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Setup

Data

In preparation for this lesson, you will need to download 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][template_script] and [plot_precipitation_climatology.py][precip_script] 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_ACCESS1-3_historical_r1i1p1_200101-200512.nc][pr_access_file]
    • [pr_Amon_CSIRO-Mk3-6-0_historical_r1i1p1_200101-200512.nc][pr_csiro_file]
    • [sftlf_fx_ACCESS1-3_historical_r0i0p0.nc][sftlf_access_file]
    • [sftlf_fx_CSIRO-Mk3-6-0_historical_r0i0p0.nc][sftlf_csiro_file]

Software installation

If your instructor hasn't sent you instructions on how to install the required software, follow the default Carpentries instructions. You need to install the bash shell, git, text editor and Python.

The conda command is not automatically available using Git Bash. This means that Windows users cannot create and activate a conda environment from the bash shell, which is an option in the first lesson. While this is not a big issue (the first lesson can be completed without creating a new environment), Windows users who would like to be able create and activate conda environments from the bash shell can do so by following one of these two options:

Option 1: Access the bash shell from the Anaconda Prompt using the posix package

  • Open the Anaconda Prompt program (from the Windows start menu)
  • Type conda install posix (this only needs to be done once)
  • Type bash to run the Bash Shell

Option 2: Update your Anaconda path so that conda is available using Git Bash

  • Open the Anaconda Prompt and enter where python to find the path of the Anaconda3 directory (the output should show a path similar to C:\Users\Username\Anaconda3\python.exe)
  • Convert that path for use in the next step by doing the following:
    • Replace all instances of \ with /
    • Replace C: with /c
    • Replace python.exe with Scripts/activate
    • e.g. if you got C:\Users\Username\Anaconda3\python.exe from the previous step, you will use /c/Users/Username/Anaconda3/Scripts/activate for the next step
  • Go back to the terminal and run echo "source [Anaconda path]" >> ~/.profile && source ~/.profile, replacing [Anaconda path] with the path you generated in the previous step

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 (standard setup): Open the Git Bash program via the Windows start menu.
  • Windows (alternative setup): Open the Anaconda Prompt program via the Windows start menu. Type conda install posix (this only needs to be done once). Type bash to run the Bash Shell.

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).
  • In the Bash Shell, type conda --version. You should see the version of your conda program listed.

[pr_access_file]: {{ "/data/pr_Amon_ACCESS1-3_historical_r1i1p1_200101-200512.nc" | relative_url }} [pr_csiro_file]: {{ "/data/pr_Amon_CSIRO-Mk3-6-0_historical_r1i1p1_200101-200512.nc" | relative_url }} [sftlf_access_file]: {{"/data/sftlf_fx_ACCESS1-3_historical_r0i0p0.nc" | relative_url }} [sftlf_csiro_file]: {{ "/data/sftlf_fx_CSIRO-Mk3-6-0_historical_r0i0p0.nc" | relative_url }} [template_script]: {{ "/code/script_template.py" | relative_url }} [precip_script]: {{ "code/plot_precipitation_climatology.py" | relative_url }}