Modelling biological diversity in a geological context

This repository contains a collection of Jupyter notebooks to introduce AdaScape, a coupled adaptive speciation with a landscape evolution model built into the FastScape Framework. This short course was part of the CRC 1211 Training Week 2022 and San Pedro de Atacama field school. This introduction builds on a previous short course on the landscape evolution modelling framework FastScape for the CRC-1211 taught by Jean Braun with the help of Benoît Bovy.

• How to run the notebooks?
  • Run in the cloud (Binder)
  • Install and run locally (Conda)

How to run the notebooks?

Run in the cloud (Binder)

You can run the notebooks in your browser without installing anything thanks to binder. Just follow the link below or click on the "launch binder" badge above and it will launch remotely a new notebook server for you:

• Run on binder

This service is for demo purposes only, do not rely on it for doing more serious work.

Install and run locally (Conda)

Assuming that you have git and conda installed, you can install all the packages required to run the notebooks in a new conda environment using the following commands:

$ git clone https://github.com/EstebanAce/adascape-intro
$ cd adascape-intro
$ conda env create -f environment.yml
$ conda activate adascape-intro

Note: you could use mamba instead of conda. mamba is a faster alternative to conda.

Note: If you have a new Mac with an M1 processor. FastScape has not been ported to this architecture yet. So you will need to install the intel version. This means that you need to install the intel version of all other necessary packages in your environment. For this, you need to change the command:

$ conda env create -f environment.yml

to:

$ CONDA_SUBDIR=osx-64 conda env create -f environment.yml

Finally, run the command below to start the Jupyterlab application. It should open a new tab in your browser.

$ jupyter lab

How to contribute?

Your contribution is welcome! You can do so by reporting issues, suggesting new notebook examples or improvements to the current examples.

A few extra steps are required to prepare your contributions. You can first update the conda environment using the following command:

$ conda env update -n adascape-intro --file environment-dev.yml 

This installs a few additional packages like pre-commit, which is used to ensure that all notebook cell outputs are cleared before adding or updating notebooks in this git repository. Run the command below to enable pre-commit (you only need to do this once):

$ pre-commit install

The script below is useful if you want to ensure that all notebooks are running without error:

$ python execute_all_notebooks.py

This script (as well as a script to build the Docker image) is run each time you open or update a pull-request on GitHub.