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earth-chris / elapid-wrapper

Convenience functions to support species distribution modeling, including a python wrapper for MaxEnt
MIT License
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elapid

the amazon

Convenience functions and scripts for species distribution modeling (SDM) in python. This includes a MaxEnt wrapper and tools for working with GBIF- and MaxEnt-format datasets.

The name was chosen as homage to the paper by H.A. Nix, A Biogeographic Analysis of Australian Elapid Snakes (1986), which is widely credited with defining the essential bioclimatic variables to use in species distribution modeling. It's also a snake pun (a python wrapper for mapping snake biogeography).

Dependencies

The source repository contains a conda environment with the packages required to run this software. If you want to install it on your own machine, there are three external dependencies you'll need to setup.

gdal is notoriously difficult to install and work with, and is beyond the scope of this readme. openjdk installs java, which is used to run the Maxent software. This can be installed on linux via:

sudo apt-get install openjdk-11-jre

It can also be installed install via conda.

conda install openjdk

Installation

pip install elapid should do the trick.

via conda

git clone https://github.com/earth-chris/elapid.git
cd elapid/
conda env update

Then you should have a conda environment you can actiave with conda activate elapid. You can then e.g. run the executable vector-to-maxent -h, or import elapid in python from this environment.

If you're interested in using the default ipython profile, you can set an environment variable to do this for you. From the base repository directory, run the following:

conda env config vars set IPYTHONDIR=$PWD/ipython

You'll have to run conda deactivate then conda activate elapid for the changes to take effect. After that you'll be able to run ipython with our default settings.

License

The Maxent software is bundled and served with this package, and is available under an MIT license. You can read more about the Maxent software here.

This source code is likewise available under MIT license.

Contributing

External contribution guidelines are not formally supported at this time--reach out to the package developers to facilitate contributions.

The elapid conda environment contains code formatting libraries, including black, flake8, isort and pytest. These tools are automatically applied to all code commits via the pre-commit library. To install pre-commit, run the following command:

pre-commit install

pre-commit behavior is defined in .pre-commit-config.yaml, specifying how to format the code, and cleaning up any formatting issues prior to accepting any commit. This should ensure that all pull requests are well-formatted.

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