init
ci/woodpecker/push/woodpecker Pipeline failed
Details
ci/woodpecker/push/woodpecker Pipeline failed
Details
This commit is contained in:
Malte Grosse
parent
c7e213cd72
commit
6cbee7a51e
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@ -1,16 +1,16 @@
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steps:
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steps:
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publish-container:
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build_and_release:
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image: taywee/woodpecker-buildah:amd64
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image: maltegrosse/woodpecker-buildah:0.0.12
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pull: true
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environment:
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environment:
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- CONDA_CUDA_OVERRIDE=11.2
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- CONDA_CUDA_OVERRIDE=11.2
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- NVIDIA_VISIBLE_DEVICES=all
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- NVIDIA_VISIBLE_DEVICES=all
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settings:
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settings:
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registry: git.sandbox.iuk.hdm-stuttgart.de
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registry: git.sandbox.iuk.hdm-stuttgart.de
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repo: grosse/jupyterlab-datascience-gpu
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repository: grosse/jupyterlab-datascience-gpu
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cache: false
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tag: 4.0.x-gpu-torch
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tag: git.sandbox.iuk.hdm-stuttgart.de/grosse/jupyterlab-datascience-gpu:test
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architectures: aarch64 amd64
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context: Dockerfile
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context: Dockerfile
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imagename: jupyterlab-datascience
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username:
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username:
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from_secret: docker_username
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from_secret: docker_username
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password:
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password:
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182
Dockerfile
182
Dockerfile
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@ -1,183 +1,5 @@
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FROM python:3.10.8-slim-bullseye
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FROM git.sandbox.iuk.hdm-stuttgart.de/grosse/jupyterlab-datascience:4.0.12c
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# debian:bullseye-20230109-slim
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# debian:bullseye-20230109-slim
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ARG NB_USER="jovyan"
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ARG NB_USER="jovyan"
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ARG NB_UID="1000"
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ARG NB_UID="1000"
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ARG NB_GID="100"
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ARG NB_GID="100"
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RUN apt-get 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-get upgrade --yes && \
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apt-get install --yes --no-install-recommends \
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# - bzip2 is necessary to extract the micromamba executable.
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bzip2 \
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ca-certificates \
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ffmpeg \
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git \
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git-lfs \
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locales \
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curl \
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libportaudio2 \
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dnsutils \
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sudo \
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nano \
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build-essential \
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tini \
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wget && \
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apt-get 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 ${NB_UID}
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# Pin python version here, or set it to "default"
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ARG PYTHON_VERSION=3.10
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# Setup work directory for backward-compatibility
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RUN mkdir "/home/${NB_USER}/work" && \
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fix-permissions "/home/${NB_USER}"
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COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
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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 \
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# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
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arch="64"; \
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fi && \
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wget -qO /tmp/micromamba.tar.bz2 \
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"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
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tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
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rm /tmp/micromamba.tar.bz2 && \
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PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
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if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
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# Install the packages
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./micromamba install \
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--root-prefix="${CONDA_DIR}" \
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--prefix="${CONDA_DIR}" \
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--yes \
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"${PYTHON_SPECIFIER}" \
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'mamba' \
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'jupyter_core' && \
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rm micromamba && \
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# Pin major.minor version of python
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mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 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 conda update --all --yes
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#RUN conda install -c conda-forge tensorflow-gpu=2.11 -y
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#RUN CONDA_CUDA_OVERRIDE="11.2" mamba install --yes -c conda-forge tensorflow==2.10.0=cuda112py310*
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ENV CONDA_CUDA_OVERRIDE="11.2"
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ENV NUM_GPUS=1
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#RUN mamba install -y tensorflow cudatoolkit>=11.2 -c conda-forge
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#==2.11.0=cuda*
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#RUN mamba install -y -c conda-forge tensorflow-gpu
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RUN CONDA_OVERRIDE_CUDA="11.2" conda install tensorflow-gpu==2.11.0 -c conda-forge
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RUN CONDA_OVERRIDE_CUDA="11.2" conda install -c conda-forge pytorch-gpu
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WORKDIR /tmp
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RUN mamba install --quiet --yes \
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'notebook==6.4.12' \
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'jupyterhub==2.3.1' \
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'mathjax' \
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'voila==0.3.7' \
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'jupyterlab-git' \
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'numba' \
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'cython' \
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'matplotlib' \
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'pandas' \
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'scipy' \
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'scikit-image' \
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'scikit-learn' \
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'jupyterlab==3.4.3' \
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'ipywebrtc' && \
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jupyter notebook --generate-config && \
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mamba clean --all -f -y && \
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# npm cache clean --force && \
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jupyter lab clean && \
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rm -rf "/home/${NB_USER}/.cache/yarn" && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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ENV JUPYTER_PORT=8888
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EXPOSE $JUPYTER_PORT
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#RUN pip install ipywidgets voila jupyter-collaboration mathjax
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RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-theme
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#RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-data-pool
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#RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-training
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#RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-synthetic-data
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RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-announcement
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RUN pip install sounddevice wavio
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RUN pip install torch==1.13.1+cu116 torchvision==0.14.1+cu116 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu116
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RUN pip install opencv-python-headless
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# Configure container startup
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CMD ["start-notebook.sh"]
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# Copy local files as late as possible to avoid cache busting
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COPY start-notebook.sh start-singleuser.sh /usr/local/bin/
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# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
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COPY jupyter_server_config.py /etc/jupyter/
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# Fix permissions on /etc/jupyter as root
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USER root
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RUN echo 'export PATH=/opt/conda/bin:$PATH' >> /etc/profile
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#RUN source /etc/profile
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# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
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RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
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/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
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fix-permissions /etc/jupyter/
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# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
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||||||
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
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||||||
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
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HEALTHCHECK --interval=5s --timeout=3s --start-period=5s --retries=3 \
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CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
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||||||
http${GEN_CERT:+s}://localhost:${JUPYTER_PORT}${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
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||||||
# Switch back to jovyan to avoid accidental container runs as root
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USER ${NB_UID}
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RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"
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||||||
#USER root
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||||||
WORKDIR "${HOME}"
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||||||
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@ -1,35 +0,0 @@
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#!/bin/bash
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|
||||||
# set permissions on a directory
|
|
||||||
# after any installation, if a directory needs to be (human) user-writable,
|
|
||||||
# run this script on it.
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|
||||||
# It will make everything in the directory owned by the group ${NB_GID}
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|
||||||
# and writable by that group.
|
|
||||||
# Deployments that want to set a specific user id can preserve permissions
|
|
||||||
# by adding the `--group-add users` line to `docker run`.
|
|
||||||
|
|
||||||
# uses find to avoid touching files that already have the right permissions,
|
|
||||||
# which would cause massive image explosion
|
|
||||||
|
|
||||||
# right permissions are:
|
|
||||||
# group=${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 "$@"; do
|
|
||||||
find "${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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||||||
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@ -1,6 +0,0 @@
|
||||||
# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
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|
||||||
|
|
||||||
auto_update_conda: false
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|
||||||
show_channel_urls: true
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|
||||||
channels:
|
|
||||||
- conda-forge
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|
||||||
|
|
@ -1,57 +0,0 @@
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
# mypy: ignore-errors
|
|
||||||
import os
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|
||||||
import stat
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|
||||||
import subprocess
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|
||||||
|
|
||||||
from jupyter_core.paths import jupyter_data_dir
|
|
||||||
|
|
||||||
c = get_config() # noqa: F821
|
|
||||||
c.ServerApp.ip = "0.0.0.0"
|
|
||||||
c.ServerApp.port = 8888
|
|
||||||
c.ServerApp.open_browser = False
|
|
||||||
|
|
||||||
# https://github.com/jupyter/notebook/issues/3130
|
|
||||||
c.FileContentsManager.delete_to_trash = False
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|
||||||
|
|
||||||
# Generate a self-signed certificate
|
|
||||||
OPENSSL_CONFIG = """\
|
|
||||||
[req]
|
|
||||||
distinguished_name = req_distinguished_name
|
|
||||||
[req_distinguished_name]
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|
||||||
"""
|
|
||||||
if "GEN_CERT" in os.environ:
|
|
||||||
dir_name = jupyter_data_dir()
|
|
||||||
pem_file = os.path.join(dir_name, "notebook.pem")
|
|
||||||
os.makedirs(dir_name, exist_ok=True)
|
|
||||||
|
|
||||||
# Generate an openssl.cnf file to set the distinguished name
|
|
||||||
cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
|
|
||||||
if not os.path.isfile(cnf_file):
|
|
||||||
with open(cnf_file, "w") as fh:
|
|
||||||
fh.write(OPENSSL_CONFIG)
|
|
||||||
|
|
||||||
# Generate a certificate if one doesn't exist on disk
|
|
||||||
subprocess.check_call(
|
|
||||||
[
|
|
||||||
"openssl",
|
|
||||||
"req",
|
|
||||||
"-new",
|
|
||||||
"-newkey=rsa:2048",
|
|
||||||
"-days=365",
|
|
||||||
"-nodes",
|
|
||||||
"-x509",
|
|
||||||
"-subj=/C=XX/ST=XX/L=XX/O=generated/CN=generated",
|
|
||||||
f"-keyout={pem_file}",
|
|
||||||
f"-out={pem_file}",
|
|
||||||
]
|
|
||||||
)
|
|
||||||
# Restrict access to the file
|
|
||||||
os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
|
|
||||||
c.ServerApp.certfile = pem_file
|
|
||||||
|
|
||||||
# Change default umask for all subprocesses of the notebook server if set in
|
|
||||||
# the environment
|
|
||||||
if "NB_UMASK" in os.environ:
|
|
||||||
os.umask(int(os.environ["NB_UMASK"], 8))
|
|
||||||
|
|
@ -1,13 +0,0 @@
|
||||||
pipeline:
|
|
||||||
publish-container:
|
|
||||||
image: woodpeckerci/plugin-docker-buildx:2.1.0
|
|
||||||
secrets: [ docker_username, docker_password ]
|
|
||||||
group: docker
|
|
||||||
environment:
|
|
||||||
- CONDA_CUDA_OVERRIDE=11.2
|
|
||||||
- NVIDIA_VISIBLE_DEVICES=all
|
|
||||||
settings:
|
|
||||||
registry: https://git.sandbox.iuk.hdm-stuttgart.de
|
|
||||||
repo: git.sandbox.iuk.hdm-stuttgart.de/grosse/jupyterlab-datascience-gpu
|
|
||||||
dockerfile: Dockerfile
|
|
||||||
tags: latest
|
|
||||||
393
old/Dockerfile
393
old/Dockerfile
|
|
@ -1,393 +0,0 @@
|
||||||
ARG NVIDIA_IMAGE=nvcr.io/nvidia/tensorflow:22.12-tf2-py3
|
|
||||||
|
|
||||||
FROM ${NVIDIA_IMAGE}
|
|
||||||
############################################################################
|
|
||||||
#################### Dependency: jupyter/base-image ########################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
#### copied from https://github.com/jupyter/docker-stacks/tree/main/docker-stacks-foundation
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
# Ubuntu 22.04 (jammy)
|
|
||||||
# https://hub.docker.com/_/ubuntu/tags?page=1&name=jammy
|
|
||||||
ARG ROOT_CONTAINER=ubuntu:22.04
|
|
||||||
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
ARG NB_USER="jovyan"
|
|
||||||
ARG NB_UID="1000"
|
|
||||||
ARG NB_GID="100"
|
|
||||||
|
|
||||||
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
|
|
||||||
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
|
|
||||||
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install all OS dependencies for notebook server that starts but lacks all
|
|
||||||
# features (e.g., download as all possible file formats)
|
|
||||||
ENV DEBIAN_FRONTEND noninteractive
|
|
||||||
RUN apt-get update --yes && \
|
|
||||||
# - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
|
|
||||||
# the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
|
|
||||||
apt-get upgrade --yes && \
|
|
||||||
apt-get install --yes --no-install-recommends \
|
|
||||||
# - bzip2 is necessary to extract the micromamba executable.
|
|
||||||
bzip2 \
|
|
||||||
ca-certificates \
|
|
||||||
locales \
|
|
||||||
sudo \
|
|
||||||
# - tini is installed as a helpful container entrypoint that reaps zombie
|
|
||||||
# processes and such of the actual executable we want to start, see
|
|
||||||
# https://github.com/krallin/tini#why-tini for details.
|
|
||||||
tini \
|
|
||||||
wget && \
|
|
||||||
apt-get clean && rm -rf /var/lib/apt/lists/* && \
|
|
||||||
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
|
|
||||||
locale-gen
|
|
||||||
|
|
||||||
# Configure environment
|
|
||||||
ENV CONDA_DIR=/opt/conda \
|
|
||||||
SHELL=/bin/bash \
|
|
||||||
NB_USER="${NB_USER}" \
|
|
||||||
NB_UID=${NB_UID} \
|
|
||||||
NB_GID=${NB_GID} \
|
|
||||||
LC_ALL=en_US.UTF-8 \
|
|
||||||
LANG=en_US.UTF-8 \
|
|
||||||
LANGUAGE=en_US.UTF-8
|
|
||||||
ENV PATH="${CONDA_DIR}/bin:${PATH}" \
|
|
||||||
HOME="/home/${NB_USER}"
|
|
||||||
|
|
||||||
# Copy a script that we will use to correct permissions after running certain commands
|
|
||||||
COPY fix-permissions /usr/local/bin/fix-permissions
|
|
||||||
RUN chmod a+rx /usr/local/bin/fix-permissions
|
|
||||||
|
|
||||||
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
|
|
||||||
# hadolint ignore=SC2016
|
|
||||||
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
|
|
||||||
# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
|
|
||||||
echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
|
|
||||||
|
|
||||||
# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
|
|
||||||
# and make sure these dirs are writable by the `users` group.
|
|
||||||
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
|
|
||||||
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
|
|
||||||
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
|
|
||||||
useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
|
|
||||||
mkdir -p "${CONDA_DIR}" && \
|
|
||||||
chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
|
|
||||||
chmod g+w /etc/passwd && \
|
|
||||||
fix-permissions "${HOME}" && \
|
|
||||||
fix-permissions "${CONDA_DIR}"
|
|
||||||
|
|
||||||
USER ${NB_UID}
|
|
||||||
|
|
||||||
# Pin python version here, or set it to "default"
|
|
||||||
ARG PYTHON_VERSION=3.10
|
|
||||||
|
|
||||||
# Setup work directory for backward-compatibility
|
|
||||||
RUN mkdir "/home/${NB_USER}/work" && \
|
|
||||||
fix-permissions "/home/${NB_USER}"
|
|
||||||
|
|
||||||
# Download and install Micromamba, and initialize Conda prefix.
|
|
||||||
# <https://github.com/mamba-org/mamba#micromamba>
|
|
||||||
# Similar projects using Micromamba:
|
|
||||||
# - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
|
|
||||||
# - repo2docker: <https://github.com/jupyterhub/repo2docker>
|
|
||||||
# Install Python, Mamba and jupyter_core
|
|
||||||
# Cleanup temporary files and remove Micromamba
|
|
||||||
# Correct permissions
|
|
||||||
# Do all this in a single RUN command to avoid duplicating all of the
|
|
||||||
# files across image layers when the permissions change
|
|
||||||
|
|
||||||
COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
|
|
||||||
WORKDIR /tmp
|
|
||||||
RUN set -x && \
|
|
||||||
arch=$(uname -m) && \
|
|
||||||
if [ "${arch}" = "x86_64" ]; then \
|
|
||||||
# Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
|
|
||||||
arch="64"; \
|
|
||||||
fi && \
|
|
||||||
wget -qO /tmp/micromamba.tar.bz2 \
|
|
||||||
"https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
|
|
||||||
tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
|
|
||||||
rm /tmp/micromamba.tar.bz2 && \
|
|
||||||
PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
|
|
||||||
if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
|
|
||||||
# Install the packages
|
|
||||||
./micromamba install \
|
|
||||||
--root-prefix="${CONDA_DIR}" \
|
|
||||||
--prefix="${CONDA_DIR}" \
|
|
||||||
--yes \
|
|
||||||
"${PYTHON_SPECIFIER}" \
|
|
||||||
'mamba' \
|
|
||||||
'jupyter_core' && \
|
|
||||||
rm micromamba && \
|
|
||||||
# Pin major.minor version of python
|
|
||||||
mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
|
|
||||||
mamba clean --all -f -y && \
|
|
||||||
fix-permissions "${CONDA_DIR}" && \
|
|
||||||
fix-permissions "/home/${NB_USER}"
|
|
||||||
|
|
||||||
EXPOSE 8888
|
|
||||||
|
|
||||||
# Configure container startup
|
|
||||||
ENTRYPOINT ["tini", "-g", "--"]
|
|
||||||
CMD ["start-notebook.sh"]
|
|
||||||
|
|
||||||
# Copy local files as late as possible to avoid cache busting
|
|
||||||
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
|
|
||||||
# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
|
|
||||||
COPY jupyter_server_config.py /etc/jupyter/
|
|
||||||
|
|
||||||
# Fix permissions on /etc/jupyter as root
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
|
|
||||||
RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
|
|
||||||
/etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
|
|
||||||
fix-permissions /etc/jupyter/
|
|
||||||
|
|
||||||
# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
|
|
||||||
# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
|
|
||||||
# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
|
|
||||||
HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
|
|
||||||
CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
|
|
||||||
http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER ${NB_UID}
|
|
||||||
|
|
||||||
WORKDIR "${HOME}"
|
|
||||||
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
################# Dependency: jupyter/minimal-notebook #####################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
ARG OWNER=jupyter
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
|
|
||||||
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
|
|
||||||
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install all OS dependencies for fully functional notebook server
|
|
||||||
RUN apt-get update --yes && \
|
|
||||||
apt-get install --yes --no-install-recommends \
|
|
||||||
# Common useful utilities
|
|
||||||
git \
|
|
||||||
nano-tiny \
|
|
||||||
tzdata \
|
|
||||||
unzip \
|
|
||||||
vim-tiny \
|
|
||||||
# Inkscape is installed to be able to convert SVG files
|
|
||||||
inkscape \
|
|
||||||
# git-over-ssh
|
|
||||||
openssh-client \
|
|
||||||
# less is needed to run help in R
|
|
||||||
# see: https://github.com/jupyter/docker-stacks/issues/1588
|
|
||||||
less \
|
|
||||||
# nbconvert dependencies
|
|
||||||
# https://nbconvert.readthedocs.io/en/latest/install.html#installing-tex
|
|
||||||
texlive-xetex \
|
|
||||||
texlive-fonts-recommended \
|
|
||||||
texlive-plain-generic && \
|
|
||||||
apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
# Create alternative for nano -> nano-tiny
|
|
||||||
RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER ${NB_UID}
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
################# Dependency: jupyter/scipy-notebook #######################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
ARG OWNER=jupyter
|
|
||||||
|
|
||||||
LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
|
|
||||||
|
|
||||||
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
|
|
||||||
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
|
|
||||||
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
RUN apt-get update --yes && \
|
|
||||||
apt-get install --yes --no-install-recommends \
|
|
||||||
# for cython: https://cython.readthedocs.io/en/latest/src/quickstart/install.html
|
|
||||||
build-essential \
|
|
||||||
# for latex labels
|
|
||||||
cm-super \
|
|
||||||
dvipng \
|
|
||||||
# for matplotlib anim
|
|
||||||
ffmpeg && \
|
|
||||||
apt-get clean && rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
USER ${NB_UID}
|
|
||||||
|
|
||||||
# Install Python 3 packages
|
|
||||||
RUN mamba install --quiet --yes \
|
|
||||||
'altair' \
|
|
||||||
'beautifulsoup4' \
|
|
||||||
'bokeh' \
|
|
||||||
'bottleneck' \
|
|
||||||
'cloudpickle' \
|
|
||||||
'conda-forge::blas=*=openblas' \
|
|
||||||
'cython' \
|
|
||||||
'dask' \
|
|
||||||
'dill' \
|
|
||||||
'h5py' \
|
|
||||||
'ipympl'\
|
|
||||||
'ipywidgets' \
|
|
||||||
'matplotlib-base' \
|
|
||||||
'numba' \
|
|
||||||
'numexpr' \
|
|
||||||
'pandas' \
|
|
||||||
'patsy' \
|
|
||||||
'protobuf' \
|
|
||||||
'pytables' \
|
|
||||||
'scikit-image' \
|
|
||||||
'scikit-learn' \
|
|
||||||
'scipy' \
|
|
||||||
'seaborn' \
|
|
||||||
'sqlalchemy' \
|
|
||||||
'statsmodels' \
|
|
||||||
'sympy' \
|
|
||||||
'widgetsnbextension'\
|
|
||||||
'xlrd' && \
|
|
||||||
mamba clean --all -f -y && \
|
|
||||||
fix-permissions "${CONDA_DIR}" && \
|
|
||||||
fix-permissions "/home/${NB_USER}"
|
|
||||||
|
|
||||||
# Install facets which does not have a pip or conda package at the moment
|
|
||||||
WORKDIR /tmp
|
|
||||||
RUN git clone https://github.com/PAIR-code/facets.git && \
|
|
||||||
jupyter nbextension install facets/facets-dist/ --sys-prefix && \
|
|
||||||
rm -rf /tmp/facets && \
|
|
||||||
fix-permissions "${CONDA_DIR}" && \
|
|
||||||
fix-permissions "/home/${NB_USER}"
|
|
||||||
|
|
||||||
# Import matplotlib the first time to build the font cache.
|
|
||||||
ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
|
|
||||||
|
|
||||||
RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
|
|
||||||
fix-permissions "/home/${NB_USER}"
|
|
||||||
|
|
||||||
USER ${NB_UID}
|
|
||||||
|
|
||||||
WORKDIR "${HOME}"
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
################ copied from https://github.com/iot-salzburg/gpu-jupyter/tree/master/src
|
|
||||||
|
|
||||||
|
|
||||||
# LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
|
|
||||||
|
|
||||||
#tensorflow 2.10.1 requires keras<2.11,>=2.10.0, but you have keras 2.11.0
|
|
||||||
|
|
||||||
# Install Tensorflow, check compatibility here:
|
|
||||||
# https://www.tensorflow.org/install/source#gpu
|
|
||||||
# installation via conda leads to errors in version 4.8.2
|
|
||||||
RUN pip install --upgrade pip && \
|
|
||||||
pip install --no-cache-dir "tensorflow==2.11.0"
|
|
||||||
RUN pip install --upgrade pip && \
|
|
||||||
pip install --no-cache-dir keras==2.11.0
|
|
||||||
|
|
||||||
# Install PyTorch with dependencies
|
|
||||||
RUN conda install --quiet --yes \
|
|
||||||
pyyaml mkl mkl-include setuptools cmake cffi typing && \
|
|
||||||
conda clean --all -f -y && \
|
|
||||||
fix-permissions $CONDA_DIR && \
|
|
||||||
fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
# Check compatibility here:
|
|
||||||
# https://pytorch.org/get-started/locally/
|
|
||||||
# Installation via conda leads to errors installing cudatoolkit=11.1
|
|
||||||
RUN pip install --no-cache-dir torch torchvision torchaudio torchviz --extra-index-url https://download.pytorch.org/whl/cu116
|
|
||||||
|
|
||||||
ENV CUDA_PATH=/opt/conda/
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
# Install nvtop to monitor the gpu tasks
|
|
||||||
RUN apt-get update && \
|
|
||||||
apt-get install -y cmake libncurses5-dev libncursesw5-dev git && \
|
|
||||||
rm -rf /var/lib/apt/lists/*
|
|
||||||
|
|
||||||
RUN git clone https://github.com/Syllo/nvtop.git /run/nvtop && \
|
|
||||||
mkdir -p /run/nvtop/build && cd /run/nvtop/build && \
|
|
||||||
(cmake .. -DNVML_RETRIEVE_HEADER_ONLINE=True 2> /dev/null || echo "cmake was not successful") && \
|
|
||||||
(make 2> /dev/null || echo "make was not successful") && \
|
|
||||||
(make install 2> /dev/null || echo "make install was not successful") && \
|
|
||||||
cd /tmp && rm -rf /tmp/nvtop
|
|
||||||
|
|
||||||
RUN fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
|
|
||||||
############################################################################
|
|
||||||
############################ Useful packages ###############################
|
|
||||||
############################################################################
|
|
||||||
|
|
||||||
LABEL authors="Christoph Schranz <christoph.schranz@salzburgresearch.at>, Mathematical Michael <consistentbayes@gmail.com>"
|
|
||||||
|
|
||||||
USER root
|
|
||||||
|
|
||||||
RUN pip install --no-cache-dir ipyleaflet "plotly>=4.14.3" "ipywidgets>=7.5"
|
|
||||||
RUN conda install -c conda-forge nodejs
|
|
||||||
# Install important packages and Graphviz
|
|
||||||
RUN set -ex \
|
|
||||||
&& buildDeps=' \
|
|
||||||
graphviz==0.19.1 \
|
|
||||||
' \
|
|
||||||
&& apt-get update \
|
|
||||||
&& apt-get -y install htop apt-utils iputils-ping graphviz libgraphviz-dev openssh-client \
|
|
||||||
&& pip install --no-cache-dir $buildDeps
|
|
||||||
|
|
||||||
# Install various extensions
|
|
||||||
RUN fix-permissions $CONDA_DIR
|
|
||||||
|
|
||||||
# RUN jupyter labextension install @jupyterlab/github
|
|
||||||
# RUN pip install jupyterlab-git
|
|
||||||
RUN pip install jupyterlab-drawio
|
|
||||||
RUN jupyter nbextension enable --py --sys-prefix ipyleaflet
|
|
||||||
|
|
||||||
RUN jupyter labextension install jupyterlab-plotly
|
|
||||||
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager plotlywidget
|
|
||||||
# RUN pip install --no-cache-dir jupyter-tabnine --user && \
|
|
||||||
# jupyter nbextension install --py jupyter_tabnine --user && \
|
|
||||||
# jupyter nbextension enable --py jupyter_tabnine --user && \
|
|
||||||
# jupyter serverextension enable --py jupyter_tabnine --user
|
|
||||||
RUN pip install --no-cache-dir jupyter_contrib_nbextensions \
|
|
||||||
jupyter_nbextensions_configurator rise
|
|
||||||
# jupyter nbextension enable codefolding/main
|
|
||||||
RUN jupyter labextension install @ijmbarr/jupyterlab_spellchecker
|
|
||||||
|
|
||||||
RUN fix-permissions /home/$NB_USER
|
|
||||||
|
|
||||||
|
|
||||||
## add sandbox plugins
|
|
||||||
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-theme
|
|
||||||
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-data-pool
|
|
||||||
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-training
|
|
||||||
RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-synthetic-data
|
|
||||||
|
|
||||||
# Switch back to jovyan to avoid accidental container runs as root
|
|
||||||
USER $NB_UID
|
|
||||||
|
|
||||||
# Copy jupyter_notebook_config.json
|
|
||||||
#COPY jupyter_notebook_config.json /etc/jupyter/
|
|
||||||
|
|
@ -1,5 +0,0 @@
|
||||||
{
|
|
||||||
"NotebookApp": {
|
|
||||||
"password": "sha1:3b4b6378355:642693b20f0a33bcad27b94293d0ed7db3408322"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
262
old/start.sh
262
old/start.sh
|
|
@ -1,262 +0,0 @@
|
||||||
#!/bin/bash
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
set -e
|
|
||||||
|
|
||||||
# The _log function is used for everything this script wants to log. It will
|
|
||||||
# always log errors and warnings, but can be silenced for other messages
|
|
||||||
# by setting JUPYTER_DOCKER_STACKS_QUIET environment variable.
|
|
||||||
_log () {
|
|
||||||
if [[ "$*" == "ERROR:"* ]] || [[ "$*" == "WARNING:"* ]] || [[ "${JUPYTER_DOCKER_STACKS_QUIET}" == "" ]]; then
|
|
||||||
echo "$@"
|
|
||||||
fi
|
|
||||||
}
|
|
||||||
_log "Entered start.sh with args:" "$@"
|
|
||||||
|
|
||||||
# The run-hooks function looks for .sh scripts to source and executable files to
|
|
||||||
# run within a passed directory.
|
|
||||||
run-hooks () {
|
|
||||||
if [[ ! -d "${1}" ]] ; then
|
|
||||||
return
|
|
||||||
fi
|
|
||||||
_log "${0}: running hooks in ${1} as uid / gid: $(id -u) / $(id -g)"
|
|
||||||
for f in "${1}/"*; do
|
|
||||||
case "${f}" in
|
|
||||||
*.sh)
|
|
||||||
_log "${0}: running script ${f}"
|
|
||||||
# shellcheck disable=SC1090
|
|
||||||
source "${f}"
|
|
||||||
;;
|
|
||||||
*)
|
|
||||||
if [[ -x "${f}" ]] ; then
|
|
||||||
_log "${0}: running executable ${f}"
|
|
||||||
"${f}"
|
|
||||||
else
|
|
||||||
_log "${0}: ignoring non-executable ${f}"
|
|
||||||
fi
|
|
||||||
;;
|
|
||||||
esac
|
|
||||||
done
|
|
||||||
_log "${0}: done running hooks in ${1}"
|
|
||||||
}
|
|
||||||
|
|
||||||
# A helper function to unset env vars listed in the value of the env var
|
|
||||||
# JUPYTER_ENV_VARS_TO_UNSET.
|
|
||||||
unset_explicit_env_vars () {
|
|
||||||
if [ -n "${JUPYTER_ENV_VARS_TO_UNSET}" ]; then
|
|
||||||
for env_var_to_unset in $(echo "${JUPYTER_ENV_VARS_TO_UNSET}" | tr ',' ' '); do
|
|
||||||
echo "Unset ${env_var_to_unset} due to JUPYTER_ENV_VARS_TO_UNSET"
|
|
||||||
unset "${env_var_to_unset}"
|
|
||||||
done
|
|
||||||
unset JUPYTER_ENV_VARS_TO_UNSET
|
|
||||||
fi
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
# Default to starting bash if no command was specified
|
|
||||||
if [ $# -eq 0 ]; then
|
|
||||||
cmd=( "bash" )
|
|
||||||
else
|
|
||||||
cmd=( "$@" )
|
|
||||||
fi
|
|
||||||
|
|
||||||
# NOTE: This hook will run as the user the container was started with!
|
|
||||||
run-hooks /usr/local/bin/start-notebook.d
|
|
||||||
|
|
||||||
# If the container started as the root user, then we have permission to refit
|
|
||||||
# the jovyan user, and ensure file permissions, grant sudo rights, and such
|
|
||||||
# things before we run the command passed to start.sh as the desired user
|
|
||||||
# (NB_USER).
|
|
||||||
#
|
|
||||||
if [ "$(id -u)" == 0 ] ; then
|
|
||||||
# Environment variables:
|
|
||||||
# - NB_USER: the desired username and associated home folder
|
|
||||||
# - NB_UID: the desired user id
|
|
||||||
# - NB_GID: a group id we want our user to belong to
|
|
||||||
# - NB_GROUP: a group name we want for the group
|
|
||||||
# - GRANT_SUDO: a boolean ("1" or "yes") to grant the user sudo rights
|
|
||||||
# - CHOWN_HOME: a boolean ("1" or "yes") to chown the user's home folder
|
|
||||||
# - CHOWN_EXTRA: a comma separated list of paths to chown
|
|
||||||
# - CHOWN_HOME_OPTS / CHOWN_EXTRA_OPTS: arguments to the chown commands
|
|
||||||
|
|
||||||
# Refit the jovyan user to the desired the user (NB_USER)
|
|
||||||
if id jovyan &> /dev/null ; then
|
|
||||||
if ! usermod --home "/home/${NB_USER}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
|
|
||||||
_log "Updated the jovyan user:"
|
|
||||||
_log "- username: jovyan -> ${NB_USER}"
|
|
||||||
_log "- home dir: /home/jovyan -> /home/${NB_USER}"
|
|
||||||
fi
|
|
||||||
elif ! id -u "${NB_USER}" &> /dev/null; then
|
|
||||||
_log "ERROR: Neither the jovyan user or '${NB_USER}' exists. This could be the result of stopping and starting, the container with a different NB_USER environment variable."
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
# Ensure the desired user (NB_USER) gets its desired user id (NB_UID) and is
|
|
||||||
# a member of the desired group (NB_GROUP, NB_GID)
|
|
||||||
if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
|
|
||||||
_log "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
|
|
||||||
# Ensure the desired group's existence
|
|
||||||
if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
|
|
||||||
groupadd --force --gid "${NB_GID}" --non-unique "${NB_GROUP:-${NB_USER}}"
|
|
||||||
fi
|
|
||||||
# Recreate the desired user as we want it
|
|
||||||
userdel "${NB_USER}"
|
|
||||||
useradd --home "/home/${NB_USER}" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 --no-log-init "${NB_USER}"
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Move or symlink the jovyan home directory to the desired users home
|
|
||||||
# directory if it doesn't already exist, and update the current working
|
|
||||||
# directory to the new location if needed.
|
|
||||||
if [[ "${NB_USER}" != "jovyan" ]]; then
|
|
||||||
if [[ ! -e "/home/${NB_USER}" ]]; then
|
|
||||||
_log "Attempting to copy /home/jovyan to /home/${NB_USER}..."
|
|
||||||
mkdir "/home/${NB_USER}"
|
|
||||||
if cp -a /home/jovyan/. "/home/${NB_USER}/"; then
|
|
||||||
_log "Success!"
|
|
||||||
else
|
|
||||||
_log "Failed to copy data from /home/jovyan to /home/${NB_USER}!"
|
|
||||||
_log "Attempting to symlink /home/jovyan to /home/${NB_USER}..."
|
|
||||||
if ln -s /home/jovyan "/home/${NB_USER}"; then
|
|
||||||
_log "Success creating symlink!"
|
|
||||||
else
|
|
||||||
_log "ERROR: Failed copy data from /home/jovyan to /home/${NB_USER} or to create symlink!"
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
# Ensure the current working directory is updated to the new path
|
|
||||||
if [[ "${PWD}/" == "/home/jovyan/"* ]]; then
|
|
||||||
new_wd="/home/${NB_USER}/${PWD:13}"
|
|
||||||
_log "Changing working directory to ${new_wd}"
|
|
||||||
cd "${new_wd}"
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Optionally ensure the desired user get filesystem ownership of it's home
|
|
||||||
# folder and/or additional folders
|
|
||||||
if [[ "${CHOWN_HOME}" == "1" || "${CHOWN_HOME}" == "yes" ]]; then
|
|
||||||
_log "Ensuring /home/${NB_USER} is owned by ${NB_UID}:${NB_GID} ${CHOWN_HOME_OPTS:+(chown options: ${CHOWN_HOME_OPTS})}"
|
|
||||||
# shellcheck disable=SC2086
|
|
||||||
chown ${CHOWN_HOME_OPTS} "${NB_UID}:${NB_GID}" "/home/${NB_USER}"
|
|
||||||
fi
|
|
||||||
if [ -n "${CHOWN_EXTRA}" ]; then
|
|
||||||
for extra_dir in $(echo "${CHOWN_EXTRA}" | tr ',' ' '); do
|
|
||||||
_log "Ensuring ${extra_dir} is owned by ${NB_UID}:${NB_GID} ${CHOWN_EXTRA_OPTS:+(chown options: ${CHOWN_EXTRA_OPTS})}"
|
|
||||||
# shellcheck disable=SC2086
|
|
||||||
chown ${CHOWN_EXTRA_OPTS} "${NB_UID}:${NB_GID}" "${extra_dir}"
|
|
||||||
done
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Update potentially outdated environment variables since image build
|
|
||||||
export XDG_CACHE_HOME="/home/${NB_USER}/.cache"
|
|
||||||
|
|
||||||
# Prepend ${CONDA_DIR}/bin to sudo secure_path
|
|
||||||
sed -r "s#Defaults\s+secure_path\s*=\s*\"?([^\"]+)\"?#Defaults secure_path=\"${CONDA_DIR}/bin:\1\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
|
|
||||||
|
|
||||||
# Optionally grant passwordless sudo rights for the desired user
|
|
||||||
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == "yes" ]]; then
|
|
||||||
_log "Granting ${NB_USER} passwordless sudo rights!"
|
|
||||||
echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/added-by-start-script
|
|
||||||
fi
|
|
||||||
|
|
||||||
# NOTE: This hook is run as the root user!
|
|
||||||
run-hooks /usr/local/bin/before-notebook.d
|
|
||||||
|
|
||||||
unset_explicit_env_vars
|
|
||||||
_log "Running as ${NB_USER}:" "${cmd[@]}"
|
|
||||||
exec sudo --preserve-env --set-home --user "${NB_USER}" \
|
|
||||||
PATH="${PATH}" \
|
|
||||||
PYTHONPATH="${PYTHONPATH:-}" \
|
|
||||||
"${cmd[@]}"
|
|
||||||
# Notes on how we ensure that the environment that this container is started
|
|
||||||
# with is preserved (except vars listed in JUPYTER_ENV_VARS_TO_UNSET) when
|
|
||||||
# we transition from running as root to running as NB_USER.
|
|
||||||
#
|
|
||||||
# - We use `sudo` to execute the command as NB_USER. What then
|
|
||||||
# happens to the environment will be determined by configuration in
|
|
||||||
# /etc/sudoers and /etc/sudoers.d/* as well as flags we pass to the sudo
|
|
||||||
# command. The behavior can be inspected with `sudo -V` run as root.
|
|
||||||
#
|
|
||||||
# ref: `man sudo` https://linux.die.net/man/8/sudo
|
|
||||||
# ref: `man sudoers` https://www.sudo.ws/man/1.8.15/sudoers.man.html
|
|
||||||
#
|
|
||||||
# - We use the `--preserve-env` flag to pass through most environment
|
|
||||||
# variables, but understand that exceptions are caused by the sudoers
|
|
||||||
# configuration: `env_delete` and `env_check`.
|
|
||||||
#
|
|
||||||
# - We use the `--set-home` flag to set the HOME variable appropriately.
|
|
||||||
#
|
|
||||||
# - To reduce the default list of variables deleted by sudo, we could have
|
|
||||||
# used `env_delete` from /etc/sudoers. It has higher priority than the
|
|
||||||
# `--preserve-env` flag and the `env_keep` configuration.
|
|
||||||
#
|
|
||||||
# - We preserve PATH and PYTHONPATH explicitly. Note however that sudo
|
|
||||||
# resolves `${cmd[@]}` using the "secure_path" variable we modified
|
|
||||||
# above in /etc/sudoers.d/path. Thus PATH is irrelevant to how the above
|
|
||||||
# sudo command resolves the path of `${cmd[@]}`. The PATH will be relevant
|
|
||||||
# for resolving paths of any subprocesses spawned by `${cmd[@]}`.
|
|
||||||
|
|
||||||
# The container didn't start as the root user, so we will have to act as the
|
|
||||||
# user we started as.
|
|
||||||
else
|
|
||||||
# Warn about misconfiguration of: granting sudo rights
|
|
||||||
if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == "yes" ]]; then
|
|
||||||
_log "WARNING: container must be started as root to grant sudo permissions!"
|
|
||||||
fi
|
|
||||||
|
|
||||||
JOVYAN_UID="$(id -u jovyan 2>/dev/null)" # The default UID for the jovyan user
|
|
||||||
JOVYAN_GID="$(id -g jovyan 2>/dev/null)" # The default GID for the jovyan user
|
|
||||||
|
|
||||||
# Attempt to ensure the user uid we currently run as has a named entry in
|
|
||||||
# the /etc/passwd file, as it avoids software crashing on hard assumptions
|
|
||||||
# on such entry. Writing to the /etc/passwd was allowed for the root group
|
|
||||||
# from the Dockerfile during build.
|
|
||||||
#
|
|
||||||
# ref: https://github.com/jupyter/docker-stacks/issues/552
|
|
||||||
if ! whoami &> /dev/null; then
|
|
||||||
_log "There is no entry in /etc/passwd for our UID=$(id -u). Attempting to fix..."
|
|
||||||
if [[ -w /etc/passwd ]]; then
|
|
||||||
_log "Renaming old jovyan user to nayvoj ($(id -u jovyan):$(id -g jovyan))"
|
|
||||||
|
|
||||||
# We cannot use "sed --in-place" since sed tries to create a temp file in
|
|
||||||
# /etc/ and we may not have write access. Apply sed on our own temp file:
|
|
||||||
sed --expression="s/^jovyan:/nayvoj:/" /etc/passwd > /tmp/passwd
|
|
||||||
echo "${NB_USER}:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
|
|
||||||
cat /tmp/passwd > /etc/passwd
|
|
||||||
rm /tmp/passwd
|
|
||||||
|
|
||||||
_log "Added new ${NB_USER} user ($(id -u):$(id -g)). Fixed UID!"
|
|
||||||
|
|
||||||
if [[ "${NB_USER}" != "jovyan" ]]; then
|
|
||||||
_log "WARNING: user is ${NB_USER} but home is /home/jovyan. You must run as root to rename the home directory!"
|
|
||||||
fi
|
|
||||||
else
|
|
||||||
_log "WARNING: unable to fix missing /etc/passwd entry because we don't have write permission. Try setting gid=0 with \"--user=$(id -u):0\"."
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Warn about misconfiguration of: desired username, user id, or group id.
|
|
||||||
# A misconfiguration occurs when the user modifies the default values of
|
|
||||||
# NB_USER, NB_UID, or NB_GID, but we cannot update those values because we
|
|
||||||
# are not root.
|
|
||||||
if [[ "${NB_USER}" != "jovyan" && "${NB_USER}" != "$(id -un)" ]]; then
|
|
||||||
_log "WARNING: container must be started as root to change the desired user's name with NB_USER=\"${NB_USER}\"!"
|
|
||||||
fi
|
|
||||||
if [[ "${NB_UID}" != "${JOVYAN_UID}" && "${NB_UID}" != "$(id -u)" ]]; then
|
|
||||||
_log "WARNING: container must be started as root to change the desired user's id with NB_UID=\"${NB_UID}\"!"
|
|
||||||
fi
|
|
||||||
if [[ "${NB_GID}" != "${JOVYAN_GID}" && "${NB_GID}" != "$(id -g)" ]]; then
|
|
||||||
_log "WARNING: container must be started as root to change the desired user's group id with NB_GID=\"${NB_GID}\"!"
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Warn if the user isn't able to write files to ${HOME}
|
|
||||||
if [[ ! -w /home/jovyan ]]; then
|
|
||||||
_log "WARNING: no write access to /home/jovyan. Try starting the container with group 'users' (100), e.g. using \"--group-add=users\"."
|
|
||||||
fi
|
|
||||||
|
|
||||||
# NOTE: This hook is run as the user we started the container as!
|
|
||||||
run-hooks /usr/local/bin/before-notebook.d
|
|
||||||
unset_explicit_env_vars
|
|
||||||
_log "Executing the command:" "${cmd[@]}"
|
|
||||||
exec "${cmd[@]}"
|
|
||||||
fi
|
|
||||||
|
|
@ -1,22 +0,0 @@
|
||||||
#!/bin/bash
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
set -e
|
|
||||||
|
|
||||||
# The Jupyter command to launch
|
|
||||||
# JupyterLab by default
|
|
||||||
DOCKER_STACKS_JUPYTER_CMD="${DOCKER_STACKS_JUPYTER_CMD:=lab}"
|
|
||||||
|
|
||||||
if [[ -n "${JUPYTERHUB_API_TOKEN}" ]]; then
|
|
||||||
echo "WARNING: using start-singleuser.sh instead of start-notebook.sh to start a server associated with JupyterHub."
|
|
||||||
exec /usr/local/bin/start-singleuser.sh "$@"
|
|
||||||
fi
|
|
||||||
|
|
||||||
wrapper=""
|
|
||||||
if [[ "${RESTARTABLE}" == "yes" ]]; then
|
|
||||||
wrapper="run-one-constantly"
|
|
||||||
fi
|
|
||||||
|
|
||||||
# shellcheck disable=SC1091,SC2086
|
|
||||||
exec /usr/local/bin/start.sh ${wrapper} jupyter ${DOCKER_STACKS_JUPYTER_CMD} ${NOTEBOOK_ARGS} "$@"
|
|
||||||
|
|
@ -1,13 +0,0 @@
|
||||||
#!/bin/bash
|
|
||||||
# Copyright (c) Jupyter Development Team.
|
|
||||||
# Distributed under the terms of the Modified BSD License.
|
|
||||||
|
|
||||||
set -e
|
|
||||||
|
|
||||||
# set default ip to 0.0.0.0
|
|
||||||
if [[ "${NOTEBOOK_ARGS} $*" != *"--ip="* ]]; then
|
|
||||||
NOTEBOOK_ARGS="--ip=0.0.0.0 ${NOTEBOOK_ARGS}"
|
|
||||||
fi
|
|
||||||
|
|
||||||
# shellcheck disable=SC1091,SC2086
|
|
||||||
. /usr/local/bin/start.sh jupyterhub-singleuser ${NOTEBOOK_ARGS} "$@"
|
|
||||||
Loading…
Reference in New Issue