creating links (optional)
-
-logo: images/logo_light.png
-
-# NOTE turning this OFF while we figure out how to not override the `html` options
-# sphinx:
-#   config:
-#     html_theme_options:
-#       logo:
-#         image_light: images/logo_light.png
-#         image_dark: images/logo_dark.svg
-
-# Add GitHub buttons to your book
-# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
-html:
-  use_issues_button: true
-  use_repository_button: true
-  use_edit_page_button: true
-  logo: true
-
-execute:
-  # Force re-execution of notebooks on each build.
-  # See https://jupyterbook.org/content/execute.html
-  execute_notebooks: force
-  timeout: -1  # Disable timeouts for executing notebooks cells
-  # allow_errors: true  # Allow errors in notebook cells
-
-parse:
-  myst_enable_extensions:
-    # don't forget to list any other extensions you want enabled,
-    # including those that are enabled by default!
-    - amsmath
-    - dollarmath
-
-launch_buttons:
-  notebook_interface: "jupyterlab"
-  binderhub_url: "https://mybinder.org"
-  thebe: true
\ No newline at end of file
diff --git a/book/_toc.yml b/book/_toc.yml
deleted file mode 100644
index 6cac4fa..0000000
--- a/book/_toc.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-# Table of contents
-# Learn more at https://jupyterbook.org/customize/toc.html
-
-format: jb-book
-root: intro
-parts:
-  - caption: Getting started
-    chapters:
-    - file: content/applications/task01
-
-  - caption: Meshing
-    chapters:
-    - file: content/meshes/mesh_festim
-    - file: content/meshes/mesh_fenics
-    - file: content/meshes/mesh_gmsh
-    - file: content/meshes/mesh_salome
-
-  - caption: Materials
-    chapters: 
-    - file: content/material/material_basics
-    - file: content/material/material_htm
-    - file: content/material/material_advanced
-
-  - caption: Species & Reactions
-    chapters:
-    - file: content/species_reactions/species
-    - file: content/species_reactions/reactions
-    - file: content/species_reactions/surface_reactions
-
-  - caption: Applications
-    chapters:
-    - file: content/applications/task02
-    - file: content/applications/task03
-    - file: content/applications/task04
-    - file: content/applications/task07
-    - file: content/applications/task08
-    - file: content/applications/task06
-    - file: content/applications/task10
-    - file: content/applications/microstructure
\ No newline at end of file

From 9bb112f063d9b06e0c3b5633da033e565d3f56e1 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 2 Oct 2025 17:25:10 -0400
Subject: [PATCH 03/38] moved jupy2 dependencies

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 90498a9..035e294 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - jupyter-book==2.*
   - jupytext # necessary to open MyST files using BinderHub https://jupyterbook.org/en/stable/interactive/launchbuttons.html#launchbuttons-binder
   - sphinx-tags
   - matplotlib
@@ -17,6 +16,7 @@ dependencies:
   - shapely
   - scipy
   - pip:
+    - jupyter-book==2.*
     - pyparsing
     - h-transport-materials==0.16
     - pyvista[all,trame]  # trame cannot be installed on conda
\ No newline at end of file

From 34c48e72118e6bcb782851974a787b28b6927cd2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Fri, 3 Oct 2025 11:39:05 -0400
Subject: [PATCH 04/38] pre release

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 035e294..037aa6e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,7 +16,7 @@ dependencies:
   - shapely
   - scipy
   - pip:
-    - jupyter-book==2.*
+    - jupyter-book==2.* --pre
     - pyparsing
     - h-transport-materials==0.16
     - pyvista[all,trame]  # trame cannot be installed on conda
\ No newline at end of file

From 6362a7029df092f61dcc667f9748f8bce9e8810d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Fri, 3 Oct 2025 11:44:12 -0400
Subject: [PATCH 05/38] quotes in pip command + dark logo

---
 book/myst.yml   | 1 +
 environment.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/book/myst.yml b/book/myst.yml
index 6f3e4a1..2c84806 100644
--- a/book/myst.yml
+++ b/book/myst.yml
@@ -44,5 +44,6 @@ project:
 site:
   options:
     logo: images/logo_light.png
+    logo_dark: images/logo_dark.svg
     folders: true
   template: book-theme
diff --git a/environment.yml b/environment.yml
index 037aa6e..1bce839 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,7 +16,7 @@ dependencies:
   - shapely
   - scipy
   - pip:
-    - jupyter-book==2.* --pre
+    - "--pre jupyter-book==2.*"
     - pyparsing
     - h-transport-materials==0.16
     - pyvista[all,trame]  # trame cannot be installed on conda
\ No newline at end of file

From 565b6ab9154a22bc366602214235ef7365a76505 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Fri, 3 Oct 2025 12:26:05 -0400
Subject: [PATCH 06/38] python command

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 04fa9f6..07d429f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -11,7 +11,7 @@ build:
   jobs:
     pre_build:
       # Generate the Sphinx configuration for this Jupyter Book so it builds.
-      - "jupyter-book config sphinx book/"
+      - "python -m jupyter-book config sphinx book/"
 
 conda:
   environment: environment.yml
@@ -19,4 +19,4 @@ conda:
 sphinx:
   builder: html
   fail_on_warning: true
-  configuration: book/_config.yml
\ No newline at end of file
+  configuration: book/_config.yml

From 2e61d17113e5f5a9577e72dd0dbb1cb609076ee6 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 3 Oct 2025 13:02:22 -0400
Subject: [PATCH 07/38] fixed install of jupyterbook2

---
 environment.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 1bce839..feecef9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: festim-workshop
+name: festim-workshop-jupyter2
 channels:
   - conda-forge
   - defaults
@@ -16,7 +16,8 @@ dependencies:
   - shapely
   - scipy
   - pip:
-    - "--pre jupyter-book==2.*"
+    - "jupyter-book>=2.0.0a0"
+    - "--pre"
     - pyparsing
     - h-transport-materials==0.16
     - pyvista[all,trame]  # trame cannot be installed on conda
\ No newline at end of file

From c1484494bf98c238bac0b87e3b9aad2f706857c6 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 3 Oct 2025 13:09:22 -0400
Subject: [PATCH 08/38] attempt to fix the build

---
 .readthedocs.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 07d429f..66a8a9b 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -8,15 +8,11 @@ build:
     - libglx-mesa0
     - libgl1
     - xvfb
-  jobs:
-    pre_build:
-      # Generate the Sphinx configuration for this Jupyter Book so it builds.
-      - "python -m jupyter-book config sphinx book/"
+  commands:
+  # this may need the --execute flag to run the notebooks
+    - cd book && jupyter book build --html
 
 conda:
   environment: environment.yml
 
-sphinx:
-  builder: html
-  fail_on_warning: true
-  configuration: book/_config.yml
+formats: []

From fced6af81009b264cf5df534fdec8c17241272c4 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 3 Oct 2025 13:10:47 -0400
Subject: [PATCH 09/38] post build

---
 .readthedocs.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 66a8a9b..c763ba4 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -8,9 +8,10 @@ build:
     - libglx-mesa0
     - libgl1
     - xvfb
-  commands:
-  # this may need the --execute flag to run the notebooks
-    - cd book && jupyter book build --html
+  jobs:
+    post_build:
+      # this may need the --execute flag to run the notebooks
+      - cd book && jupyter book build --html
 
 conda:
   environment: environment.yml

From 8890cbacff5e15ef925684283ba7ca688bd154d3 Mon Sep 17 00:00:00 2001
From: RemDelaporteMathurin <rdelaportemathurin@gmail.com>
Date: Fri, 3 Oct 2025 13:13:10 -0400
Subject: [PATCH 10/38] build and move html

---
 .readthedocs.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index c763ba4..8c9406a 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,5 +1,8 @@
 version: 2
 
+conda:
+  environment: environment.yml
+
 build:
   os: ubuntu-22.04
   tools:
@@ -12,8 +15,6 @@ build:
     post_build:
       # this may need the --execute flag to run the notebooks
       - cd book && jupyter book build --html
-
-conda:
-  environment: environment.yml
+      - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
 
 formats: []

From 657fc4b4883d2f38166e07a123e0614eb1be67d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Delaporte-Mathurin?=
 <40028739+RemDelaporteMathurin@users.noreply.github.com>
Date: Fri, 3 Oct 2025 21:09:31 -0400
Subject: [PATCH 11/38] override build

Co-authored-by: Matt Fisher <3608264+mfisher87@users.noreply.github.com>
---
 .readthedocs.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 8c9406a..8306025 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -12,9 +12,10 @@ build:
     - libgl1
     - xvfb
   jobs:
-    post_build:
-      # this may need the --execute flag to run the notebooks
-      - cd book && jupyter book build --html
-      - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
+    build:
+      html:
+        # this may need the --execute flag to run the notebooks
+        - cd book && jupyter book build --html
+        - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
 
 formats: []

From f9f55e6596dd3a26e4aae85d3e8b3546a5ca4894 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@mac.mynetworksettings.com>
Date: Mon, 6 Oct 2025 16:17:24 -0400
Subject: [PATCH 12/38] added hyphen

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 8306025..5fe29b1 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,7 +15,7 @@ build:
     build:
       html:
         # this may need the --execute flag to run the notebooks
-        - cd book && jupyter book build --html
+        - cd book && jupyter-book build --html
         - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
 
 formats: []

From 7edbec429176f9f497ab08930abfa73a806d7f05 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 13:51:37 -0400
Subject: [PATCH 13/38] overriding build and creating environment with command

---
 .readthedocs.yml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5fe29b1..1adab6c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,7 +1,7 @@
 version: 2
 
-conda:
-  environment: environment.yml
+# conda:
+#   environment: environment.yml
 
 build:
   os: ubuntu-22.04
@@ -11,11 +11,10 @@ build:
     - libglx-mesa0
     - libgl1
     - xvfb
-  jobs:
-    build:
-      html:
-        # this may need the --execute flag to run the notebooks
-        - cd book && jupyter-book build --html
-        - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
+  commands:
+    - conda env create --name festim-workshop-jupyter2 --file environment.yml
+    - conda activate festim-workshop-jupyter2
 
-formats: []
+    - cd book
+    - python -m jupyter_book build --html .
+    - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 3152e3231b8d9571dc1e3bc83265d43aa996c493 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 13:56:38 -0400
Subject: [PATCH 14/38] added conda init

---
 .readthedocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 1adab6c..3db91c4 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -13,6 +13,7 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
+    - conda init
     - conda activate festim-workshop-jupyter2
 
     - cd book

From 19093dee925b8cacbbf501a169319d8206854cfe Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 14:00:52 -0400
Subject: [PATCH 15/38] not using conda activate anymore

---
 .readthedocs.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 3db91c4..aa5ce76 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -13,9 +13,6 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - conda init
-    - conda activate festim-workshop-jupyter2
-
-    - cd book
-    - python -m jupyter_book build --html .
-    - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
+    - conda run -n festim-workshop-jupyter2 python -m jupyter_book build --html book
+    - mkdir -p $READTHEDOCS_OUTPUT/html
+    - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 3c0836c2803fa0e452bd021e68277e8b618555ca Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 14:06:50 -0400
Subject: [PATCH 16/38] added node.js to dependancies

---
 .readthedocs.yml | 4 +++-
 environment.yml  | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index aa5ce76..65aa317 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -8,11 +8,13 @@ build:
   tools:
     python: "miniconda-latest"
   apt_packages:
+    - nodejs
+    - npm
     - libglx-mesa0
     - libgl1
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - conda run -n festim-workshop-jupyter2 python -m jupyter_book build --html book
+    - conda run -n festim-workshop-jupyter2 python -m jupyter-book build --html book
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index feecef9..1e766f3 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,6 +5,7 @@ channels:
 dependencies:
   - 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

From 3be70ad726a3a1e2b4297bddbac8ffdde489bf9d Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 14:15:10 -0400
Subject: [PATCH 17/38] fixed hyphen?

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 65aa317..a140816 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,6 +15,6 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - conda run -n festim-workshop-jupyter2 python -m jupyter-book build --html book
+    - conda run -n festim-workshop-jupyter2 python -m jupyter_book build --html book
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 03323cbae1f72573bd3fa180c8844cdd7e52d1cb Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 14:24:47 -0400
Subject: [PATCH 18/38] updated syntax

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index a140816..2ff68ad 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,6 +15,6 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - conda run -n festim-workshop-jupyter2 python -m jupyter_book build --html book
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From cbf2b5afce9e13bdf56b067214e19ff46e3a3a14 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Wed, 8 Oct 2025 14:38:26 -0400
Subject: [PATCH 19/38] syntax update

---
 .readthedocs.yml | 3 ++-
 book/myst.yml    | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 2ff68ad..15a1b54 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,6 +15,7 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
+    - cd book
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book build
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
diff --git a/book/myst.yml b/book/myst.yml
index 2c84806..09fa9fe 100644
--- a/book/myst.yml
+++ b/book/myst.yml
@@ -8,7 +8,7 @@ project:
     binder:
       repo: festim-dev/FESTIM-workshop
       provider: github
-      url: https://mybinder.org
+      url: https://github.com/festim-dev/FESTIM-workshop
       ref: festim2
   toc:
     - file: intro.md

From 3d85caa713b1edf9ed79b180ebcc9a170c2faf87 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 15:44:19 -0400
Subject: [PATCH 20/38] added html to command line

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 15a1b54..c90047b 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,6 +16,6 @@ build:
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - cd book
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book build
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 96764d2fdad91acc58e592c809102c7bfa1bfaa7 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:02:59 -0400
Subject: [PATCH 21/38] fixing path location

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index c90047b..aff6c92 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -18,4 +18,4 @@ build:
     - cd book
     - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
     - mkdir -p $READTHEDOCS_OUTPUT/html
-    - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
+    - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From cda3f220ce35e62bd069af82e3f0e70f254d88b0 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:11:52 -0400
Subject: [PATCH 22/38] added init for jupy book

---
 .readthedocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index aff6c92..645d44d 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,6 +16,7 @@ build:
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - cd book
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book init
     - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From db86959f97272b9f65138dc4e466a386dc2d6e6e Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:16:27 -0400
Subject: [PATCH 23/38] changed init to start

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 645d44d..2044646 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,7 +16,7 @@ build:
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - cd book
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book init
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book start
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html --all
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 4d4a3d86ac2d667d2592ecc462e6cb24b9475090 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:27:55 -0400
Subject: [PATCH 24/38] listing folder to see what builds

---
 .readthedocs.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 2044646..ef425db 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,7 +16,8 @@ build:
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - cd book
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book start
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html --all
+    # - conda run -n festim-workshop-jupyter2 python -m jupyter book start
+    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
+    - !ls
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From f1ce3ade701d0cdf702db17e29b7e5368f9f7ec0 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:32:29 -0400
Subject: [PATCH 25/38] debugging fix

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index ef425db..201a77f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -18,6 +18,6 @@ build:
     - cd book
     # - conda run -n festim-workshop-jupyter2 python -m jupyter book start
     - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
-    - !ls
+    - ls -la
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 8f52c15c7a784dcce0f7f476b63222d681fb4456 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 16:44:23 -0400
Subject: [PATCH 26/38] bash command

---
 .readthedocs.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 201a77f..e3bb95d 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,9 +15,10 @@ build:
     - xvfb
   commands:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    - cd book
+    # - cd book
     # - conda run -n festim-workshop-jupyter2 python -m jupyter book start
-    - conda run -n festim-workshop-jupyter2 python -m jupyter book build --html
-    - ls -la
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book && python -m jupyter book build --html"
+    - ls
     - mkdir -p $READTHEDOCS_OUTPUT/html
+    - ls
     - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From 50d6728f5d84d6d3d2a9999f554aec258fb3c700 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 8 Oct 2025 17:10:51 -0400
Subject: [PATCH 27/38] removed markdown text in reactions.ipynb temporarily

---
 .../content/species_reactions/reactions.ipynb | 53 +++----------------
 1 file changed, 8 insertions(+), 45 deletions(-)

diff --git a/book/content/species_reactions/reactions.ipynb b/book/content/species_reactions/reactions.ipynb
index 0d9b934..da598c1 100644
--- a/book/content/species_reactions/reactions.ipynb
+++ b/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."
    ]

From f21337957a17d6df1c4b9c7d9d460f13bdac0d24 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 10:19:56 -0400
Subject: [PATCH 28/38] adding /book to path

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index e3bb95d..d00aa33 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -17,8 +17,8 @@ build:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     # - cd book
     # - conda run -n festim-workshop-jupyter2 python -m jupyter book start
-    - conda run -n festim-workshop-jupyter2 bash -c "cd book && python -m jupyter book build --html"
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book && HOST="127.0.0.1" python -m jupyter book build --html"
     - ls
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - ls
-    - cp -r _build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
+    - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file

From c0fb70c074b9dd1f455830000eee973ac420b607 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 11:05:57 -0400
Subject: [PATCH 29/38] trying example from jupy2 gh

---
 .readthedocs.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index d00aa33..ae46b76 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -7,18 +7,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "miniconda-latest"
+    nodejs: "20"
   apt_packages:
-    - nodejs
-    - npm
     - libglx-mesa0
     - libgl1
     - xvfb
   commands:
+    - npm install -g mystmd
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
-    # - cd book
-    # - conda run -n festim-workshop-jupyter2 python -m jupyter book start
-    - conda run -n festim-workshop-jupyter2 bash -c "cd book && HOST="127.0.0.1" python -m jupyter book build --html"
-    - ls
     - mkdir -p $READTHEDOCS_OUTPUT/html
-    - ls
-    - cp -r book/_build/html/* $READTHEDOCS_OUTPUT/html/
\ No newline at end of file
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html"
+    - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/_build
\ No newline at end of file

From 5f42702718a9bd2845c2a37a179015f49dc6d0c2 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 11:11:34 -0400
Subject: [PATCH 30/38] typo fix

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index ae46b76..04bd00f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -17,4 +17,4 @@ build:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/html
     - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html"
-    - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r docs/_build
\ No newline at end of file
+    - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build
\ No newline at end of file

From 577b3401e177960ebe232d91c68be1cf147a98b2 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 11:36:58 -0400
Subject: [PATCH 31/38] added keep-host

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 04bd00f..cf08245 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,5 +16,5 @@ build:
     - npm install -g mystmd
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/html
-    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html"
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html --keep-host"
     - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build
\ No newline at end of file

From 0a57eb39032e253537718437030c16cbcfef1439 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 11:54:34 -0400
Subject: [PATCH 32/38] not creating environment to test if host connects

---
 .readthedocs.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index cf08245..ad69bed 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -14,7 +14,8 @@ build:
     - xvfb
   commands:
     - npm install -g mystmd
-    - conda env create --name festim-workshop-jupyter2 --file environment.yml
+    # - pip install "jupyter-book>=2.0.0a0"
+    # - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/html
-    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html --keep-host"
+    - cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html
     - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build
\ No newline at end of file

From 85887e527d9e0f310fdf7a4848e91710c91b69cb Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 11:59:48 -0400
Subject: [PATCH 33/38] changing host location

---
 .readthedocs.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index ad69bed..18ce17c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -17,5 +17,6 @@ build:
     # - pip install "jupyter-book>=2.0.0a0"
     # - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/html
-    - cd book/ && BASE_URL="/$READTHEDOCS_LANGUAGE/$READTHEDOCS_VERSION" myst build --html
+    - ls
+    - cd book/ && BASE_URL="127.0.0.1" myst build --html
     - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build
\ No newline at end of file

From fc39efbd983980c14bdc7a6e39517473c305ac85 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 12:02:32 -0400
Subject: [PATCH 34/38] changing html to site

---
 .readthedocs.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 18ce17c..731327d 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,7 +16,7 @@ build:
     - 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/html
+    - mkdir -p $READTHEDOCS_OUTPUT/site
     - ls
-    - cd book/ && BASE_URL="127.0.0.1" myst build --html
-    - cp -a book/_build/html/. "$READTHEDOCS_OUTPUT/html" && rm -r book/_build
\ No newline at end of file
+    - cd book/ && BASE_URL="127.0.0.1" myst build --site
+    - cp -a book/_build/site/. "$READTHEDOCS_OUTPUT/site" && rm -r book/_build
\ No newline at end of file

From 35b1fc700d7671bef5dc319949e80a3e99957e3e Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 12:04:39 -0400
Subject: [PATCH 35/38] adding back env

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 731327d..cb1c1bc 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,8 +15,8 @@ build:
   commands:
     - npm install -g mystmd
     # - pip install "jupyter-book>=2.0.0a0"
-    # - conda env create --name festim-workshop-jupyter2 --file environment.yml
+    - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/site
     - ls
-    - cd book/ && BASE_URL="127.0.0.1" myst build --site
+    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="127.0.0.1" myst build --site"
     - cp -a book/_build/site/. "$READTHEDOCS_OUTPUT/site" && rm -r book/_build
\ No newline at end of file

From 700d407ca27e70fced97966180f9c157f4adfd56 Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Thu, 9 Oct 2025 12:15:58 -0400
Subject: [PATCH 36/38] change host location before running commands

---
 .readthedocs.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index cb1c1bc..b5b592e 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -18,5 +18,7 @@ build:
     - conda env create --name festim-workshop-jupyter2 --file environment.yml
     - mkdir -p $READTHEDOCS_OUTPUT/site
     - ls
-    - conda run -n festim-workshop-jupyter2 bash -c "cd book/ && BASE_URL="127.0.0.1" myst build --site"
-    - cp -a book/_build/site/. "$READTHEDOCS_OUTPUT/site" && rm -r book/_build
\ No newline at end of file
+    - 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
\ No newline at end of file

From 29c2de8ec1c53db31065ab9e10b388c17dcef81e Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@Lap-khurana.local>
Date: Tue, 14 Oct 2025 16:58:54 -0400
Subject: [PATCH 37/38] changed template

---
 book/myst.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/book/myst.yml b/book/myst.yml
index 09fa9fe..b64529a 100644
--- a/book/myst.yml
+++ b/book/myst.yml
@@ -46,4 +46,4 @@ site:
     logo: images/logo_light.png
     logo_dark: images/logo_dark.svg
     folders: true
-  template: book-theme
+  template: "https://github.com/myst-templates/book-theme/archive/de4c1e9c09c6cd12fc529c1f22e8abf8e7f35381.zip"

From ba867e18e53d0d40175588ddc59c1eddb5b3798e Mon Sep 17 00:00:00 2001
From: ckhurana <ckhurana@lap-khurana.psfc.mit.edu>
Date: Wed, 15 Oct 2025 16:18:46 -0400
Subject: [PATCH 38/38] changed binder url

---
 book/intro.md | 26 ++++++++++++++++++++++++--
 book/myst.yml |  4 ++--
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/book/intro.md b/book/intro.md
index 119f518..19b44f3 100644
--- a/book/intro.md
+++ b/book/intro.md
@@ -1,3 +1,25 @@
-# The FESTIM tutorial
+# FESTIM-workshop
 
-Welcome to the FESTIM tutorial!
\ No newline at end of file
+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
\ No newline at end of file
diff --git a/book/myst.yml b/book/myst.yml
index b64529a..360ed6f 100644
--- a/book/myst.yml
+++ b/book/myst.yml
@@ -1,6 +1,6 @@
 version: 1
 project:
-  title: FESTIM tutorial
+  title: FESTIM workshop
   authors:
     - name: The FESTIM community
   github: festim-dev/FESTIM-workshop
@@ -8,7 +8,7 @@ project:
     binder:
       repo: festim-dev/FESTIM-workshop
       provider: github
-      url: https://github.com/festim-dev/FESTIM-workshop
+      url: https://mybinder.org
       ref: festim2
   toc:
     - file: intro.md