Jupyter Notebooks Tutorial FAQ#

Here is a compilation of questions and issues that arose during the Jupyter Notebooks session of the Python Tutorial Seminar Series.

Q. I installed Miniconda but it doesn’t seem to be working. conda is not a recognized command. What should I do?

A. This is possible if Miniconda is not visible from your workspace, according to the Conda trouble shooting site this happens if you answered “NO” instead of “YES” when asked if you’d like to prepend the conda prompt to your path. You have two options:

  1. Manually edit your (hidden) .baschrc file to include the line:

    export PATH=/Users/your-username/anaconda3/bin:$PATH
  2. Try uninstalling and re-installing Conda, making sure to answer “YES” this time,

Q. I executed jupyter lab and received the message, “Could not determine jupyterlab build status without nodejs”. Do I need to exit somehow and or fix something?

A. This is only a warning, not an error message. No fix is necessary.

Q. How do you specify what browser Jupyter opens with?

A. If you don’t want to use your default browser (which Jupyter will automatically open), you can specify a different one with jupyter lab —browser=chrome (e.g., for Chrome)

Q. Jupyter opens to my base environment, not the environment I launched jupyter lab from. Is this an error?

A. This is the expected behavior. You can double check your environment by typing conda env list from your Jupyter terminal to see all of your environments. The one with the asterisks next to it is your activated environment.

Q. The Jupyter workspace autocompletion of quotation marks and parenthesis is causing errors. Is there a way to disable this?

A. Yes according to this this stack overflow post, in any code cell type:

from notebook.services.config import ConfigManager
c = ConfigManager()
c.update('notebook', {"CodeCell": {"cm_config": {"autoCloseBrackets": False}}})

You may have to restart the Jupyter session for the changes to take effect.

Q. Is converting a cell from code to raw a good way to basically “comment out” an entire cell? Is that good practice or bad practice?

A. This is the easiest way to “comment out” a cell.

Q. How do I use Jupyter with an R kernel (instead of Python)?

A. You would need to create a new Conda environment with R and jupyter installed.

Q. Does Jupyter Lab care about being shut down gracefully? If I you just ctrl-C it from the command-line, does that do anything bad?

A. As long as your notebook is saved, ctrl-C is fine. Otherwise, you will lose the contents of your notebooks that weren’t saved before the shutdown.

On a Mac you can double check that your Jupyter Notebook isn’t still running in the background, type jupyter notebook list in the terminal to list all active sessions.

Q. How do different environments affect resource usage in virtual environments?

A. Running code uses resources, different environments use disc space. It is possible to have a ton of duplication (e.g., every single user of the virtual environment has installed numpy) but this gives you a lot of control over your own software versioning. You can prune unused virtual environments to save disc space with the command conda env remove —name my_env, or try conda clean -a to clean up any cached downloaded packages.

Q. Where are the packages physically installed in a virtual environment?

A. In the directory where miniconda was installed, you will see a directory called envs, and every single named environment will be put into that directory.

Q. Why do we install Miniconda instead of Anaconda?

A. Miniconda is much more lightweight than Anaconda. It contains fewer packages and takes up less disc space.