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CIROH-UA / awi-ciroh-image

2i2c JupyterHub user image for the Alabama Water Institute CIROH hub
BSD 3-Clause "New" or "Revised" License
2 stars 6 forks source link

Add R kernel to docker image #55

Open manjilasingh opened 1 month ago

manjilasingh commented 1 month ago

Users currently need to reinstall r kernel every time they start a server. Adding r kernel directly to the image would eliminate the need of repeated installations. The following line can be added to the Dockerfile: RUN conda install -c r r-irkernel

benlee0423 commented 1 month ago

@manjilasingh How many users are requesting this feature, and which organization are they belongs to?

benlee0423 commented 1 month ago

Before

$ jupyter kernelspec list
[ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`.
Available kernels:
  python3    /srv/conda/envs/notebook/share/jupyter/kernels/python3

After

$ jupyter kernelspec list                          
[ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`.                                                                        
Available kernels:                                                                       
  ir         /srv/conda/envs/notebook/share/jupyter/kernels/ir                           
  python3    /srv/conda/envs/notebook/share/jupyter/kernels/python3
manjilasingh commented 1 month ago

@manjilasingh How many users are requesting this feature, and which organization are they belongs to?

@arpita0911patel might have that info

benlee0423 commented 1 month ago

Correct command to use RUN conda install -c r r-irkernel -y After rebuild and use the image to launch instance in staging.

$ jupyter kernelspec list
[ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`.
Available kernels:
  python3    /srv/conda/envs/notebook/share/jupyter/kernels/python3
(notebook) jovyan@jupyter-benlee0423:~$

This means conda command is not compatible with Dockerfile, and the command does not install R kernel to the image built.

benlee0423 commented 1 month ago

@arpita0911patel We like to ask new image built tested by requester in staging if it works. Can you share the email address who requested r kernel, and I will send instruction how to test in staging?

arpita0911patel commented 1 month ago

Pabitra Dash pabitra.dash@usu.edu