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Upgrade Workbench JupyterLab to 4.x #852

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Oct 2, 2024
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Upgrade Workbench JupyterLab to 4.x #852

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d502705
Upgrade JupyterLab to 4.x
ianpittwood Oct 1, 2024
27dfcbc
Upgrade Jupyterlab in r-session-complete
ianpittwood Oct 1, 2024
ce16390
Fix PYTHON_VERSION_JUPYTER usage
ianpittwood Oct 1, 2024
3bcd170
Fix test jupyter path
ianpittwood Oct 1, 2024
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27 changes: 12 additions & 15 deletions r-session-complete/Dockerfile.ubuntu2204
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Expand Up @@ -43,21 +43,18 @@ RUN ln -s /lib/rstudio-server/bin/quarto/bin/quarto /usr/local/bin/quarto
### Install TinyTeX using Quarto ###
RUN $SCRIPTS_DIR/install_quarto.sh --install-tinytex --add-path-tinytex

RUN /opt/python/"${PYTHON_VERSION}"/bin/pip install \
jupyter \
jupyterlab=="${JUPYTERLAB_VERSION}" \
rsconnect_jupyter \
rsconnect_python \
rsp_jupyter \
workbench_jupyterlab \
&& ln -s /opt/python/"${PYTHON_VERSION}"/bin/jupyter /usr/local/bin/jupyter \
&& /opt/python/"${PYTHON_VERSION}"/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter \
&& /opt/python/"${PYTHON_VERSION}"/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter \
&& /opt/python/"${PYTHON_VERSION}"/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter \
&& /opt/python/"${PYTHON_VERSION}"/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/"${PYTHON_VERSION}"/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter

ENV PATH="/opt/python/${PYTHON_VERSION}/bin:${PATH}"
RUN /opt/python/"${PYTHON_VERSION}"/bin/python -m venv /opt/python/jupyter \
&& /opt/python/jupyter/bin/python -m pip install \
jupyterlab~=4.2.4 \
notebook \
pwb_jupyterlab~=1.0 \
&& ln -s /opt/python/jupyter/bin/jupyter /usr/local/bin/jupyter \
&& /opt/python/jupyter/bin/python -m pip install ipykernel \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION_ALT} --display-name "Python ${PYTHON_VERSION_ALT}" \
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@bjfletcher bjfletcher Oct 11, 2024 •
edited
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Hi @ianpittwood, JupyterLab has stopped working for us.

If I run:

docker run -it --platform linux/amd64 rstudio/r-session-complete:ubuntu2204-2024.09.0 bash

I see that the two python -m ipykernel install lines in your Dockerfile produce the following kernel configurations:

/usr/local/share/jupyter/kernels/py3.11.10/kernel.json

{
...
  "/opt/python/jupyter/bin/python",
...
 "display_name": "Python 3.11.10",
...
}

/usr/local/share/jupyter/kernels/py3.12.6/kernel.json

{
...
  "/opt/python/jupyter/bin/python",
...
 "display_name": "Python 3.12.6",
...
}

Note how the paths for both 3.11 and 3.12 point to the same one Python binary, which is 3.12.

It'd be great if this is fixed because 3.12 doesn't work with most ML libraries/models.

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Thanks for pointing this out. This should fix the issue: #855

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Thanks @ianpittwood . Sorry to be a pain, but !pip install <pkg> has been broken too.

&& /opt/python/jupyter/bin/python -m pip cache purge

ENV PATH="/opt/python/jupyter/bin:${PATH}"

COPY vscode.extensions.conf /etc/rstudio/vscode.extensions.conf

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2 changes: 1 addition & 1 deletion r-session-complete/test/goss.yaml
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Expand Up @@ -23,7 +23,7 @@ file:
filetype: symlink

command:
"echo '{ \"cells\": [], \"metadata\": {}, \"nbformat\": 4, \"nbformat_minor\": 2}' | /opt/python/{{.Env.PYTHON_VERSION}}/bin/jupyter nbconvert --to notebook --stdin --stdout":
"echo '{ \"cells\": [], \"metadata\": {}, \"nbformat\": 4, \"nbformat_minor\": 2}' | /opt/python/jupyter/bin/jupyter nbconvert --to notebook --stdin --stdout":
title: jupyter_works
timeout: 60000
exit-status: 0
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20 changes: 6 additions & 14 deletions workbench-for-google-cloud-workstations/Dockerfile.ubuntu2204
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Expand Up @@ -118,23 +118,15 @@ RUN mkdir -p /opt/rstudio-license/ \

### Install Jupyter and extensions ###
RUN /opt/python/"${PYTHON_VERSION_JUPYTER}"/bin/python -m venv /opt/python/jupyter \
&& /opt/python/jupyter/bin/pip install \
jupyter \
jupyterlab=="${JUPYTERLAB_VERSION}" \
rsconnect_jupyter \
rsconnect_python \
rsp_jupyter \
workbench_jupyterlab \
&& /opt/python/jupyter/bin/python -m pip install\
jupyterlab~=4.2.4 \
notebook \
pwb_jupyterlab~=1.0 \
&& ln -s /opt/python/jupyter/bin/jupyter /usr/local/bin/jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/python -m pip install ipykernel \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION_ALT} --display-name "Python ${PYTHON_VERSION_ALT}" \
&& /opt/python/${PYTHON_VERSION}/bin/python3 -m pip cache purge \
&& /opt/python/${PYTHON_VERSION_ALT}/bin/python3 -m pip cache purge
&& /opt/python/jupyter/bin/python3 -m pip cache purge

ADD --chmod=755 https://raw.githubusercontent.com/rstudio/wait-for-it/master/wait-for-it.sh /usr/local/bin/wait-for-it.sh

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3 changes: 1 addition & 2 deletions workbench-for-google-cloud-workstations/conf/jupyter.conf
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@@ -1,7 +1,6 @@
notebooks-enabled=1
labs-enabled=1

jupyter-exe=/usr/local/bin/jupyter
jupyter-exe=/opt/python/jupyter/bin/jupyter
lab-args=--no-browser --allow-root --ip=0.0.0.0 --ServerApp.allow_origin="*" --ServerApp.allow_remote_access=True --LabApp.token="" --debug

default-session-cluster=Local
28 changes: 7 additions & 21 deletions workbench-for-microsoft-azure-ml/Dockerfile.ubuntu2204
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Expand Up @@ -89,28 +89,14 @@ RUN apt-get update --fix-missing -qq \
### Install Jupyter and extensions ###
RUN /opt/python/"${PYTHON_VERSION_JUPYTER}"/bin/python -m venv /opt/python/jupyter \
&& /opt/python/jupyter/bin/pip install \
jupyter \
jupyterlab=="${JUPYTERLAB_VERSION}" \
rsconnect_jupyter \
rsconnect_python \
rsp_jupyter \
workbench_jupyterlab \
&& /opt/python/jupyter/bin/jupyter kernelspec remove python3 -f \
&& /opt/python/jupyter/bin/pip uninstall -y ipykernel \
jupyterlab~=4.2.4 \
notebook \
pwb_jupyterlab~=1.0 \
&& ln -s /opt/python/jupyter/bin/jupyter /usr/local/bin/jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/${PYTHON_VERSION}/bin/pip install \
ipykernel \
virtualenv \
&& /opt/python/${PYTHON_VERSION}/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" \
&& /opt/python/${PYTHON_VERSION_ALT}/bin/pip install \
ipykernel \
virtualenv \
&& /opt/python/${PYTHON_VERSION_ALT}/bin/python -m ipykernel install --name py${PYTHON_VERSION_ALT} --display-name "Python ${PYTHON_VERSION_ALT}"
&& /opt/python/jupyter/bin/python -m pip install ipykernel \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION_ALT} --display-name "Python ${PYTHON_VERSION_ALT}" \
&& /opt/python/jupyter/bin/python3 -m pip cache purge

### Install basic data science packages for Python and R ###
COPY deps/* /
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3 changes: 1 addition & 2 deletions workbench-for-microsoft-azure-ml/conf/jupyter.conf
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@@ -1,7 +1,6 @@
notebooks-enabled=1
labs-enabled=1

jupyter-exe=/usr/local/bin/jupyter
jupyter-exe=/opt/python/jupyter/bin/jupyter
lab-args=--no-browser --allow-root --ip=0.0.0.0 --ServerApp.allow_origin="*" --ServerApp.allow_remote_access=True --LabApp.token="" --debug

default-session-cluster=Local
20 changes: 8 additions & 12 deletions workbench/Dockerfile.ubuntu2204
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Expand Up @@ -80,19 +80,15 @@ COPY startup/* /startup/base/
COPY supervisord.conf /etc/supervisor/supervisord.conf

RUN /opt/python/"${PYTHON_VERSION_JUPYTER}"/bin/python -m venv /opt/python/jupyter \
&& /opt/python/jupyter/bin/pip install \
jupyter \
jupyterlab=="${JUPYTERLAB_VERSION}" \
rsconnect_jupyter \
rsconnect_python \
rsp_jupyter \
workbench_jupyterlab \
&& /opt/python/jupyter/bin/python -m pip install \
jupyterlab~=4.2.4 \
notebook \
pwb_jupyterlab~=1.0 \
&& ln -s /opt/python/jupyter/bin/jupyter /usr/local/bin/jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsp_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension install --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-nbextension enable --sys-prefix --py rsconnect_jupyter \
&& /opt/python/jupyter/bin/jupyter-serverextension enable --sys-prefix --py rsconnect_jupyter
&& /opt/python/jupyter/bin/python -m pip install ipykernel \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION} --display-name "Python ${PYTHON_VERSION}" \
&& /opt/python/jupyter/bin/python -m ipykernel install --name py${PYTHON_VERSION_ALT} --display-name "Python ${PYTHON_VERSION_ALT}" \
&& /opt/python/jupyter/bin/python -m pip cache purge

RUN curl -fsSL -o /usr/local/bin/wait-for-it.sh https://raw.githubusercontent.com/rstudio/wait-for-it/master/wait-for-it.sh && \
chmod +x /usr/local/bin/wait-for-it.sh
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3 changes: 1 addition & 2 deletions workbench/conf/jupyter.conf
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@@ -1,6 +1,5 @@
notebooks-enabled=1
labs-enabled=1

# jupyter-exe=/usr/local/bin/jupyter
jupyter-exe=/opt/python/jupyter/bin/jupyter

default-session-cluster=Local
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