Using Jupyter server/installing lsmlsda environment

[mlane22]

Hi, I have been trying to set up a notebook on the Jupyter server with the lsmlsda environment according to the instructions in the Logistics file. To install and activate the environment I ran:

!conda env create -f environment.yml
!conda init
!ipython kernel install --user --name lsmlsda

When I try to activate the environment via !conda activate lsmlsda

I get the following error message: CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run $ conda init Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options. IMPORTANT: You may need to close and restart your shell after running 'conda init'.

I've tried logging in and out, restarting the kernel, etc. Any advice on what else to try would be very much appreciated. Thank you!

[poornimaramesh]

Hey, are you running these commands from inside a Jupyter notebook? That might be why you get this error. If you want to set up the conda environment, then you need to run the conda ... commands in a terminal on JupyterHub, before you open a notebook. The instructions for how to do this are under the section "Logging into JupyterHub" (Step 4) of logistics.md from Module 0.

Also, if you already installed the conda environment in the week when we presented Module 0, then you don't need to repeat these steps again i.e. you don't need to reinstall the environment. You can directly log in to the server, and start working from a notebook.

I hope this helps. If not, please us know -- we can try and give you more detailed instructions.

[mlane22]

Hi Poornima,

Ahh okay, I was a bit confused then as I was running the commands from inside a Jupyter notebook after I logged on to the server. I will try again using the JupyterHub terminal :)

Thank you!!