Draft: Organise notebooks into website content

_config.yml

@@ -7,8 +7,28 @@ author: The Python in Chemistry Community
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
+only_build_toc_files: true
 execute:
   execute_notebooks: force
+  allow_errors: true
+
+launch_buttons:
+  notebook_interface: classic
+  binderhub_url: "https://mybinder.org"
+  colab_url: "https://colab.research.google.com"
+
+parse:
+  myst_enable_extensions:
+    - colon_fence
+    # - deflist
+    - dollarmath
+    # - html_admonition
+    - html_image
+    - linkify
+    # - replacements
+    # - smartquotes
+    - substitution
+    - tasklist
 
 # Define the name of the latex output file for PDF builds
 latex:
@@ -42,4 +62,4 @@ sphinx:
     html_theme_options: 
       logo:
         image_light: ./logo/logo-light.png
-        image_dark: ./logo/logo-dark.png
+        image_dark: ./logo/logo-dark.png

_toc.yml

@@ -10,6 +10,32 @@ parts:
       sections:
       - file: lessons/basics/write_run_python.md
       - file: lessons/basics/notebook.md
+    - file: lessons/manipulating_variables.md
+      sections:
+      - file: lessons/variables/Variable_data_types.ipynb
+      - file: lessons/variables/mathematical-operators.ipynb
+      - file: lessons/variables/Conditions.ipynb
+    - file: lessons/organising_code.md
+      sections:
+      - file: lessons/loops_functions/For_Loop_Lesson.ipynb
+      - file: lessons/loops_functions/PyinC_while_loops_WIP.ipynb
+      - file: lessons/loops_functions/functions_and_scope.ipynb
+    - file: lessons/files.md
+      sections:
+      - file: lessons/files/reading_files.ipynb
+      - file: lessons/files/writing_files.ipynb
+    - file: lessons/common_libraries.md
+      sections:
+      - file: lessons/common_libs/python-in-chem_pyplot_basics_SM.ipynb
+      - file: lessons/common_libs/Matplotlib_Documentation.ipynb
+      - file: lessons/common_libs/Introduction_to_NumPy.ipynb
+      - file: lessons/common_libs/NumPy_axes_operations.ipynb
+      - file: lessons/common_libs/intro_to_pandas.ipynb
+    - file: lessons/advanced_libraries.md
+      sections:
+      - file: lessons/advanced_libs/Intro_to_ASE.ipynb
+      - file: lessons/advanced_libs/PiC_scipy.ipynb
+      - file: lessons/advanced_libs/RDKit_drawing.ipynb
   - caption: Teaching Python in Chemistry Meeting Blogs
     chapters:
     - file: 2025-meeting

lessons/advanced_libraries.md

@@ -0,0 +1,3 @@
+# Advanced Libraries
+
+This section gives a quick introduction to a few chemistry-specific libraries.

lessons/advanced_libs/Asprin.mol

@@ -0,0 +1,47 @@
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+  -OEChem-04102511032D
+
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+M  END