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variables:

  docker_registry_user: "robot$$gitlab"

stages:

stages:

  - build

  - build

    - tags

    - tags

  tags:

  tags:

    - shell-runner

    - shell-runner

build_latest_dev_image:

  stage: build

  script:

    - docker build -f base/Dockerfile -t docker-registry.ebrains.eu/clb-jupyter-image/ebrains:dev-$CI_COMMIT_SHORT_SHA .

    - docker login -u $docker_registry_user -p $docker_registry_prod_token docker-registry.ebrains.eu

    - docker push docker-registry.ebrains.eu/clb-jupyter-image/ebrains:dev-$CI_COMMIT_SHORT_SHA

  when: manual

  tags:

    - shell-runner

[Machine]

spalloc_server = https://spinnaker.cs.man.ac.uk/spalloc/

[Java]

use_java = True

FROM ubuntu:focal

# https://jupyter-docker-stacks.readthedocs.io/en/latest/#using-old-images

FROM quay.io/jupyter/minimal-notebook:b74418220768

LABEL maintainer="Collaboratory Platform <platform@humanbrainproject.eu>"

LABEL maintainer="Collaboratory Platform <platform@humanbrainproject.eu>"

ARG NB_USER="jovyan"

ARG NB_UID=1000

ARG NB_GID=100

ENV GIT_COMMITTER_NAME=platform@humanbrainproject.eu \

ENV GIT_COMMITTER_NAME=platform@humanbrainproject.eu \

    GIT_COMMITTER_EMAIL=platform@humanbrainproject.eu \

    GIT_COMMITTER_EMAIL=platform@humanbrainproject.eu \

    USER="${NB_USER}" \

    USER="${NB_USER}" \

RUN ln -sf /usr/share/zoneinfo/Europe/Zurich /etc/localtime

RUN ln -sf /usr/share/zoneinfo/Europe/Zurich /etc/localtime

# Set to noninteractive for install

# Set to noninteractive for install

ENV DEBIAN_FRONTEND noninteractive

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update --yes && \

RUN apt-get update --yes && \

    apt-get install --yes \

    apt-get install --yes \

    ca-certificates \

    cmake \

    csh \

    curl \

    cython \

    gcc \

    gcc \

    gettext \

    git \

    libnss-wrapper \

    llvm \

    lsof \

    mpich \

    pandoc \

    python-dev \

    python3-venv \

    python3-pip \

    r-base \

    r-base \

    swig \

    lsof \

    unzip \

    vim  && \

    vim  && \

    apt-get clean && rm -rf /var/lib/apt/lists/*

    apt-get clean && rm -rf /var/lib/apt/lists/*

# install nodejs

RUN curl -fsSL https://deb.nodesource.com/setup_17.x | bash

RUN apt-get install -y nodejs

# install min texlive (necessary for nb exports)

RUN apt-get update --yes && \

    apt-get install --yes --no-install-recommends \

    texlive-xetex \

    texlive-fonts-recommended \

    texlive-plain-generic && \

    apt-get clean && rm -rf /var/lib/apt/lists/*

# jupyter install in /opt/app-root/ for legacy reasons (previously based on centos base image)

# jupyter install in /opt/app-root/ for legacy reasons (previously based on centos base image)

RUN mkdir -p /opt/app-root/etc /opt/app-root/clb/ /opt/app-root/src

RUN mkdir -p /opt/app-root/etc /opt/app-root/clb/ /opt/app-root/src

COPY base/jupyter_notebook_config.py /opt/app-root/etc/

# folders for drive integration

# folders for drive integration

RUN mkdir -p /mnt/user/

RUN mkdir -p /mnt/user/

COPY base/requirements.txt /tmp

COPY base/requirements.txt /tmp

RUN pip install --no-cache-dir -r /tmp/requirements.txt

RUN pip install --no-cache-dir -r /tmp/requirements.txt

# fix missing template issue in nbgitpuller: https://github.com/jupyterhub/nbgitpuller/issues/235

# remove this once it has been fixed in project

RUN ln -s /usr/local/lib/python3.8/dist-packages/nbgitpuller/templates/status.html /usr/local/lib/python3.8/dist-packages/notebook/templates/

# disable ipcluster extension

# disable ipcluster extension

RUN jupyter labextension disable ipcluster \

RUN jupyter labextension disable ipcluster \

                              ipyparallel-labextension

                              ipyparallel-labextension

# install additional labextensions

# install additional labextensions (TODO: install with pip, if possible)

RUN jupyter labextension install --no-build \

RUN jupyter labextension install --no-build \

                             clb-jupyter-ext-query-params@3.2.0

                             clb-jupyter-ext-query-params-dev@3.2.0 \

                             clb-lab-extension@0.9.2

RUN jupyter lab build

RUN jupyter lab build

RUN jupyter notebook --generate-config

RUN jupyter notebook --generate-config

RUN mkdir -p /opt/app-root/src/.ipython/profile_default/startup/ /opt/app-root/src/.local/lib/python3.8/site-packages/ /tmp/cache/

RUN mkdir -p /opt/app-root/src/.ipython/profile_default/startup/ /tmp/cache/

# Preload clb_oauth

# Preload clb_oauth

RUN echo 'from clb_nb_utils import oauth as clb_oauth' >> /opt/app-root/src/.ipython/profile_default/startup/50-clb-nb-utils.py

RUN echo 'from clb_nb_utils import oauth as clb_oauth' >> /opt/app-root/src/.ipython/profile_default/startup/50-clb-nb-utils.py

# install R kernel

# install R kernel

RUN R --slave -e "install.packages('IRkernel')"

RUN R --slave -e "install.packages('IRkernel')"

RUN R --slave -e "IRkernel::installspec(name = 'ir363', displayname = 'R 3.6.3')"

RUN R --slave -e "IRkernel::installspec(name = 'ir', displayname = 'R 4.3.3')"

# disable core dumps

RUN echo "* - core 0" >> /etc/security/limits.conf

# fix permissions so NB_USER has permissions to run notebooks and install packages

# allow the script to fail (because of symlinks) without failing the build (TODO: fix)

COPY base/fix-permissions /usr/local/bin/fix-permissions

RUN sed -i 's/set -e/set +e/' $(which fix-permissions)

RUN chmod +x /usr/local/bin/fix-permissions

RUN fix-permissions /opt/app-root/ && \

RUN fix-permissions /opt/app-root/ && \

    fix-permissions /tmp/cache/ && \

    fix-permissions /tmp/cache/ && \

    fix-permissions /usr/local/share/jupyter/ && \

    fix-permissions /opt/conda/share/jupyter/ && \

    fix-permissions /usr/local/etc/jupyter && \

    fix-permissions /opt/conda/etc/jupyter && \

    fix-permissions /usr/local/lib/R/site-library && \

    fix-permissions /usr/local/lib/R/site-library

    fix-permissions /usr/etc/jupyter/

# to support OpenShift's arbitrary UIDs

# more info: https://docs.openshift.com/enterprise/3.1/creating_images/guidelines.html

COPY base/passwd.template /tmp/passwd.template

COPY base/group.template /tmp/group.template

COPY base/start-notebook.sh /opt/app-root/etc/

RUN chmod +x /opt/app-root/etc/start-notebook.sh

WORKDIR /opt/app-root/src/

COPY base/.spynnaker.cfg /opt/app-root/src/

EXPOSE 8080

WORKDIR /opt/app-root/src/

USER ${NB_UID}

USER ${NB_UID}

CMD /opt/app-root/etc/start-notebook.sh

#!/bin/sh

# source: https://github.com/sclorg/s2i-base-container/blob/master/core/root/usr/bin/fix-permissions

# Allow this script to fail without failing a build

set +e

SYMLINK_OPT=${2:--L}

# Fix permissions on the given directory or file to allow group read/write of

# regular files and execute of directories.

[ $(id -u) -ne 0 ] && CHECK_OWNER=" -uid $(id -u)"

# If argument does not exist, script will still exit with 0,

# but at least we'll see something went wrong in the log

if ! [ -e "$1" ] ; then

  echo "ERROR: File or directory $1 does not exist." >&2

  # We still want to end successfully

  exit 0

fi

find $SYMLINK_OPT "$1" ${CHECK_OWNER} \! -gid 0 -exec chgrp 0 {} +

find $SYMLINK_OPT "$1" ${CHECK_OWNER} \! -perm -g+rw -exec chmod g+rw {} +

find $SYMLINK_OPT "$1" ${CHECK_OWNER} -perm /u+x -a \! -perm /g+x -exec chmod g+x {} +

find $SYMLINK_OPT "$1" ${CHECK_OWNER} -type d \! -perm /g+x -exec chmod g+x {} +

# Always end successfully

exit 0

 No newline at end of file

nb_group:x:${GROUP_ID}:

nb_group_user:x:${USER_ID}:

 No newline at end of file

import os

port = int(os.environ.get('JUPYTER_NOTEBOOK_PORT', '8080'))

c.NotebookApp.ip = '0.0.0.0'

c.NotebookApp.port = port

c.NotebookApp.open_browser = False

c.NotebookApp.quit_button = False

c.WebPDFExporter.enabled = False

if os.environ.get('JUPYTERHUB_SERVICE_PREFIX'):

    c.NotebookApp.base_url = os.environ.get('JUPYTERHUB_SERVICE_PREFIX')

password = os.environ.get('JUPYTER_NOTEBOOK_PASSWORD')

if password:

    import notebook.auth

    c.NotebookApp.password = notebook.auth.passwd(password)

    del password

    del os.environ['JUPYTER_NOTEBOOK_PASSWORD']

image_config_file = '/opt/app-root/src/.jupyter/jupyter_notebook_config.py'

if os.path.exists(image_config_file):

    with open(image_config_file) as fp:

        exec(compile(fp.read(), image_config_file, 'exec'), globals())

root:x:0:0:root:/root:/bin/bash

bin:x:1:1:bin:/bin:/sbin/nologin

daemon:x:2:2:daemon:/sbin:/sbin/nologin

adm:x:3:4:adm:/var/adm:/sbin/nologin

lp:x:4:7:lp:/var/spool/lpd:/sbin/nologin

sync:x:5:0:sync:/sbin:/bin/sync

shutdown:x:6:0:shutdown:/sbin:/sbin/shutdown

halt:x:7:0:halt:/sbin:/sbin/halt

mail:x:8:12:mail:/var/spool/mail:/sbin/nologin

operator:x:11:0:operator:/root:/sbin/nologin

games:x:12:100:games:/usr/games:/sbin/nologin

ftp:x:14:50:FTP User:/var/ftp:/sbin/nologin

nobody:x:99:99:Nobody:/:/sbin/nologin

${USER}:x:${USER_ID}:${GROUP_ID}:${USER_DESCRIPTION}:${HOME}:/bin/bash

 No newline at end of file

beautifulsoup4==4.10.0

git+https://github.com/HumanBrainProject/clb-nb-utils.git

bluepyopt==1.11.5

ipympl==0.8.8

bokeh==2.4.2

ipywidgets==7.7.0

Cython==0.29.26

jupyterlab==3.4.8

cffi==1.14.5

jupyterlab-git==0.44.0

cryptography==36.0.1

ebrains-drive==0.4.0

elephant==0.10.0

h5py==3.6.0

ipympl==0.8.5

ipywidgets==7.6.5

jupyterlab-widgets==1.0.2

jupyterlab-topbar==0.6.1

jupyterlab-system-monitor==0.8.0

jupyterlab-system-monitor==0.8.0

jupyterhub==1.5.0

jupyterlab-topbar==0.6.1

jupyterlab==3.2.8

jupyterlab-widgets==1.1.11

jupyterlab-git==0.34.1

nbdime==3.2.1

jupyter-server==1.13.5

nbgitpuller==1.2.2

lazyarray==0.5.1

lxml==4.7.1

matplotlib==3.5.1

mpi4py==3.1.3

nbdime==3.1.1

nbgitpuller==1.0.2

nbresuse==0.4.0

nbresuse==0.4.0

neo==0.10.0

neurom==3.1.0

nglview==3.0.3

nibabel==3.2.1

numba==0.54.1

numexpr==2.8.1

numpy==1.20.3

pandas==1.3.5

patsy==0.5.2

plotly==5.5.0

Pygments==2.11.2

python-swiftclient==3.13.0

PyJWT==2.3.0

pyunicore==0.9.13

requests-oauthlib==1.3.0

rise==5.7.1

rpy2==3.4.5

scikit-image==0.19.1

scikit-learn==1.0.2

scipy==1.7.3

seaborn==0.11.2

statsmodels==0.13.1

sympy==1.9

tvb-ext-unicore==0.1.3

vincent==0.4.4

widgetsnbextension==3.5.2

xlrd==2.0.1

git+https://github.com/HumanBrainProject/clb-nb-utils.git

#!/bin/bash

set -e

# to support OpenShift's arbitrary UIDs

# more info: https://docs.openshift.com/enterprise/3.1/creating_images/guidelines.html

export USER_ID=$(id -u)

export GROUP_ID=$(id -g)

export USER_DESCRIPTION="Notebook User"

envsubst < /tmp/passwd.template > /tmp/passwd

envsubst < /tmp/group.template > /tmp/group

export LD_PRELOAD=libnss_wrapper.so

export NSS_WRAPPER_PASSWD=/tmp/passwd

export NSS_WRAPPER_GROUP=/tmp/group

exec jupyter labhub --NotebookApp.default_url=/lab --config=/opt/app-root/etc/jupyter_notebook_config.py $@