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# References regarding our base image:
# - ubuntu:22.04
# - pangeo/base-image definition: https://github.com/pangeo-data/pangeo-docker-images/blob/master/base-image
# - pangeo/pytorch-notebook definition: https://github.com/pangeo-data/pangeo-docker-images/tree/master/pytorch-notebook
# - pangeo/pytorch-notebook tags: https://hub.docker.com/r/pangeo/pytorch-notebook/tags
# - pytorch-notebook conda package: https://github.com/conda-forge/pytorch-notebook-feedstock/blob/master/recipe/meta.yaml
#
FROM pangeo/pytorch-notebook:master
# While NB_GID is often defined in these jupyter images, it isn't for
# pangeo/base-image and derivative images. Let's define it here so copy pasting
# various Dockerfile snippets will work.
ENV NB_GID=$NB_UID
USER root
# We only need to install packages not listed in this file already:
# https://github.com/pangeo-data/pangeo-docker-images/blob/master/pytorch-notebook/apt.txt
RUN echo "Installing apt-get packages..." \
&& apt-get -y update > /dev/null \
&& apt-get -y install \
curl \
emacs-nox emacs-goodies-el \
# Basic Emacs configuration for general development.
#
# python-mode was part of this list, but removed as it was not
# available for ubuntu 22.04 that is now used.
nano \
# A terminal file editor, vim is already made available
micro \
# A friendly terminal editor, even easier than nano for new users
mc \
# powerful terminal-based file manager, better than the one in JLab
build-essential gfortran \
# Regular build tools for compiling common stuff
texlive-xetex texlive-fonts-recommended texlive-plain-generic \
# Dependencies for nbconvert
rsync \
# for use with jupyterhub-ssh, generate a token at
# hub.jupytearth.org/hub/token and connect to
# <hub-username>@hub.jupytearth.org using the token as password
unrar \
# zipp is installed in the base image, but I think zipp provides
# `zip` and `unzip` which doesn't help us decompress .rar files. See
# https://github.com/pangeo-data/pangeo-docker-images/issues/366 for
# an issue about installing this in the base image.
# /desktop part 1: install desktop UI via apt
#
dbus-x11 \
xfce4 \
xfce4-panel \
xfce4-session \
xfce4-settings \
xorg \
xubuntu-icon-theme \
# qgis
gnupg \
software-properties-common \
> /dev/null \
&& apt-get -y remove \
xfce4-screensaver \
# /desktop part 2: xfce4-screensaver removal
#
# There is no great option to avoid installing it while installing
# other xfce4 packages above it seems.
#
> /dev/null \
# chown $HOME to workaround that the xorg installation creates a
# /home/jovyan/.cache directory owned by root
&& chown -R $NB_UID:$NB_GID $HOME \
&& rm -rf /var/lib/apt/lists/*
# /desktop part 3: firefox as default browswer
#
RUN sed -i 's/WebBrowser=.*/WebBrowser=firefox/' /etc/xdg/xfce4/helpers.rc
# Install visual studio code-server
# ref: https://github.com/cdr/code-server
#
RUN export VERSION=4.7.1 \
&& curl -fsSL https://code-server.dev/install.sh | sh \
&& rm -rf "${HOME}/.cache"
# qgis, used by geographers, display gis data
# ref: https://qgis.org/en/site/forusers/alldownloads.html#debian-ubuntu
RUN wget -qO - https://qgis.org/downloads/qgis-2022.gpg.key \
| gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/qgis-archive.gpg --import \
&& chmod a+r /etc/apt/trusted.gpg.d/qgis-archive.gpg \
&& add-apt-repository "deb https://qgis.org/ubuntu $(lsb_release -c -s) main" \
&& apt-get -y update > /dev/null \
&& apt-get -y install \
qgis \
qgis-plugin-grass \
> /dev/null \
&& rm -rf /var/lib/apt/lists/*
# Install TurboVNC (https://github.com/TurboVNC/turbovnc)
ARG TURBOVNC_VERSION=3.0.1
RUN wget -q "https://sourceforge.net/projects/turbovnc/files/${TURBOVNC_VERSION}/turbovnc_${TURBOVNC_VERSION}_amd64.deb/download" -O turbovnc.deb \
&& apt-get install -y ./turbovnc.deb > /dev/null \
&& rm ./turbovnc.deb \
&& ln -s /opt/TurboVNC/bin/* /usr/local/bin/
# Install Julia itself (Julia part 1/2)
#
# NOTE: Needs to be followed up by installing the Julia kernel in a location not
# overridden by mounting the user storage as done below when we are no
# longer acting as root.
#
# NOTE: The following issue was observed, and we added the workaround of copying
# libstdc++.so.6 from the system to the julia directory:
# https://github.com/pangeo-data/jupyter-earth/issues/126.
#
# I've concluded that julia declares a version of CSL
# (CompilerSupportLibraries) as defined here
# https://github.com/JuliaLang/julia/blob/35ac6e1823a2145fdbd8273d62cc19f10bde3543/stdlib/CompilerSupportLibraries_jll/Project.toml#L4-L7,
# and that CSL version ships with stdlibc++.so.6 of a certain version. The
# version can be found by inspecting the .tar files in the releases of CSL
# as defined in
# https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl/releases.
#
# At this point in time, Julia 1.7.3 and 1.8.0-beta.3 is referencing CSL
# 0.5.2, and only CSL 0.6.0+ included stdlibc++.so.6 version 6.0.30 as
# required. Due to that, we remove the stdlibc++.so.6 symlink and the
# stdlibc++.so.6.0.29 file provided by the julia installation currently
# and copy the more modern ubuntu 22.04 symlink to 6.0.30.
#
# There was one open PR to bump to a modern version of CSL to 0.6.1 that
# that has stdlibc++.so.6.0.30 see https://github.com/JuliaLang/julia/pull/45582.
#
# Latest Julia version at https://julialang.org/downloads/
#
ARG JULIA_VERSION=1.8.1
ARG JULIA_PATH=/srv/julia
ENV JULIA_DEPOT_PATH=${JULIA_PATH}/pkg
ENV PATH=$PATH:${JULIA_PATH}/bin
RUN mkdir -p ${JULIA_PATH} \
&& curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" \
| tar -xz -C ${JULIA_PATH} --strip-components 1 \
&& mkdir -p ${JULIA_DEPOT_PATH} \
&& chown ${NB_UID}:${NB_UID} ${JULIA_DEPOT_PATH} \
&& rm $JULIA_PATH/lib/julia/libstdc++.so.6* \
&& cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $JULIA_PATH/lib/julia/
# Install the nix package manager, step 1/2
RUN mkdir -m 0755 /nix \
&& chown jovyan /nix
# Switch user away from ROOT for the rest
USER ${NB_USER}
# Install the nix package manager, step 2/2
RUN curl -L https://nixos.org/nix/install | sh
# Install Julia kernel (Julia part 2/2)
#
# NOTE: If we are not not setting JUPYTER_DATA_DIR, the Julia kernel gets
# installed in ~/.local/share/jupyter/kernels, and that folder may be
# overridden by a home directory mount. This was found out by using
# "jupyter kernelspec list" during debugging.
#
# Julia's installkernel function relates to JUPYTER_DATA_DIR via logic
# defined at https://github.com/JuliaLang/IJulia.jl/blob/cc2a9bf61a2515596b177339f9a3514de8c38573/deps/kspec.jl#L32-L37
#
# NB_PYTHON_PREFIX is presumed to be /srv/conda/envs/notebook in this
# case, which is defined in this specific Dockerfile's base image.
#
RUN export JUPYTER_DATA_DIR="$NB_PYTHON_PREFIX/share/jupyter" \
&& julia --eval 'using Pkg; Pkg.add("IJulia"); using IJulia; installkernel("Julia");' \
&& julia --eval 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"'
# Make additional julia packages be installed in the home folder while retaining
# access to julia packages installed outside the home folder as well.
#
ENV JULIA_DEPOT_PATH=$HOME/.julia/pkg:$JULIA_DEPOT_PATH
# We only need to install packages not listed in this file already:
# https://github.com/pangeo-data/pangeo-docker-images/blob/master/pytorch-notebook/packages.txt
RUN echo "Installing conda packages..." \
&& mamba install -n ${CONDA_ENV} -y \
# temporary upgrades, because sometimes we wish to have a more modern
# version than installed in the base image.
#
# Should be possible to remove very soon
"ipyspin>=1.0.1" \
#
# visualization:
altair \
# https://anaconda.org/conda-forge/altair
# https://github.com/conda-forge/altair-feedstock/blob/main/recipe/meta.yaml
bqplot \
# https://anaconda.org/conda-forge/bqplot
# https://github.com/conda-forge/bqplot-feedstock/blob/main/recipe/meta.yaml
plotly \
# https://anaconda.org/conda-forge/plotly
# https://github.com/conda-forge/plotly-feedstock/blob/main/recipe/meta.yaml
python-kaleido \
# https://anaconda.org/conda-forge/python-kaleido
# https://github.com/conda-forge/python-kaleido-feedstock/blob/main/recipe/meta.yaml
seaborn \
# https://anaconda.org/conda-forge/seaborn
# https://github.com/conda-forge/seaborn-feedstock/blob/main/recipe/meta.yaml
ipycanvas \
# https://anaconda.org/conda-forge/ipycanvas
# https://github.com/conda-forge/ipycanvas-feedstock/blob/main/recipe/meta.yaml
ipympl \
# https://anaconda.org/conda-forge/ipympl
# https://github.com/conda-forge/ipympl-feedstock/blob/main/recipe/meta.yaml
jupyter_bokeh \
# https://anaconda.org/conda-forge/jupyter_bokeh
# https://github.com/conda-forge/jupyter_bokeh-feedstock/blob/main/recipe/meta.yaml
jupyterlab-geojson \
# https://anaconda.org/conda-forge/jupyterlab-geojson
# https://github.com/conda-forge/jupyterlab-geojson-feedstock/blob/main/recipe/meta.yaml
#
# common geospatial dependencies:
qgis \
# https://anaconda.org/conda-forge/qgis
# https://github.com/conda-forge/qgis-feedstock/blob/main/recipe/meta.yaml
#
# We install this as an apt-get package but on startup we got errors
# about Python integration not being available. But installing this
# by itself didn't seem to give us the application. Installing both
# though makes things work, but seem to cause an initial install
# followed by a downgrade as the conda-forge version isn't as well
# updated. It also makes the installation take ~5-10 minutes longer.
#
# FIXME: Install qgis in a way that provides us with a recent
# version, a shortcut from the desktop UI, and with Python
# support - without also taking 5-10 minutes more than needed
# to install.
#
# FIXME: Installing qgis downgrades pytorch and lots of other files,
# causing a 1 GB download. The reason is unclear.
#
# NOTE: qgis depends on libspatialindex, geos, proj, but not
# proj-data. Fernando added these as apt packages initially.
#
proj-data \
# https://anaconda.org/conda-forge/proj-data
# https://github.com/conda-forge/proj-data-feedstock/blob/main/recipe/meta.yaml
#
# tests and formatting:
black \
# https://anaconda.org/conda-forge/black
# https://github.com/conda-forge/black-feedstock/blob/main/recipe/meta.yaml
flake8 \
# https://anaconda.org/conda-forge/flake8
# https://github.com/conda-forge/flake8-feedstock/blob/main/recipe/meta.yaml
pep8 \
# https://anaconda.org/conda-forge/pep8
# https://github.com/conda-forge/pep8-feedstock/blob/main/recipe/meta.yaml
pyflakes \
# https://anaconda.org/conda-forge/pyflakes
# https://github.com/conda-forge/pyflakes-feedstock/blob/main/recipe/meta.yaml
pylint \
# https://anaconda.org/conda-forge/pylint
# https://github.com/conda-forge/pylint-feedstock/blob/main/recipe/meta.yaml
pytest \
# https://anaconda.org/conda-forge/pytest
# https://github.com/conda-forge/pytest-feedstock/blob/main/recipe/meta.yaml
pytest-cov \
# https://anaconda.org/conda-forge/pytest-cov
# https://github.com/conda-forge/pytest-cov-feedstock/blob/main/recipe/meta.yaml
#
# documentation:
jupyter-book \
# https://anaconda.org/conda-forge/jupyter-book
# https://github.com/conda-forge/jupyter-book-feedstock/blob/main/recipe/meta.yaml
jupytext \
# https://anaconda.org/conda-forge/jupytext
# https://github.com/conda-forge/jupytext-feedstock/blob/main/recipe/meta.yaml
numpydoc \
# https://anaconda.org/conda-forge/numpydoc
# https://github.com/conda-forge/numpydoc-feedstock/blob/main/recipe/meta.yaml
sphinx \
# https://anaconda.org/conda-forge/sphinx
# https://github.com/conda-forge/sphinx-feedstock/blob/main/recipe/meta.yaml
#
# data:
ipydatagrid \
# FIXME: currently holding back ipywidgets to 7.*, see
# https://github.com/bloomberg/ipydatagrid/pull/282 for a
# resolution.
#
# https://anaconda.org/conda-forge/ipydatagrid
# https://github.com/conda-forge/ipydatagrid-feedstock/blob/main/recipe/meta.yaml
ipyparallel \
# https://anaconda.org/conda-forge/ipyparallel
# https://github.com/conda-forge/ipyparallel-feedstock/blob/main/recipe/meta.yaml
lxml \
# https://anaconda.org/conda-forge/lxml
# https://github.com/conda-forge/lxml-feedstock/blob/main/recipe/meta.yaml
pyhdf \
# https://anaconda.org/conda-forge/pyhdf
# https://github.com/conda-forge/pyhdf-feedstock/blob/main/recipe/meta.yaml
vaex \
# https://anaconda.org/conda-forge/vaex
# https://github.com/conda-forge/vaex-feedstock/blob/main/recipe/meta.yaml
mhealpy \
# https://anaconda.org/conda-forge/mhealpy
# https://github.com/conda-forge/mhealpy-feedstock/blob/main/recipe/meta.yaml
pytables \
# https://anaconda.org/conda-forge/pytables
# https://github.com/conda-forge/pytables-feedstock/blob/main/recipe/meta.yaml
statsmodels \
# https://anaconda.org/conda-forge/statsmodels
# https://github.com/conda-forge/statsmodels-feedstock/blob/main/recipe/meta.yaml
xlrd \
# https://anaconda.org/conda-forge/xlrd
# https://github.com/conda-forge/xlrd-feedstock/blob/main/recipe/meta.yaml
jupyter-repo2docker \
# https://anaconda.org/conda-forge/jupyter-repo2docker
# https://github.com/conda-forge/jupyter-repo2docker-feedstock/blob/main/recipe/meta.yaml
#
# IDE:
jupyter-vscode-proxy \
# https://anaconda.org/conda-forge/jupyter-vscode-proxy
# https://github.com/conda-forge/jupyter-vscode-proxy-feedstock/blob/main/recipe/meta.yaml
# NOTE: Requires code-server to be installed.
# https://pypi.org/project/jupyter-vscode-proxy/
jupyterlab-link-share \
# https://anaconda.org/conda-forge/jupyterlab-link-share
# https://github.com/conda-forge/jupyterlab-link-share-feedstock/blob/main/recipe/meta.yaml
# ref: https://github.com/jupyterlab-contrib/jupyterlab-link-share
jupyterlab-git \
# https://anaconda.org/conda-forge/jupyterlab-git
# https://github.com/conda-forge/jupyterlab-git-feedstock/blob/main/recipe/meta.yaml
jupyterlab-system-monitor \
# https://anaconda.org/conda-forge/jupyterlab-system-monitor
# https://github.com/conda-forge/jupyterlab-system-monitor-feedstock/blob/main/recipe/meta.yaml
jupyterlab-favorites \
# https://anaconda.org/conda-forge/jupyterlab-favorites
# https://github.com/conda-forge/jupyterlab-favorites-feedstock/blob/main/recipe/meta.yaml
nbdime \
# https://anaconda.org/conda-forge/nbdime
# https://github.com/conda-forge/nbdime-feedstock/blob/main/recipe/meta.yaml
gh-scoped-creds \
# https://anaconda.org/conda-forge/gh-scoped-creds
# https://github.com/conda-forge/gh-scoped-creds-feedstock/blob/main/recipe/meta.yaml
#
# Additional setup instructions: https://github.com/yuvipanda/gh-scoped-creds#installation
# Additional setup done: https://github.com/2i2c-org/infrastructure/commit/5a9f69b11727965fd4f07571c03eb65de5279fa4
# Related issue: https://github.com/pangeo-data/jupyter-earth/issues/96
retrolab \
# https://anaconda.org/conda-forge/retrolab
# https://github.com/conda-forge/retrolab-feedstock/blob/main/recipe/meta.yaml
ipydrawio \
# a drawio IDE launchable from jupyterlab's launcher
# https://anaconda.org/conda-forge/ipydrawio
# https://github.com/conda-forge/ipydrawio-feedstock/blob/main/recipe/meta.yaml
cython \
fortran-magic \
# https://anaconda.org/conda-forge/fortran-magic
# https://github.com/conda-forge/fortran-magic-feedstock/blob/main/recipe/meta.yaml
google-cloud-sdk \
# https://anaconda.org/conda-forge/google-cloud-sdk
# https://github.com/conda-forge/google-cloud-sdk-feedstock/blob/main/recipe/meta.yaml
sympy \
# https://anaconda.org/conda-forge/sympy
# https://github.com/conda-forge/sympy-feedstock/blob/main/recipe/meta.yaml
# Storage related
#
syncthing \
# https://anaconda.org/conda-forge/syncthing
# We also install jupyter-syncthing-proxy from pip.
#
# /desktop part 4: websockify and firefox
websockify \
# https://anaconda.org/conda-forge/websockify
# optional performance benefit for jupyter-remote-desktop-proxy
firefox \
# https://anaconda.org/conda-forge/firefox
# optional good to have for use with jupyter-remote-desktop-proxy,
# note that we also set it as a default in a command below.
#
&& echo "Installing conda packages complete!"
# We use a conda first approach in this Dockerfile, so only install pip packages
# if you have a clear reason to not use conda.
# https://github.com/pangeo-data/pangeo-docker-images/blob/master/pytorch-notebook/packages.txt
#
RUN echo "Installing pip packages..." \
&& export PATH=${NB_PYTHON_PREFIX}/bin:${PATH} \
&& pip install --no-cache-dir \
https://github.com/jupyterhub/jupyter-remote-desktop-proxy/archive/main.zip \
# /desktop part 5: jupyter-remote-desktop-proxy
#
# jupyter-remote-desktop-proxy enables us to visit the /desktop path
# just like we visit the /lab path. Visiting /desktop provides us
# with an actual remote desktop experience.
#
# NOTE: This package is not available on conda-forge, but available
# on PyPI as jupyter-desktop-server I think but maybe not.
#
# NOTE: This install requires websockify to be installed via
# conda-forge. We have also installed TurboVNC for performance
# I think, and also various apt packages to get a desktop UI.
#
https://github.com/minrk/jupyter-keepalive/archive/main.zip \
# This is a jupyter_server extension that is controllable via a
# JupyterLab plugin to keep a server running.
#
# ref: https://github.com/minrk/jupyter-keepalive
julia \
# To enable doing Julia stuff from Python
# ref: https://pyjulia.readthedocs.io/en/latest/index.html
jupyter-syncthing-proxy \
# We install the conda-forge package syncthing along with this, as
# this is just the glue to expose syncthing.
#
# ref, request: https://github.com/pangeo-data/jupyter-earth/issues/103
# ref, source: https://github.com/yuvipanda/jupyter-syncthing-proxy
# ref, dependency: https://anaconda.org/conda-forge/syncthing
plotly-geo \
# NOTE: This package is not available in conda (conda-forge or
# plotly), even though they describe it to be.
# ref: https://github.com/plotly/plotly.py#extended-geo-support
# jupyter-datasette-proxy \
# FIXME: this is disabled because it malfunctions, and when it does,
# all other jupyter-server-proxy processes fail and we
# observe for example the vscode launcher entry in the
# jupyterlab UI disappears.
# This package is not available in conda
&& echo "Installing pip packages complete!"
# Configure conda/mamba to create new environments within the home folder by
# default. This allows the environments to remain in between restarts of the
# container if only the home folder is persisted.
RUN conda config --system --prepend envs_dirs '~/.conda/envs'
# User environment variables
# Configure PIP always installs to the user's home directory
ENV PIP_USER=True
# Set up micro as the default EDITOR (git, etc). Advanced users will reconfigure
# this to vim/emacs/etc, but this will ensure that less unix-experienced ones
# have a good first experience
ENV EDITOR=micro
ENV VISUAL=micro