Setup and software installation

1. Setup and software installation#

1.1. Storage requirements#

You will need at least 2 GB free on your computer’s hard drive.

1.3. Install Visual Studio Code#

VS Code is a text editor designed for programming. VS Code is available on all operating systems and has some cool custom plugins. Follow the instructions for setting up Visual Studio Code for your operating system. For Windows and Linux users, just follow the steps under “Installation.” For Mac users, follow the steps under “Installation” and “Launching from the command line.”

1.4. Install Miniconda#

What is Miniconda?#

Anaconda is a popular distribution of Python and a set of programs built specifically for data science. Miniconda is stripped-down version of Anaconda. We will use Miniconda, and add additional programs manually, so that it does not take up as much space on your computer. Miniconda includes:

Python: Programming language (we’ll be using version 3.11)
Conda: Package manager

Conda is a package manager. It maintains the directories (folder pathways) and versions of external (non-default) python packages. A package is a set of Python tools designed for a specific purpose. Some of these are included with Python, but others have to be downloaded from an external source.

If you have Anaconda or Miniconda already installed#

If you have Anaconda or Miniconda already installed on your computer, follow the steps below. If not, move on to Miniconda installation.

First run Python and check which version you have. The version number is displayed when Python starts up.

To maintain consistency, we will be using Python version 3.10 in this class. Previous versions of Python 3.x will work most of the time in classroom demonstrations and other course materials, but you may run into a few cases where certain commands are invalid or not available. Python 2.x is completely incompatible with this course material. If your version is already 3.10, and you are fine with installing additional packages to your existing version, proceed to installing additional tools.

If you have a different version of Python, you have two options:

Uninstall the previous installation. Note that option 2 below may be better if you already have Python code that you want to keep running on the same version of Python. If you choose option 1, find the uninstall instructions for your operating system at https://conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation. For Mac and Windows installations, be sure to remove the Miniconda or Anaconda directory from your home folder. Restart your terminal and proceed with the Miniconda installation steps below.
Advanced: Create a new environment for this class.

Option 2 will allow you to use the same Python version and packages used in the course material, without altering your existing setup. For more information on environments, see https://conda.io/docs/user-guide/tasks/manage-environments.html

Open a terminal (Mac) or Anaconda prompt (Windows) and type:

conda create --name ms263-24 python=3.11

You can replace ms263-24 with any name you like for your environment. To enter the new environment, type:

conda activate ms263-24

Note

To access the environment you just created at later time, you will have to repeat this command whenever you start a new terminal or Anaconda prompt.

Keep this window open and proceed to Installing additional tools

Miniconda installation#

Go to: https://conda.io/miniconda.html

Download the appropriate installer for your operating system and run. The default options will be fine.

Mac: There are different options for installers. Download the .pkg installer for the processor on your Mac (Intel for older Macs and Apple M1 for newer Macs) and click on it. If you don’t know what type of processor you have, see this guide.

Open a terminal or command prompt#

Windows instructions
Mac instructions

Windows instructions#

After installing Anaconda, open the program ”Anaconda Prompt” You might have to search for this in the start menu.

Clicking Anaconda Prompt will bring up a screen where you can type commands. Keep this window open and follow the steps under Installing additional tools

Mac instructions#

After installing Anaconda, open the program ”Terminal”

This is located in Applications -> Utilities

Or you can search for “Terminal” in the spotlight (use press cmd-space).

This will bring up a screen where you can type commands. Continue to the next section on Installing additional tools using conda

1.5. Installing additional tools#

Now that you have a command line open, type these commands to install additional programs and Python packages that we will use throughout the semester.

First, add the “conda-forge” channel as a source for obtaining packages. This is a community-driven project that makes sure that none of the packages you download conflict with each other. Type (or copy and paste) the following on the command line and press Enter:

conda config --add channels conda-forge

Now, install the additional programs and Python packages. This will take a while. Copy and paste the following onto the command line and press Enter (note: this command is very long and probably extends beyond the width of your browser; the easiest way to copy it is to click the “copy” button that appears when you hover the cursor over the right side of the text box):

conda install jupyter jupyterlab matplotlib pandas seaborn xarray netCDF4 cartopy cmocean gsw scikit-image scikit-learn statsmodels uncertainties pingouin nb_conda_kernels ipympl openpyxl autograd

Here, conda is the name of the package management program and install is a command given to this program, followed by the names of programs to install. A description of the packages that you have just installed can be found here.

1.6. Install PyCO2SYS#

When those package installations have finished, there is one more tool that has be installed with a different package manager called pip. Enter this command:

pip install --no-deps PyCO2SYS

1.7. Install Git#

Git is version control system that is commonly used in developing software projects. Enter this command:

conda install git

Choose the default options if prompted to make selections. If for some reason that method of installing Git does not work, you can download and install Git for your operating system by following the instructions at https://git-scm.com

Windows only: Git Bash command line#

Check to make sure that you can open the Git Bash command prompt. You should be able to find Git Bash in the list of programs when you open the Windows Start menu. It may be listed under the heading Anaconda3.

1.8. Open a text editor from the command line#

Make sure that you can open a text editor from the command line. Open the Terminal application (Mac) or Git Bash (Windows).

VS Code#

First, try the VS Code text editor. On the command line, enter:

code

This should open a window in the VS Code text editor. If that worked, then proceed to Setup for Unix shell tutorial

Nano#

If for some reason you cannot open Visual Studio Code from the command line, try the Nano text editor:

nano

This brings up a text editor in the terminal window. Enter Control-X to exit Nano.

System default text editor#

You can also try the default text editor for your operating system. These do not have as many features as Visual Studio Code but will get the job done.

TextEdit (Mac)#

open -e

Notepad (Windows)#

notepad

If you are using Windows, it is highly recommended that you install the free Notepad++ editor instead of using the default Notepad.

1.9. Setup for Unix shell tutorial#

On the first day of our data analysis course, we go through parts of the Software Carpentry Unix shell tutorial. Software Carpentry is an organization that develops lessons and workshops to teach skills in research computing.

You will need to download some files to follow this lesson. To prepare for this lesson, follow the steps listed under “download files” (you have already installed all of the necessary software).