added tools

Dockerfile

@@ -1,8 +1,12 @@
 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.
 
@@ -97,8 +101,8 @@ RUN mkdir "/home/${NB_USER}/work" && \
 # Correct permissions
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
-RUN sleep 120
+
-COPY --chown="${NB_UID}:${NB_GID}" ./jupyterlab-datascience-gpu/initial-condarc "${CONDA_DIR}/.condarc"
+COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
 WORKDIR /tmp
 RUN set -x && \
     arch=$(uname -m) && \
@@ -139,8 +143,138 @@ 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>"
 
 
@@ -183,4 +317,50 @@ RUN git clone https://github.com/Syllo/nvtop.git /run/nvtop && \
 
 RUN fix-permissions /home/$NB_USER
 
-USER $NB_UID
+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"
+
+# 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
+
+# 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/