Python for Atmosphere and Ocean Scientists: Setup

Data

In preparation for these lessons, you will need to download the following two Python scripts and four netCDF files and place them in a new folder/directory:

1. Make a new folder in your Desktop called data-carpentry.
2. Download script_template.py and plot_precipitation_climatology.py and move them into that folder.
3. Make a new folder in your data_carpentry folder called data. Download the following files and place them in that folder:
   • pr_Amon_ACCESS-CM2_historical_r1i1p1f1_gn_201001-201412.nc
   • pr_Amon_ACCESS-ESM1-5_historical_r1i1p1f1_gn_201001-201412.nc
   • sftlf_fx_ACCESS-CM2_historical_r1i1p1f1_gn.nc
   • sftlf_fx_ACCESS-ESM1-5_historical_r1i1p1f1_gn.nc

Software installation

In order to complete the lessons, you will need access to the following:

• The bash shell (the Z-shell is also fine, which is default on new Macs)
• A text editor
• Git
• Anaconda (which is a Python distribution)

If you don’t already have these installed, please follow The Carpentries software installation instructions. (You do not need to install R, which is also listed at that site.)

Troubeshooting

If you have any trouble with software installation, The Carpentries maintain a list of common issues on their Configuration Problems and Solutions wiki page.

Your workshop instructor may also ask that you install the python packages introduced in the first lesson ahead of time. You can do this via the command line or by using the Anaconda Navigator:

Installation of python packages: via the command line

(Windows users may need to open the Anaconda Prompt program and run conda init bash to make conda available at the Bash Shell.)

Step 1

Add the conda-forge channel:

$ conda config --add channels conda-forge

Option 1 for Step 2 (recommended if you’re new to using Anaconda)

Install the packages in the base conda environment:

$ conda install xarray dask netCDF4 cartopy cmocean cmdline_provenance

Option 2 for Step 2

Create a new environment called pyaos-lesson and install the packages there:

$ conda create -n pyaos-lesson jupyter xarray dask netCDF4 cartopy cmocean cmdline_provenance

You can activate this new environment as follows:

$ conda activate pyaos-lesson

(Or source activate pyaos-lesson if that doesn’t work.)

Type conda deactivate to exit that environment.

Installation of python packages: via the Anaconda Navigator

Once you’ve opened the Anaconda Navigator program (which can be found at the start menu on Windows), head to the “Environments” tab.

You can install the packages into the “base” environment (recommended if you’re new to Anaconda) OR create a new environment called pyaos-lesson by clicking the “create” button at the bottom of the environment list before doing the following:

Step 1

Add the conda-forge channel.

Step 2

Install the xarray, dask, netCDF4, cartopy, cmocean and cmdline_provenance packages one-by-one (click “apply” to install once selected). If you’ve created a new environment, you’ll need to install jupyter too.

Software check

To check that everything is installed correctly, follow the instructions below.

Bash Shell

• Linux: Open the Terminal program via the applications menu. The default shell is usually Bash. If you aren’t sure what yours is, type echo $SHELL. If the shell listed is not bash, type bash and press Enter to access Bash.
• Mac: Open the Applications Folder, and in Utilities select Terminal.
• Windows: Open the Git Bash program via the Windows start menu.

Git

• At the Bash Shell, type git --version. You should see the version of your Git program listed.

Anaconda

• At the Bash Shell, type python --version. You should see the version of your Python program listed, with a reference to Anaconda (i.e. the default Python program on your laptop needs to be the Anaconda installation of Python).