Python for Ecologists: Setup

Data

Data for this lesson is from the Portal Project Teaching Database - available on FigShare.

We will use the eight files listed below for the data in this lesson. Download these files to your computer either by clicking this link , which will give you everything in a single compressed file. You’ll need to unzip this file after downloading it.

Or download each file indvidually with the following links:

Software

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

For this workshop we use Python version 3.x.

Required Python Packages for this workshop

Install the workshop packages

For installing these packages we will use Anaconda or Miniconda. They both use Conda, the main difference is that Anaconda comes with a lot of packages pre-installed. With Miniconda you will need to install the required packages.

Anaconda installation

Anaconda will install the workshop packages for you.

Download and install Anaconda

Download and install Anaconda. Remember to download and install the installer for Python 3.x.

Download plotting package

The plotting package plotnine is not installed by default. From the terminal, type:

conda install -c conda-forge plotnine

Miniconda installation

Miniconda is a “light” version of Anaconda. If you install and use Miniconda you will also need to install the workshop packages.

Download and install Miniconda

Download and install Miniconda following the instructions. Remember to download and run the installer for Python 3.x.

Check the installation of Miniconda

From the terminal, type:

conda list

Install the required workshop packages with conda

From the terminal, type:

conda install -y numpy pandas matplotlib jupyter
conda install -c conda-forge plotnine

Launch a Jupyter notebook

After installing either Anaconda or Miniconda and the workshop packages, launch a Jupyter notebook by typing this command from the terminal:

jupyter notebook

The notebook should open automatically in your browser. If it does not or you wish to use a different browser, open this link: http://localhost:8888.

For a bried introduction to Jupyter Notebooks, please consult with our Introduction to Jupyter Notebooks page.