Update cube-in-box to install the latest version of deafrica-tools (#9)

.gitignore

@@ -19,3 +19,5 @@ notebooks/.python_history
 .env
 data
 __pycache__
+**/.idea/
+**/core

Dockerfile

@@ -1,35 +1,109 @@
-FROM osgeo/gdal:ubuntu-full-3.4.2
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.8.5
 
 ENV DEBIAN_FRONTEND=noninteractive \
     LC_ALL=C.UTF-8 \
     LANG=C.UTF-8 \
+    USE_PYGEOS=0 \
+    SPATIALITE_LIBRARY_PATH='mod_spatialite.so' \
+    SHELL=bash \
     TINI_VERSION=v0.19.0
 
 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
 RUN chmod +x /tini
 
-RUN apt-get update && \
-    apt-get install -y \
-      build-essential \
-      git \
-      # For Psycopg2
-      libpq-dev python3-dev \
-      python3-pip \
-      wget \
-    && apt-get autoclean \
-    && apt-get autoremove \
-    && rm -rf /var/lib/{apt,dpkg,cache,log}
+RUN apt update \
+  && apt install -y curl \
+  && curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
+  && apt update \
+  && apt install -y --fix-missing --no-install-recommends \
+    python3-full \
+    python3-dev \
+    python3-venv \
+    python3-pip \
+    # developer convenience
+    file \
+    fish \
+    git \
+    graphviz \
+    htop \
+    iproute2 \
+    iputils-ping \
+    jq \
+    less \
+    libtiff-tools \
+    net-tools \
+    openssh-client \
+    postgresql \
+    postgresql-client \
+    rsync \
+    simpleproxy \
+    sudo \
+    tig \
+    time \
+    tmux \
+    unzip \
+    vim \
+    wget \
+    xz-utils \
+    zip  \
+    # rgsislib dependencies
+    libboost-date-time1.74.0 \
+    libboost-dev \
+    libboost-filesystem1.74.0 \
+    libboost-system1.74.0 \
+    libcgal-dev \
+    libgeos-dev \
+    libgsl-dev \
+    libmuparser2v5 \
+    libpq-dev \
+    libproj-dev \
+    # for cython to work need compilers
+    build-essential \
+    # for pyRAT install or something
+    libfftw3-dev \
+    liblapack-dev \
+    # install libhdf5
+    libhdf5-dev \
+    # install ffmpeg the normal way
+    ffmpeg \
+    nodejs \
+    # install texlive
+    texlive-fonts-recommended \
+    texlive-plain-generic\
+    texlive-xetex \
+    # Spatialite support
+    libsqlite3-mod-spatialite \
+  && apt clean autoclean \
+  && apt autoremove \
+  && rm -rf /var/lib/{apt,dpkg,cache}
+
+# Install yq
+RUN wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O /usr/bin/yq &&\
+    chmod +x /usr/bin/yq
+
+# install pandoc 3.4.1
+RUN wget https://github.com/jgm/pandoc/releases/download/3.4/pandoc-3.4-1-amd64.deb
+RUN dpkg -i pandoc-3.4-1-amd64.deb
+RUN rm pandoc-3.4-1-amd64.deb
+
+# Set up the python virtual environment PEP 668.
+ENV VIRTUAL_ENV=/opt/venv
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
 COPY requirements.txt /conf/
-RUN pip3 install --no-cache-dir --requirement /conf/requirements.txt
 
-RUN cd /tmp \
-  && git clone --depth 1 https://github.com/digitalearthafrica/deafrica-sandbox-notebooks.git \
-  && pip install deafrica-sandbox-notebooks/Tools \
-  && rm -rf /tmp/deafrica-sandbox-notebooks
+RUN python -m pip install --upgrade pip pip-tools
+RUN pip install --no-cache-dir --requirement /conf/requirements.txt
+
+RUN jupyter server extension enable --py --sys-prefix jupyterlab_iframe jupyter_resource_usage
+
+ENV JUPYTERLAB_DIR=$VIRTUAL_ENV/share/jupyter/lab
+COPY assets/overrides.json $JUPYTERLAB_DIR/settings/
+COPY assets/jupyter_lab_config.py /etc/jupyter/
 
 WORKDIR /notebooks
 
 ENTRYPOINT ["/tini", "--"]
+CMD ["jupyter",  "lab", "--allow-root",  "--ip=0.0.0.0", "--no-browser",  "--port=8888"]
 
-CMD ["jupyter", "notebook", "--allow-root", "--ip='0.0.0.0'", "--NotebookApp.token='secretpassword'"]