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Commit f2eed8bd authored by Christof Kaufmann's avatar Christof Kaufmann
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Merge branch 'development' into 'master'

Update code-server, install git-lfs

See merge request !37
parents bdb34155 123b113d
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1 merge request!37Update code-server, install git-lfs
...@@ -12,15 +12,16 @@ USER root ...@@ -12,15 +12,16 @@ USER root
RUN apt-get update --yes && \ RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \ apt-get install --yes --no-install-recommends \
# general purpose utils # general purpose utils
iputils-ping \ git-lfs \
htop \ htop \
iputils-ping \
# R pre-requisites # R pre-requisites
fonts-dejavu \ fonts-dejavu \
unixodbc \ gcc \
unixodbc-dev \
r-cran-rodbc \
gfortran \ gfortran \
gcc && \ r-cran-rodbc \
unixodbc \
unixodbc-dev && \
apt-get clean && rm -rf /var/lib/apt/lists/* apt-get clean && rm -rf /var/lib/apt/lists/*
USER ${NB_UID} USER ${NB_UID}
...@@ -60,7 +61,7 @@ RUN mamba install --yes \ ...@@ -60,7 +61,7 @@ RUN mamba install --yes \
USER root USER root
# install code-server and extensions # install code-server and extensions
ENV CODE_VERSION=4.95.3 ENV CODE_VERSION=4.96.2
RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \ RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \
dpkg -i code-server_${CODE_VERSION}_amd64.deb && \ dpkg -i code-server_${CODE_VERSION}_amd64.deb && \
rm -f code-server_${CODE_VERSION}_amd64.deb && \ rm -f code-server_${CODE_VERSION}_amd64.deb && \
...@@ -80,7 +81,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do ...@@ -80,7 +81,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do
tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \ tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \
rm vscode_cli.tar.gz && \ rm vscode_cli.tar.gz && \
chown ${NB_USER} /usr/local/bin/code && \ chown ${NB_USER} /usr/local/bin/code && \
fix-permissions /usr/local/bin/code fix-permissions /usr/local/bin/code && \
# fix issue with permissions of /opt/conda/share/gdb/auto-load/opt
fix-permissions "${CONDA_DIR}"
# install some packages # install some packages
USER ${NB_UID} USER ${NB_UID}
...@@ -148,6 +151,8 @@ USER root ...@@ -148,6 +151,8 @@ USER root
# activate extensions by default # activate extensions by default
COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/" COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/"
COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyter-server/resource-usage/" COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyter-server/resource-usage/"
# source mamba.sh in bash using /etc/profile.d/conda.sh (workaround for removed mamba init --system, see https://github.com/mamba-org/mamba/issues/3691)
COPY conda.sh "/etc/profile.d/"
RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
# history search with Page Up/Down # history search with Page Up/Down
sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \ sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \
...@@ -162,6 +167,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -162,6 +167,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
mkdir -p /etc/skel/.cache && \ mkdir -p /etc/skel/.cache && \
cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \ cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \
# stuff # stuff
mkdir -p "/home/${NB_USER}/.conda" && \
cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \ cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \
# VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de # VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de
printf '%s\n' \ printf '%s\n' \
...@@ -173,8 +179,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -173,8 +179,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
' fi' \ ' fi' \
'done' \ 'done' \
>> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \ >> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \
# source mamba.sh in bash using /etc/profile.d/conda.sh
mamba init --system && \
chown -R ${NB_USER} "/home/${NB_USER}/.local" && \ chown -R ${NB_USER} "/home/${NB_USER}/.local" && \
fix-permissions "/home/${NB_USER}" && \ fix-permissions "/home/${NB_USER}" && \
fix-permissions "/etc/skel" fix-permissions "/etc/skel"
......
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/conda/bin/conda' 'shell.posix' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
. "/opt/conda/etc/profile.d/conda.sh"
else
export PATH="/opt/conda/bin:$PATH"
fi
fi
unset __conda_setup
if [ -f "/opt/conda/etc/profile.d/mamba.sh" ]; then
. "/opt/conda/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<
...@@ -12,12 +12,13 @@ USER root ...@@ -12,12 +12,13 @@ USER root
# general purpose utils # general purpose utils
RUN apt-get update --yes && \ RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \ apt-get install --yes --no-install-recommends \
iputils-ping \ git-lfs \
htop && \ htop \
iputils-ping && \
apt-get clean && rm -rf /var/lib/apt/lists/* apt-get clean && rm -rf /var/lib/apt/lists/*
# install code-server and extensions # install code-server and extensions
ENV CODE_VERSION=4.95.3 ENV CODE_VERSION=4.96.2
RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \ RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \
dpkg -i code-server_${CODE_VERSION}_amd64.deb && \ dpkg -i code-server_${CODE_VERSION}_amd64.deb && \
rm -f code-server_${CODE_VERSION}_amd64.deb && \ rm -f code-server_${CODE_VERSION}_amd64.deb && \
...@@ -35,7 +36,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do ...@@ -35,7 +36,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do
tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \ tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \
rm vscode_cli.tar.gz && \ rm vscode_cli.tar.gz && \
chown ${NB_USER} /usr/local/bin/code && \ chown ${NB_USER} /usr/local/bin/code && \
fix-permissions /usr/local/bin/code fix-permissions /usr/local/bin/code && \
# fix issue with permissions of /opt/conda/share/gdb/auto-load/opt
fix-permissions "${CONDA_DIR}"
# install some packages # install some packages
USER ${NB_UID} USER ${NB_UID}
...@@ -109,6 +112,8 @@ RUN pip install --no-cache-dir \ ...@@ -109,6 +112,8 @@ RUN pip install --no-cache-dir \
USER root USER root
# activate extensions by default # activate extensions by default
COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/" COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/"
# source mamba.sh in bash using /etc/profile.d/conda.sh (workaround for removed mamba init --system, see https://github.com/mamba-org/mamba/issues/3691)
COPY conda.sh "/etc/profile.d/"
RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
# history search with Page Up/Down # history search with Page Up/Down
sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \ sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \
...@@ -123,6 +128,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -123,6 +128,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
mkdir -p /etc/skel/.cache && \ mkdir -p /etc/skel/.cache && \
cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \ cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \
# stuff # stuff
mkdir -p "/home/${NB_USER}/.conda" && \
cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \ cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \
# VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de # VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de
printf '%s\n' \ printf '%s\n' \
...@@ -134,8 +140,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -134,8 +140,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
' fi' \ ' fi' \
'done' \ 'done' \
>> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \ >> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \
# source mamba.sh in bash using /etc/profile.d/conda.sh
mamba init --system && \
chown -R ${NB_USER} "/home/${NB_USER}/.local" && \ chown -R ${NB_USER} "/home/${NB_USER}/.local" && \
fix-permissions "/home/${NB_USER}" && \ fix-permissions "/home/${NB_USER}" && \
fix-permissions "/etc/skel" fix-permissions "/etc/skel"
......
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/conda/bin/conda' 'shell.posix' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
. "/opt/conda/etc/profile.d/conda.sh"
else
export PATH="/opt/conda/bin:$PATH"
fi
fi
unset __conda_setup
if [ -f "/opt/conda/etc/profile.d/mamba.sh" ]; then
. "/opt/conda/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<
...@@ -12,12 +12,13 @@ USER root ...@@ -12,12 +12,13 @@ USER root
# general purpose utils # general purpose utils
RUN apt-get update --yes && \ RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \ apt-get install --yes --no-install-recommends \
iputils-ping \ git-lfs \
htop && \ htop \
iputils-ping && \
apt-get clean && rm -rf /var/lib/apt/lists/* apt-get clean && rm -rf /var/lib/apt/lists/*
# install code-server and extensions # install code-server and extensions
ENV CODE_VERSION=4.95.3 ENV CODE_VERSION=4.96.2
RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \ RUN wget --no-hsts -q https://github.com/coder/code-server/releases/download/v$CODE_VERSION/code-server_${CODE_VERSION}_amd64.deb && \
dpkg -i code-server_${CODE_VERSION}_amd64.deb && \ dpkg -i code-server_${CODE_VERSION}_amd64.deb && \
rm -f code-server_${CODE_VERSION}_amd64.deb && \ rm -f code-server_${CODE_VERSION}_amd64.deb && \
...@@ -35,7 +36,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do ...@@ -35,7 +36,9 @@ RUN wget --no-hsts -q -O vscode_cli.tar.gz 'https://code.visualstudio.com/sha/do
tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \ tar -xf vscode_cli.tar.gz --directory /usr/local/bin && \
rm vscode_cli.tar.gz && \ rm vscode_cli.tar.gz && \
chown ${NB_USER} /usr/local/bin/code && \ chown ${NB_USER} /usr/local/bin/code && \
fix-permissions /usr/local/bin/code fix-permissions /usr/local/bin/code && \
# fix issue with permissions of /opt/conda/share/gdb/auto-load/opt
fix-permissions "${CONDA_DIR}"
# install some packages # install some packages
# NOTE: without --no-update-deps somehow an undefined symbol error in /opt/conda/lib/python3.11/lib-dynload/_sqlite3.cpython-311-x86_64-linux-gnu.so occurs, which crashes jupyter lab. # NOTE: without --no-update-deps somehow an undefined symbol error in /opt/conda/lib/python3.11/lib-dynload/_sqlite3.cpython-311-x86_64-linux-gnu.so occurs, which crashes jupyter lab.
...@@ -109,6 +112,8 @@ RUN conda install --yes --no-update-deps \ ...@@ -109,6 +112,8 @@ RUN conda install --yes --no-update-deps \
USER root USER root
# activate extensions by default # activate extensions by default
COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/" COPY plugin.jupyterlab-settings "/home/${NB_USER}/.jupyter/lab/user-settings/@jupyterlab/extensionmanager-extension/"
# source mamba.sh in bash using /etc/profile.d/conda.sh (workaround for removed mamba init --system, see https://github.com/mamba-org/mamba/issues/3691)
COPY conda.sh "/etc/profile.d/"
RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
# history search with Page Up/Down # history search with Page Up/Down
sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \ sed -i "s/^# \(.*history-search.*\)/\1/" /etc/inputrc && \
...@@ -123,6 +128,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -123,6 +128,7 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
mkdir -p /etc/skel/.cache && \ mkdir -p /etc/skel/.cache && \
cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \ cp -r "/home/${NB_USER}/.cache/matplotlib" /etc/skel/.cache/ && \
# stuff # stuff
mkdir -p "/home/${NB_USER}/.conda" && \
cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \ cp -r "/home/${NB_USER}/.conda" "/home/${NB_USER}/.config" "/home/${NB_USER}/.jupyter" /etc/skel/ && \
# VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de # VS Code extension "gitlab-workflow", default gitlab server: gitlab.cvh-server.de
printf '%s\n' \ printf '%s\n' \
...@@ -134,8 +140,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \ ...@@ -134,8 +140,6 @@ RUN chown -R ${NB_USER} "/home/${NB_USER}/.jupyter" && \
' fi' \ ' fi' \
'done' \ 'done' \
>> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \ >> /usr/local/bin/start-notebook.d/fix-gitlab-server.sh && \
# source mamba.sh in bash using /etc/profile.d/conda.sh
mamba init --system && \
chown -R ${NB_USER} "/home/${NB_USER}/.local" && \ chown -R ${NB_USER} "/home/${NB_USER}/.local" && \
fix-permissions "/home/${NB_USER}" && \ fix-permissions "/home/${NB_USER}" && \
fix-permissions "/etc/skel" fix-permissions "/etc/skel"
......
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/conda/bin/conda' 'shell.posix' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
. "/opt/conda/etc/profile.d/conda.sh"
else
export PATH="/opt/conda/bin:$PATH"
fi
fi
unset __conda_setup
if [ -f "/opt/conda/etc/profile.d/mamba.sh" ]; then
. "/opt/conda/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<
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