Install Git, Bash Shell, Python

Authors: 
Materials adapted from Data Carpentry by NEON staff
Table of Contents

This page outlines the tools and resources that you will need to complete the Data Institute activities. Please be sure to have the laptop you will be bringing to the Institute setup by 2 June 2017 to ensure you are prepared to begin the pre-Institute materials.

Checklist

This checklist includes the tools that need to be set-up on your computer for the Institute. Detailed directions to accomplish each objective are below.

  • Install Bash shell (or shell of preference)
  • Install Git
  • Install Python 3.x

Bash/Shell Setup

Install Bash for Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Welcome to the Git Setup Wizard: Click on "Next".
    2. Information: Click on "Next".
    3. Select Destination Location: Click on "Next".
    4. Select Components: Click on "Next".
    5. Select Start Menu Folder: Click on "Next".
    6. Adjusting your PATH environment: Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the event will not work properly. If this happens rerun the installer and select the appropriate option.
    7. Configuring the line ending conversions: Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Configuring the terminal emulator to use with Git Bash: Select "Use Windows' default console window" and click on "Next".
    9. Configuring experimental performance tweaks: Click on "Next".
    10. Completing the Git Setup Wizard: Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

Install Bash for Mac OS X

The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Install Bash for Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git Setup

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on GitHub. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Git installation instructions borrowed and modified from Software Carpentry.

Git for Windows

Git should be installed on your computer as part of your Bash install.

Git on Mac OS X

Video Tutorial

Install Git on Macs by downloading and running the most recent installer for "mavericks" if you are using OS X 10.9 and higher -or- if using an earlier OS X, choose the most recent "snow leopard" installer, from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program.

Data Tip: If you are running Mac OSX El Capitan, you might encounter errors when trying to use git. Make sure you update XCODE. Read more - a Stack Overflow Issue.

Git on Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Setting Up Python

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

Regardless of how you choose to install it, **please make sure your environment is set up with Python version 3.4 (at the time of writing, gdal did not work with the newest Python version 3.6). Python 2.x is quite different from Python 3.x so you do need to install 3.x and set up with the 3.4 environment.

We will teach using Python in the Jupyter Notebook environment, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not). You can choose to not use notebooks in the course, however, we do recommend you download and install the library so that you can explore this tool.

Windows

Download and install Anaconda. Download the default Python 3 installer (3.6 -- and yes you can later set up the 3.4 environment from this). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Download and install Anaconda from Continuum. Download the Python 3.x installer, choosing either the graphical installer or the command-line installer (3.6 -- and yes you can later set up the 3.4 environment from this). For the graphical installer, use all of the defaults for installation. For the command-line installer open Terminal, navigate to the directory with the download then enter:

bash Anaconda3-4.3.1-MacOSX-x86_64.sh

Linux

We recommend the all-in-one scientific Python installer Anaconda. Download the installer that matches your operating system and save it in your home folder. Download the default Python 3 installer.

Open a terminal window. Type

bash Anaconda-

and then press tab. The name of the file you just downloaded should appear.

Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Install Python packages

We need to install several packages to the Python environment to be able to work with the remote sensing data

  • gdal
  • h5py
  • matlabpy

If you are new to working with command line you may wish to complete the next setup instructions which provides and intro to command line (bash) prior to completing these package installation instructions.

Windows

Create a new Python 3.4 environment by opening Windows Command Prompt and typing

conda create –n p34 python=3.4 anaconda

When prompted, activate the py34 environment in Command Prompt by typing

activate py34

You should see (py34) at the beginning of the command line. You can also test that you are using the correct version by typing python --version.

Install Python package(s):

  • gdal: conda install gdal
  • h5py: conda install h5py
  • matplotlib: conda install matplotlib

Note: You may need to only install gdal as the others may be included in the default.

Mac OS X

Create a new Python 3.4 environment by opening Terminal and typing

conda create –n p34 python=3.4 anaconda

When prompted, activate the py34 environment in Command Prompt by typing

source activate py34

You should see (py34) at the beginning of the command line. You can also test that you are using the correct version by typing python --version.

Install Python package(s):

  • gdal: conda install gdal
  • h5py: conda install h5py
  • matplotlib: conda install matplotlib

Linux

Open default terminal application (on Ubuntu that will be gnome-terminal).

Launch Python.

Install Python package(s):

  • gdal: conda install gdal
  • h5py: conda install h5py
  • matplotlib: conda install matplotlib

Set up Jupyter Notebook Environment

In your terminal application, navigate to the directory (cd) that where you want the Jupyter Notebooks to be saved (or where they already exist).

Open Jupyter Notebook with

jupyter notebook

Once the notebook is open, check which version of Python you are in.

Check which Python environment is running. Source: National Ecological Observatory Network (NEON)

You should now be able to work in the notebook.

The gdal package that occasionally has problems with some versions of Python. Therefore test out loading it using

import gdal.

Additional Resources

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