jupyter/base-notebook: Hardcoded PATH Environment Variable in Dockerfile

[lima4658]

Some developers need to change the PATH Environment Variable (e.g. create their own virtual environments and registrate/add their private notebooks) You can create virtual environments (conda create ...; python -m venv ...) but the activation will fail due to the hardcoded PATH environment variable.

Solution: Remove Line 'ENV PATH=$CONDA_DIR/bin:$PATH' from Dockerfile But this will cause several problems:

• tini will not be found in ENTRYPOINT command line
• conda/jupyter commands will not be found in RUN command lines
• jupyter command will not be found during startup sequence

Workarounds:

• Install tini from Ubuntu repository (same Version as from conda) and remove lines <'tini=0.18.0' && > and <conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && > from Dockerfile

• Add <export PATH=$CONDA_DIR/bin:$PATH && > to the corresponding RUN statement sections in Dockerfile

• Regarding the 'run-hooks /usr/local/bin/before-notebook.d' command in the start.sh script: Place a script conda_path.sh in directory /usr/local/bin/before-notebook.d containing the command 'export PATH=$CONDA_DIR/bin:$PATH'

Diff Dockerfile:

49,50d48
<     build-essential binutils binfmt-support \
<     tini \
70c68,69
< ENV HOME=/home/$NB_USER \
---
> ENV PATH=$CONDA_DIR/bin:$PATH \
>     HOME=/home/$NB_USER \
112d110
<     export PATH=$CONDA_DIR/bin:$PATH && \
120c118,119
<     'pip' && \
---
>     'pip' \
>     'tini=0.18.0' && \
121a121
>     conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
133,134c133
< RUN export PATH=$CONDA_DIR/bin:$PATH && \
<     conda install --quiet --yes \
---
> RUN conda install --quiet --yes \
159,163d157
<
< RUN mkdir -p /usr/local/bin/before-notebook.d && \
<     printf '#!/bin/bash\n\nexport PATH=$CONDA_DIR/bin:$PATH\n\n' > \
<               /usr/local/bin/before-notebook.d/conda_path.sh && \
<     chmod 777 /usr/local/bin/before-notebook.d/conda_path.sh

[romainx]

Hello @lima4658,

Good remark and also good suggestions!

• Install tini from Ubuntu repository (same Version as from conda) and remove lines [...]

Definitely a very good idea, I've drafted the PR #1308 to implement this change, I think it's a simplification.

• Add <export PATH=$CONDA_DIR/bin:$PATH && > to the corresponding RUN statement sections in Dockerfile

Not sure it's a good solution, it would add too much noise in the Dockerfiles -> we have to think of a better option.

• Regarding the 'run-hooks /usr/local/bin/before-notebook.d' command in the start.sh script: Place a script conda_path.sh in directory /usr/local/bin/before-notebook.d containing the command 'export PATH=$CONDA_DIR/bin:$PATH'

It could do the job in a cleaner way, however need to fix the problem of the conda path in the Dockerfiles first.

Thanks.

[lima4658]

Using a login shell could also be a solution.

Needed modifications in Dockerfile:

All notebooks:

• SHELL ["/bin/bash", "-o", "pipefail", "-l", "-c"]

Base notebook only:

• CMD ["/bin/bash", "-l", "start-notebook.sh"]

• Place desired flexible environment variables (CONDA_DIR, PATH, SHELL, LC_ALL, LANG, LANGUAGE ...) in a file (e.g. 00-base-notebook.sh) in directory /etc/profile.d.

Due to using a login shell the changes will be recognized.

[mathbunnyru]

@lima4658 I thought about this issue for a few day.

You can create virtual environments (conda create ...; python -m venv ...) but the activation will fail due to the hardcoded PATH environment variable.

Could you please give us an explicit example which doesn't work for you?

I believe some solutions won't work for us:

• PATH=$CONDA_DIR/bin:$PATH I agree with @romainx it adds too much noise. What's worse, it will break all dependent images.
• I currently think using login shell won't work well for jupyterhub users, where they don't have access to the host machine. https://github.com/jupyter/docker-stacks/pull/1935#issuecomment-1650684172

On the other hand, does your issue happen during build time or runtime?

1. If it happens during a build time, then you can set ENV PATH to the default value. It's a bit of hardcode, but I don't think the default path is likely to change.
2. If it happens during runtime, I think you can use our Startup Hooks where you can manipulate PATH as you wish.

Please, let me tell, what you think about this.

[mathbunnyru]

@lima4658 please, comment or reopen this issue if you still have an issue. I think having PATH changed in the Dockerfile is best for most of the users, so I don't think we'll be able to change this. I also proposed two solutions for how you can change PATH in your case.