Tutorial
Install Git, Bash Shell, Python
Authors: Materials adapted from Data Carpentry by NEON staff
Last Updated: Apr 9, 2021
This page outlines the tools and resources that you will need to install Git, Bash and Python applications onto your computer as the first step of our Python skills tutorial series.
Checklist
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
- Download the Git for Windows installer.
- Run the installer and follow the steps bellow:
- Welcome to the Git Setup Wizard: Click on "Next".
- Information: Click on "Next".
- Select Destination Location: Click on "Next".
- Select Components: Click on "Next".
- Select Start Menu Folder: Click on "Next".
- 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.
- Configuring the line ending conversions: Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
- Configuring the terminal emulator to use with Git Bash: Select "Use Windows' default console window" and click on "Next".
- Configuring experimental performance tweaks: Click on "Next".
- 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.
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 3.7 (at the time of writing, the gdal
package 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 3.7 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 (3.7). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
Mac OS X
Download and install Anaconda. Download the Python 3.x installer, choosing either the graphical installer or the command-line installer (3.7). 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 Anaconda3-2020.11-MacOSX-x86_64.sh
(or whatever you file name is)
Linux
Download and install 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 and navigate to your downloads folder. Type
bash Anaconda3-2020.11-Linux-ppc64le.sh
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
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 3.7 environment by opening Windows Command Prompt and typing
conda create –n py37 python=3.7 anaconda
When prompted, activate the py37 environment in Command Prompt by typing
activate py37
You should see (py37) 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
Note: You may need to only install gdal as the others may be included in the default.
Mac OS X
Create a new Python 3.7 environment by opening Terminal and typing
conda create –n py37 python=3.7 anaconda
This may take a minute or two.
When prompted, activate the py37 environment in Command Prompt by typing
source activate py37
You should see (py37) 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
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
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 by using the prompts
# check what version of Python you are using.
import sys
sys.version
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
- Setting up the Python Environment section from the Python Bootcamp
- Conda Help: setting up an environment
- iPython documentation: Kernals