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Merge pull request #62 from yuvipanda/user-image
Upgrade user image
2 parents 2ee1ee7 + c6ade7a commit 6eb075e

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‎images/singleuser/Dockerfile‎

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FROM ubuntu:18.04
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FROM ubuntu:20.04
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ENV EDITOR=/bin/nano
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ENV PYWIKIBOT2_DIR=/srv/paws
@@ -21,14 +21,15 @@ RUN adduser --disabled-password \
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WORKDIR ${HOME}
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# Base building utilities that'll always be required, probably
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RUN apt-get update --yes
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RUN apt-get install --yes \
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RUN apt-get update > /dev/null && \
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apt-get install --yes \
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git \
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locales \
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pkg-config \
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build-essential \
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gcc \
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apt-transport-https
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apt-transport-https > /dev/null
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RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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@@ -40,16 +41,23 @@ ENV LANGUAGE en_US.UTF-8
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ADD node/nodesource.gpg.key /etc/apt/trusted.gpg.d/nodesource.gpg.key
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ADD node/nodesource.list /etc/apt/sources.list.d/nodesource.list
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RUN apt-key add /etc/apt/trusted.gpg.d/nodesource.gpg.key
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RUN apt-get update --yes
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# Use newer version of R
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# Binary packages from packagemanager.rstudio.com work against this.
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# Base R from Focal is only 3.6.
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RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list
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# Install languages needed and their core dev packages
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RUN apt-get install --yes \
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RUN apt-get update --yes > /dev/null && \
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apt-get install --yes \
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python3 \
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python3-dev \
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python3-venv \
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r-recommended \
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r-base-dev \
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nodejs
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r-cran-littler \
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nodejs > /dev/null
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# Utilities
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RUN apt-get install --yes \
@@ -61,7 +69,7 @@ RUN apt-get install --yes \
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links \
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nano \
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vim \
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mariadb-client
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mariadb-client > /dev/null
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# Machine-learning type stuff
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RUN apt-get install --yes \
@@ -80,42 +88,49 @@ RUN apt-get install --yes \
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libzmq3-dev \
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libreadline-dev \
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# For R's mysql
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libmariadb-client-lgpl-dev \
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libmariadb-dev \
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# For R's curl
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libcurl4-openssl-dev \
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# For R's devtools
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libssl-dev \
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# For PDFs and stuff
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pandoc \
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texlive-xetex
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texlive-xetex > /dev/null
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# Create user owned R libs dir
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# This lets users temporarily install packages
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ENV R_LIBS_USER /srv/r
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RUN install -d -o ${NB_USER} -g ${NB_USER} ${R_LIBS_USER}
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# Create venv directory, and let users install into it
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ENV VENV_DIR /srv/paws
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RUN install -d -o ${NB_USER} -g ${NB_USER} ${VENV_DIR}
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RUN mkdir -p /srv/paws && chown ${NB_USER}:${NB_USER} /srv/paws
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ENV PATH=/srv/paws/pwb:/srv/paws/bin:/srv/paws:$PATH
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USER ${NB_USER}
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RUN python3.6 -m venv /srv/paws
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RUN python3 -m venv /srv/paws
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# Install base notebook packages
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RUN pip install --no-cache-dir \
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jupyterhub==1.1.0 \
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notebook \
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jupyterlab \
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notebook==6.3.* \
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jupyterlab==3.* \
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bash_kernel
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# Install the bash kernel
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RUN python -m bash_kernel.install --sys-prefix
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# Install the R Kernel and libraries
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COPY install-r /usr/local/bin/install-r
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# Set CRAN mirror to rspm before we install anything
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COPY Rprofile.site /usr/lib/R/etc/Rprofile.site
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# We need root simply to install the kernelspec lol
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# https://github.com/IRkernel/IRkernel/issues/495
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USER root
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RUN /usr/local/bin/install-r
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# Install the R Kernel
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RUN r -e "install.packages('IRkernel', version='1.1.1')" && \
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r -e "IRkernel::installspec(prefix='${VENV_DIR}')" && \
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rm -rf /tmp/downloaded_packages
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# Install mass amount of python libraries!
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COPY --chown=tools.paws:tools.paws requirements.txt /tmp/requirements.txt
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USER ${NB_USER}
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RUN pip --no-cache-dir install -r /tmp/requirements.txt
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@@ -130,12 +145,9 @@ RUN /usr/local/bin/install-pwb
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COPY install-extensions /usr/local/bin/
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RUN /usr/local/bin/install-extensions
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COPY banner /etc/bash.bashrc
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# use custom css to hide clusters tab
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COPY --chown=tools.paws:tools.paws hide_clusters_tab.css /home/paws/.jupyter/custom/custom.css
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USER ${NB_USER}
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EXPOSE 8888

‎images/singleuser/Rprofile.site‎

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# Use RStudio's CRAN mirror to get binary packages
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# 'latest' just means it has all available versions.
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# We can specify version numbers in devtools::install_version
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options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
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# RStudio's CRAN mirror needs this to figure out which binary package to serve.
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# If not set properly, it will just serve up source packages
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# Quite hilarious, IMO.
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# See https://docs.rstudio.com/rspm/admin/binaries.html
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options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))

‎images/singleuser/install-extensions‎

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#!/bin/bash
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set -euo pipefail
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pip install --no-cache-dir \
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pythreejs \
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ipyleaflet \
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bqplot \
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RISE \
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py-heat-magic \
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nbresuse \
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jupyter-resource-usage \
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git+https://github.com/toolforge/nbpawspublic@main \
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jupyter nbextension install --py widgetsnbextension --sys-prefix
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jupyter nbextension enable --py widgetsnbextension --sys-prefix
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jupyter nbextension install --py ipyleaflet --sys-prefix
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jupyter nbextension enable --py ipyleaflet --sys-prefix
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jupyter nbextension install --py bqplot --sys-prefix
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jupyter nbextension enable --py bqplot --sys-prefix
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jupyter nbextension install --py pythreejs --sys-prefix
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jupyter nbextension enable --py pythreejs --sys-prefix
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jupyter nbextension install --py rise --sys-prefix
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jupyter nbextension enable --py rise --sys-prefix
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jupyter serverextension enable --py nbresuse --sys-prefix
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jupyter nbextension enable --py nbresuse --sys-prefix
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jupyter serverextension enable --py jupyterlab --sys-prefix
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jupyter nbextension install --py nbpawspublic --sys-prefix
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jupyter nbextension enable --py nbpawspublic --sys-prefix
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‎images/singleuser/install-r‎

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This file was deleted.

‎images/singleuser/node/nodesource.list‎

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deb https://deb.nodesource.com/node_10.x bionic main
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deb https://deb.nodesource.com/node_14.x focal main
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