Catalysis tutorial fixes (#1674)

* small fix to toc and mermaid config (for diagram)

* fixes to the NEB section

* add google colab option

* more small fixes

* update apt first

* typo

* more small fixes to the NEB initial guess and optimization

---------

Co-authored-by: Muhammed Shuaibi <45150244+mshuaibii@users.noreply.github.com>

Author: zulissimeta

.github/workflows/build_docs.yml

@@ -45,8 +45,8 @@ jobs:
       with:
           status-context: '${{ github.job }}'
 
-    - name: Install pandoc
-      run: sudo apt-get -y install pandoc
+    - name: Install pandoc and ffmpeg
+      run: sudo apt-get update && sudo apt-get -y install pandoc ffmpeg
 
     # Install dependencies
     - name: Set up Python
@@ -73,7 +73,7 @@ jobs:
         FAST_DOCS: ${{ (github.event_name != 'push' || github.ref != 'refs/heads/main') && 'true' || '' }}
       run: |
         # Convert MyST markdown files to Jupyter notebooks if needed to get download as ipynb buttons
-        jupytext --to ipynb ./docs/uma_tutorials/uma_tutorial.md
+        jupytext --to ipynb ./docs/uma_tutorials/*.md
         # find ./docs/ -name "*.md" -exec grep -q "format_name: myst" {} \; -print0 | xargs -0 jupytext --to ipynb
         jupyter-book build docs
 

docs/_config.yml

@@ -13,7 +13,7 @@ copyright                   : "Meta Platforms, Inc"  # Copyright year to be plac
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: force
+  execute_notebooks: cache
   timeout: 14400
   allow_errors: false
 
@@ -22,6 +22,9 @@ latex:
   latex_documents:
     targetname: fairchem.tex
 
+launch_buttons:
+  colab_url: "https://colab.research.google.com"
+
 # Add a bibtex file so that we can create citations
 bibtex_bibfiles:
   - references.bib
@@ -49,6 +52,7 @@ sphinx:
   extra_extensions:
   - 'sphinx.ext.napoleon'
   - 'autoapi.extension'
+  - 'sphinxcontrib.mermaid'
   config:
     autosummary_generate: True
     autoapi_dirs: ['../src/fairchem/core','../src/fairchem/data','../src/fairchem/applications/AdsorbML/adsorbml','../src/fairchem/applications/cattsunami','../src/fairchem/demo/ocpapi']

docs/_toc.yml

@@ -27,9 +27,8 @@ parts:
   - file: uma_tutorials/summary
     sections:
     - file: uma_tutorials/uma_tutorial
-    - file: core/uma_examples/uma_catalysis_tutorial
+    - file: uma_tutorials/uma_catalysis_tutorial
   - file: core/generative_models
-
 - caption: Molecules & Molecular Crystals
   chapters:
   - file: molecules/datasets/summary