Create Jupyter Book

[rabernat]

This is a first pass at creating the actual jupyter book out of these notebooks.

Assembling everything together in this way reveals a great deal of inconsistency in how we have organized and structured this materials. Here is the full list of notebooks

./01Intro/L96-description.ipynb
./01Intro/L96-two-scale-description.ipynb
./01Intro/gcm-analog-demo.ipynb
./01Intro/slides/presentation-model-setup.ipynb
./02type-of-parametrization/estimating-gcm-parameters.ipynb
./02type-of-parametrization/gcm-parameterization-problem.ipynb
./03Data-Assimilation/DA_demo_L96.ipynb
./04Subgrid-parametrization-pytorch/Neural_network_for_Lorenz96.ipynb
./04Subgrid-parametrization-pytorch/gradient_decent.ipynb
./05Offline-DA-increments/DA_demo_repeat.ipynb
./05Offline-DA-increments/Figure-for-DA.ipynb
./05Offline-DA-increments/Learning-DA-increments.ipynb
./06Different-ML-models/random_forest_parameterization.ipynb
./07-Interpretability-of-ML/LRP-L96.ipynb
./08-Implementation/Neural Network Advection FwdEuler.ipynb
./08-Implementation/Neural Network Advection.ipynb

and python files

./01Intro/L96_model.py
./02type-of-parametrization/L96_model.py
./03Data-Assimilation/DA_methods.py
./03Data-Assimilation/L96_model.py
./04Subgrid-parametrization-pytorch/L96_model_XYtend.py
./05Offline-DA-increments/DA_methods.py
./05Offline-DA-increments/L96_model.py
./06Different-ML-models/L96_model.py
./06Different-ML-models/L96_model_XYtend.py
./07-Interpretability-of-ML/L96_model_XYtend.py
./07-Interpretability-of-ML/LRP_gradient.py
./08-Implementation/L96_model_XYtend.py

Some large-scale issues that need to be addressed

• Why are there multiple notebooks per topic? How are the sub notebooks within each topic related? How do they flow together
• Each notebook needs to use the same style and organization, including a single top level header (e.g. # Main Title) and appropriate sub-headers
• Jupyter Book is intended to share notebook content. So how do we handle the '.py' files? Are they just copied from one folder to another? Maybe we need to turn them into an actual standalone package. Ideally we would put as much content as possible into the notebooks themselves.
• Jupyter Book supports references. We need to update our notebooks to use references properly.
• There are many formatting problems in the notebooks, particularly around equations.

Resolving these issues will be lots of work.