Python Resources

The servers have several versions of python, with the default version being python 2.7. The best practice when coding in python is to set up a virtual environment with the libraries you will be using. To do this, follow these steps:

Set up a virtual environment

• Use the following command to initialize the latest conda in the servers:

  • `which conda | sed -E 's:.*[ ](/.*l7).+:\1/\*/\*/\*3-edge/bin/conda:'` init bash tcsh
  • Close the current terminal and open a new one for the changes to take place

• Use the following commands to set up the directory where the python environments and packages will be stored:

  • mkdir /path/to/save/dir
  • conda config --append envs_dirs /path/to/save/dir/envs
  • conda config --append pkgs_dirs /path/to/save/dir/pkgs

• Use the following command to create a new Anaconda (includes numpy, scipy, pandas, matplotlib, jupyter, etc)] python environment named environmentname (this can be any word without spaces):

  • Python 2

    • conda create -n environmentname python=2.7 anaconda -y

  • Python 3

    • conda create -n environmentname python=3.X anaconda -y
      • The python 3 versions available are 3.5, 3.6, 3.7, and 3.8

• To create an empty python environment, so you can add your own packages, just remove anaconda from the above command and install your own packages with:

  • conda install packagename

Using the new environment

• To activate the virtual environment use the following command:
  • conda activate environmentname
  • The name of the virtual environment will be displayed to the left of the command line
  • After activating the virtual environment, run the following command to update pip to the latest version:
    • pip install -U pip -y
• To deactivate the virtual environment use the following command:
  • conda deactivate

Conda CheatSheet

Advanced

• Refer to the Scientific Computing Services (SCS) official Python tutorial for more advanced options (requires UCSF login)