How do I create a docker container with both Python 2 and 3 available in Jupyter Notebooks?

Question

I am trying to create a docker container that has anaconda and supports Jupyter notebooks with both python 2 and 3. I created a container based on the official anaconda python 3 container like so:

FROM continuumio/anaconda3:latest

WORKDIR /app/
COPY requirements.txt /app/

RUN pip install --upgrade pip && \
    pip install -r requirements.txt

Once on the container, I am able to get python 2 and 3 working with Jupyter notebooks by entering the following commands:

conda create -y -n py2 python=2.7
conda activate py2
conda install -y notebook ipykernel
ipython kernel install --user
conda deactivate

Then when I go back to base and run jupyter kernelspec list I see:

(base) root@1683850aacf0:/app# jupyter kernelspec list
Available kernels:
  python2    /root/.local/share/jupyter/kernels/python2
  python3    /root/.local/share/jupyter/kernels/python3

and when I open a jupyter notebook server I see both python 2 and 3 options. This is the state that I would like to end up in. I tried to turn all these into docker commands like so:

RUN    conda create -y -n py2 python=2.7
RUN    conda activate py2
RUN    conda install -y notebook ipykernel
RUN    ipython kernel install --user
RUN    conda deactivate

but running the command to activate or deactivate ( RUN conda activate py2 ) a conda environment gives me an error:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

Adding RUN conda init bash before the commands doesn't change the error message.

Also, based on this SO question I tried:

RUN conda create -y -n py3 python=3.7 ipykernel
RUN conda create -y -n py2 python=2.7 ipykernel

but after I build and enter the container I only see the python 3 environment:

(base) root@b301d8ab5f1e:/app# jupyter kernelspec list
Available kernels:
  python3    /opt/conda/share/jupyter/kernels/python3

I can activate py2 and see that kernel, but not both:

(py2) root@b301d8ab5f1e:/app# jupyter kernelspec list
Available kernels:
  python2    /opt/conda/envs/py2/share/jupyter/kernels/python2

What else should I try?

EDIT:

I tried specifying the shell as Adiii suggested with the following:

FROM continuumio/anaconda3:latest

WORKDIR /app/
COPY requirements.txt /app/

RUN pip install --upgrade pip && \
    pip install -r requirements.txt

ENV BASH_ENV ~/.bashrc
SHELL ["/bin/bash", "-c"]
RUN    conda create -y -n py2 python=2.7
RUN    conda activate py2
RUN    conda install -y notebook ipykernel
RUN    ipython kernel install --user
RUN    conda deactivate

This allows the container to build but for some reason there was no python 2.7 environment:

(base) root@31169f698f14:/app# jupyter kernelspec list
Available kernels:
  python3    /root/.local/share/jupyter/kernels/python3
(base) root@31169f698f14:/app# conda info --envs
# conda environments:
#
base                  *  /opt/conda
py2                      /opt/conda/envs/py2

(base) root@31169f698f14:/app# conda activate py2
(py2) root@31169f698f14:/app# jupyter kernelspec list
Available kernels:
  python3    /root/.local/share/jupyter/kernels/python3

Answer 1

From this issue , you need sepcify the SHELL directive in the Dockerfile, like SHELL ["/bin/bash", "-c"] . The problem could be the fact that the default shell in RUN command is sh .

This is similar to the solutions above, but avoids some of the boilerplate in every RUN command:

ENV BASH_ENV ~/.bashrc
SHELL ["/bin/bash", "-c"]

Then something like this should work as expected:

RUN conda activate my-env && conda info --envs

Or, to set the environment persistently (including for an interactive shell) you could:

RUN echo "conda activate my-env" >> ~/.bashrc

Dockerfile

FROM continuumio/anaconda3:latest

WORKDIR /app/

RUN pip install --upgrade pip
ENV BASH_ENV ~/.bashrc
SHELL ["/bin/bash", "-c"]
RUN    conda create -y -n py2 python=2.7
RUN    conda activate py2
RUN    conda install -y notebook ipykernel
RUN    ipython kernel install --user
RUN    conda deactivate

Answer 2

This was what ended up working:

RUN conda env create -f py2_env.yaml
RUN conda env create -f py3_env.yaml
RUN /bin/bash -c "conda init bash && source /root/.bashrc && conda activate py2 && conda install -y notebook ipykernel && ipython kernel install --user && conda deactivate"
RUN /bin/bash -c "conda init bash && source /root/.bashrc && conda activate py3 && conda install -y notebook ipykernel && ipython kernel install --user && conda deactivate"