Topic 1 — Getting set up
Contents
Because our ultimate goal is for you to continue using computational skills beyond this course, we are not going to force you to use a ``pre-cooked’’ computer environment in the form of a container or virtual machine. Rather, we are going to help you to establish an environment in which you are comfortable working. The tools you will need installed on your computer for this class are:
- Unix-like shell (e.g., Bash)
- Git
- Python (Version 3)
- A text editor
Below we provide some resources and recommendations for installing these tools on Windows, MacOSX, and Linux. However, you are certainly free to explore other configurations.
Unix-like shell
Windows
If you are using Windows, you have several options for installing a Unix-like shell. Below, we provide information on three options. The first two options essentially install a full working version of the Linux operating system. The last option installs Git BASH, a Bash emulator within Windows.
NOTE: The option you choose will affect how you will install Git, Python, and a text editor below:
- Subsystem or virtual machine: Install Git, Python, and text editor within the Linux environment.
- Git BASH:, You already have Git. Install Python so that it is “visible” to Git BASH (see below). If you choose to install a text editor, do so within Windows.
Windows Subsystem for Linux (WSL)
If you are using Windows 10, you have the option of installing a Linux subsystem. If you go this route, I recommend you install the Ubuntu distribution of Linux. Here are links to instructions from Ubuntu and Microsoft:
Linux virtual machine
Using VirtualBox you can install a Linux virtual machine for free. Click here for instructions on how to do so. If you choose this route, I recommend you install the most recent version of Ubuntu Desktop.
Git BASH
If you don’t want to install a Linux subsystem or virtual machine, another option is to install a terminal emulator within Windows.
If you want to go this route, I recommend you install Git for Windows, and follow these instructions from the Software Carpentries.
After installing Git for Windows, you will use the Git BASH tool to access a Bash-like command-line terminal.
Mac
Just launch the Terminal application, which should be located in
/Applications/Utilities.
Linux
Just launch the Terminal application.
Git
Windows
If you installed Git for Windows, you already have Git available in Git BASH.
If you installed the Linux subsystem or virtual machine, boot your Linux environment and follow the instructions for Linux below.
Mac
If you are using MacOSX, you have two options for getting Git:
- Install Xcode from the App Store, OR
- Go to git-scm.com and download and run the installer for your version of MacOSX.
Linux
You might already have Git. At the command line, try:
git --version
If you get a command not found error, use your Linux distribution’s package
manager to install Git.
If you are using a Debian derivative of Linux (e.g., Ubuntu), you can
get Git by typing the following at the command line:
sudo apt-get install git
Python
For this class, I recommend you install Version 3 of Python via Anaconda or its smaller cousin, miniconda.
Anaconda installs Python and a bunch of popular Python packages, many of which you will probably never use. Miniconda is the same as Anaconda, but without all the extra packages (and it’s easy to install the packages you do need).
Either is fine, but I recommend Miniconda, because it will install much faster and take up less disk space.
Windows
If you installed the Linux subsystem or virtual machine, boot your Linux environment and follow the instructions for Linux below.
If you installed Git for Windows,.
follow these instructions from the Software Carpentries
to install Anaconda or miniconda.
The most important part of these instructions is to make sure to check Add
Anaconda to my PATH environment variable during the install;
this will make Python “visible” to Git BASH.
NOTE: The instructions on the Software Carpentries website are for
Anaconda, but should also work for miniconda.
After miniconda is installed, I highly recommend that you install the
conda-bash-completion package that allows you to use tab completion when
typing conda commands. You can do so by typing the following at the Git BASH
command line:
conda install -c conda-forge conda-bash-completion
Mac
Go here and download the MacOSX installer for Python 3.
If you download Miniconda3 MacOSX 64-bit pkg, then double click the download
and install it like other software (you can accept all the default setting
during the installation).
If you download Miniconda3 MacOSX 64-bit bash,
then follow along with the Linux instructions to install it below; the
only difference is that the first command will be
bash Miniconda3-latest-MacOSX-x86_64.sh.
Either way, after it’s installed, I highly recommend that you install the
conda-bash-completion package that allows you to use tab completion when
typing conda commands. You can do so by typing the following at the command
line (i.e., Terminal):
conda install -c conda-forge conda-bash-completion
Linux
Download the miniconda installation script with the following command:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
After this command finishes, you should be able to type:
ls
and see Miniconda3-latest-Linux-x86_64.sh listed.
This is a shell script that will install miniconda.
To install it, run:
bash Miniconda3-latest-Linux-x86_64.sh
You should see a prompt that looks something like:
Welcome to Miniconda3 4.8.2
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
Hit enter, then scroll down using the space bar or enter key until you see the following prompt:
Do you accept the license terms? [yes|no]
[no] >>>
Type “yes” and hit enter. Then, you will be prompted to choose the lcoation of the installation:
Miniconda3 will now be installed into this location:
/home/jamie/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/jamie/miniconda3] >>>
Simply hit enter to accept the default install location. After a while (and lots of output), you should see the following prompt:
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>>
Type “yes” and hit enter. This will add some code to your .bashrc file
that will make using conda simpler.
If all goes well, you should see:
Thank you for installing Miniconda3!
at the bottom of the output.
Next, close your terminal window and open a new one.
Then, update conda by running:
conda update conda
If there are updates available for conda you will be prompted with:
Proceed ([y]/n)? y
Type “y” (for yes) and hit enter to finish the update.
Lastly, I highly recommend that you install the conda-bash-completion
package that allows you to use tab completion when typing conda commands:
conda install -c conda-forge conda-bash-completion
Text editor
Most Unix-like shells already have text editors available that you can use
right in the command line, like nano and vim.
If you are comfortable using one of these, then there’s no need to install a
text editor.
However, some people prefer a text editor with a graphical user interface (GUI)
and some extra bells and whistles.
Text editors with a lot of bells and whistles are often called
an integrative design environment (IDE).
Here are some popular and free options for text editors/IDEs, in no particular
order:
Python-specific IDEs
Windows
If you are using Git for Windows (Git BASH), you already have nano available
in Git BASH.
If you want to install a fancier text editor, you will do so within Windows.
If you installed a Linux subsystem or virtual machine and want to install a text editor, you will want to do so within the Linux environment.