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add dockerfile and workflow to build a jupyter
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‎.github/workflows/docker-jupyter-image.yml‎

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name: ghcr
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#on:
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# push:
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# branches: [ "main" ]
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# pull_request:
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# branches: [ "main" ]
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jobs:
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build:
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runs-on: ubuntu-latest
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permissions:
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packages: write
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contents: read
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steps:
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- name: 'clone the repo'
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uses: actions/checkout@v4
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- name: 'login to ghcr'
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{github.actor}}
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password: ${{secrets.GITHUB_TOKEN}}
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: ./containers
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file: ./containters/Dockerfile.jupyter
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push: true
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tags: |
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ghcr.io/stfc/janus-core/jupyter:${{ github.sha }}
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ghcr.io/stfc/janus-core/jupyter:latest

‎containers/Dockerfile.jupyter‎

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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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# this is adapted from above.
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ARG ROOT_CONTAINER=ubuntu:25.04
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FROM $ROOT_CONTAINER
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LABEL maintainer="Alin Elena <[email protected]>"
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ARG NB_USER="jovyan"
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ARG NB_UID="1001"
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ARG NB_GID="100"
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USER root
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# Install all OS dependencies for notebook server that starts but lacks all
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# features (e.g., download as all possible file formats)
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt update --yes && \
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# - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
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# the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
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apt upgrade --yes && \
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apt install --yes --no-install-recommends \
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ca-certificates \
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fonts-liberation \
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locales \
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# - pandoc is used to convert notebooks to html files
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# it's not present in arm64 ubuntu image, so we install it here
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pandoc \
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# - run-one - a wrapper script that runs no more
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# than one unique instance of some command with a unique set of arguments,
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# we use `run-one-constantly` to support `RESTARTABLE` option
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run-one \
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sudo \
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# - tini is installed as a helpful container entrypoint that reaps zombie
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# processes and such of the actual executable we want to start, see
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# https://github.com/krallin/tini#why-tini for details.
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tini \
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wget bzip2 && \
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apt clean && rm -rf /var/lib/apt/lists/* && \
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echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
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locale-gen
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# Configure environment
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ENV CONDA_DIR=/opt/conda \
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SHELL=/bin/bash \
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NB_USER="${NB_USER}" \
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NB_UID=${NB_UID} \
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NB_GID=${NB_GID} \
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LC_ALL=en_US.UTF-8 \
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LANG=en_US.UTF-8 \
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LANGUAGE=en_US.UTF-8
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ENV PATH="${CONDA_DIR}/bin:${PATH}" \
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HOME="/home/${NB_USER}"
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# Copy a script that we will use to correct permissions after running certain commands
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COPY fix-permissions /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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# hadolint ignore=SC2016
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
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# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
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# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
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# and make sure these dirs are writable by the `users` group.
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
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sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
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useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
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mkdir -p "${CONDA_DIR}" && \
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chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
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chmod g+w /etc/passwd && \
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fix-permissions "${HOME}" && \
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fix-permissions "${CONDA_DIR}"
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USER ${NB_UID}
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ARG PYTHON_VERSION=3.12
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# Setup work directory for backward-compatibility
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RUN mkdir "/home/${NB_USER}/work" && \
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fix-permissions "/home/${NB_USER}"
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# Install conda as jovyan and check the sha256 sum provided on the download site
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WORKDIR /tmp
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RUN set -x && \
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arch=$(uname -m) && \
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if [ "${arch}" = "x86_64" ]; then arch="64"; fi && \
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wget --progress=dot:giga -O - "https://micro.mamba.pm/api/micromamba/linux-${arch}/latest" | tar -xvj bin/micromamba && \
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PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
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if [ "${PYTHON_VERSION}" = "default" ]; then PYTHON_SPECIFIER="python"; fi && \
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./bin/micromamba install \
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--root-prefix="${CONDA_DIR}" \
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--prefix="${CONDA_DIR}" \
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--yes \
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'jupyter_core' \
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'conda' \
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'mamba' \
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"${PYTHON_SPECIFIER}" && \
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rm -rf /tmp/bin/ && \
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mamba list --full-name 'python' | awk 'END{sub("[^.]*$", "*", $2); print $1 " " $2}' >> "${CONDA_DIR}/conda-meta/pinned" && \
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mamba clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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RUN rm -rf "/home/${NB_USER}/.cache/"
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# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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#============
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#minimal image now
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USER root
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RUN apt update --yes && \
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apt install --yes --no-install-recommends \
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cm-super \
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dvipng && \
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apt clean && rm -rf /var/lib/apt/lists/*
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USER ${NB_UID}
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# Install Python 3 packages
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RUN mamba install --yes \
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'altair' \
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'beautifulsoup4' \
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'bokeh' \
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'bottleneck' \
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'cloudpickle' \
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'conda-forge::blas=*=openblas' \
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'conda-forge::gfortran' \
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'conda-forge::hdf5' \
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'cython' \
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'dask' \
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'dill' \
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'h5py' \
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'ipympl'\
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'ipywidgets' \
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'matplotlib-base' \
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'numba' \
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'numexpr' \
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'pandas' \
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'openpyxl' \
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'patsy' \
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'protobuf' \
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'pytables' \
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'scikit-image' \
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'scikit-learn' \
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'scipy' \
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'seaborn' \
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'sqlalchemy' \
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'statsmodels' \
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'sympy' \
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'widgetsnbextension'\
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'xlrd' \
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'meson' \
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'spglib' && \
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mamba clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Import matplotlib the first time to build the font cache.
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ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions "/home/${NB_USER}"
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USER root
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RUN apt -y update && apt -y upgrade\
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&& apt install -y git pkg-config cmake && \
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apt clean && rm -rf /var/lib/apt/lists/*
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RUN chown -R $NB_UID:$NB_GID $HOME
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COPY --chown=$NB_UID:$NB_GID environment.yml /tmp
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USER $NB_USER
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RUN . /opt/conda/bin/activate && \
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mamba env update --quiet --file /tmp/environment.yml && \
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mamba clean --all -f -y && \
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rm -rf "/home/${NB_USER}/.cache"
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WORKDIR "${HOME}"

‎containers/environment.yml‎

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channels:
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- conda-forge
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- nodefaults
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dependencies:
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- pip
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- pip:
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- git+https://github.com/imagdau/aseMolec@main
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- skmatter
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- pymatgen
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- tqdm
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- pack-mm
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- 'janus-core[all]@git+https://github.com/stfc/janus-core.git@main'
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- git+https://github.com/ChengUCB/les.git
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# - git+https://github.com/ACEsuit/mace.git@develop
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- torch-dftd
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# - git+https://github.com/CheukHinHoJerry/torch-dftd.git
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- cuequivariance==0.5.1
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- cuequivariance-torch==0.5.1
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- cuequivariance-ops-torch-cu12==0.5.1
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- torchvision
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- weas-widget
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- seaborn
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- data-tutorials
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- opentsne

‎containers/fix-permissions‎

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#!/bin/bash
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# set permissions on a directory
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# after any installation, if a directory needs to be (human) user-writable,
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# run this script on it.
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# It will make everything in the directory owned by the group ${NB_GID}
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# and writable by that group.
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# Deployments that want to set a specific user id can preserve permissions
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# by adding the `--group-add users` line to `docker run`.
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# uses find to avoid touching files that already have the right permissions,
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# which would cause massive image explosion
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# right permissions are:
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# group=${NB_GID}
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# AND permissions include group rwX (directory-execute)
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# AND directories have setuid,setgid bits set
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set -e
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for d in "$@"; do
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find "${d}" \
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! \( \
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-group "${NB_GID}" \
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-a -perm -g+rwX \
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\) \
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-exec chgrp "${NB_GID}" {} \; \
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-exec chmod g+rwX {} \;
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# setuid, setgid *on directories only*
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find "${d}" \
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\( \
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-type d \
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-a ! -perm -6000 \
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\) \
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-exec chmod +6000 {} \;
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done

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