Create the jupyter notebook for the examples

aguspesce commented 2 years ago

I'm making a Jupyter notebook for each of the examples. Each notebook generates the input files, gives instructions to run the model using Mandyoc, and plots the results.

I am taking into account the comments of the reviewer:

[x] Please consider merging README markdown files and PYTHON scripts into a Jupyter notebook. They are easier to read, especially on GitHub. You can also take the user through the step of installing the required Python dependencies...
[x] - Please don't expect user to have PETSc installed in their HOME directory as default...
[x] - Jupyter notebooks would also help to visualize the outcome of the models / Benchmarks. As it is now, users must run the model themselves to see the result and they don't have a mean of comparison. That is also where you should compare with other codes (I2VES, UNDERWORLD, STAGYY)

addresses #47

aguspesce commented 2 years ago

@jamisonassuncao, @victorsacek, @rafaelmds, I've finished passing all the script in a Jupyter notebook. Can you give them a reviewer?