Draft: Organise notebooks into website content

_config.yml

@@ -7,9 +7,15 @@ 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
 
+launch_buttons:
+  notebook_interface: classic
+  binderhub_url: "https://mybinder.org"
+  colab_url: "https://colab.research.google.com"
+
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:
@@ -42,4 +48,4 @@ 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 @@
+2244
+  -OEChem-04102511032D
+
+ 21 21  0     0  0  0  0  0  0999 V2000
+    3.7320   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8660   -1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8660   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0000   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.0611   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.8671   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.8671   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3100    0.4769    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4631    0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6900   -0.5969    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  5  1  0  0  0  0
+  1 12  1  0  0  0  0
+  2 11  1  0  0  0  0
+  2 21  1  0  0  0  0
+  3 11  2  0  0  0  0
+  4 12  2  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  2  0  0  0  0
+  6  8  2  0  0  0  0
+  6 11  1  0  0  0  0
+  7  9  1  0  0  0  0
+  7 14  1  0  0  0  0
+  8 10  1  0  0  0  0
+  8 15  1  0  0  0  0
+  9 10  2  0  0  0  0
+  9 16  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 18  1  0  0  0  0
+ 13 19  1  0  0  0  0
+ 13 20  1  0  0  0  0
+M  END