Creating general purpose python virtual environment on CBS server

For those wishing to use Python on the CBS server, below are instructions for setting up a general purpose virtual environment.

  1. Set up a virtual environment. (current available python versions: 3.7, 3.8, and 3.9)
    python3.9 -m venv ~/venv

  2. Activate it.
    source ~/venv/bin/activate

  3. Upgrade pip and install any packages you need.
    pip install --upgrade pip
    pip install numpy scipy pandas nilearn nibabel jupyterlab

  4. Start using python, e.g., launch jupyter-lab.
    jupyter-lab

  5. When finished, deactivate the virtual environment.
    deactivate

Note 1: You will always need to activate the virtual environment before using it (e.g., run step 2).

Note 2: virtualenv (venv) is preferred over conda on the CBS server, as it more lightweight. Users have also reported strange behavior when using conda.

Note 3: If you want or need to start fresh, simply remove the venv folder from your home directory.

Note 4: It is recommended to keep separate virtual environments for softwares that may have conflicting dependencies. To create a new virtual environment, simply re-run the steps, specifying a new name for the virtual environment folder (e.g., python3.9 -m venv ~/new_venv).