Adding docker resources

.github/workflows/build-and-push-jupyterlab-image.yml

@@ -0,0 +1,44 @@
+name: build-and-push-jupyterlab-image
+
+on:
+  workflow_dispatch:  # This allows you to manually trigger the action from GitHub UI.
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Checkout
+        uses: actions/[email protected]
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/[email protected]
+
+      - name: Login to dockerhub 
+        uses: docker/[email protected]
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Get lowercase repo name (for dynamic tags)
+        id: repo_name  
+        run: |
+          lowercase_name=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]')
+          echo "::set-output name=repo_name::${lowercase_name}"
+        
+      - name: Build and push latest
+        id: docker_build_jupyterlab
+        uses: docker/[email protected]
+        with:
+          context: docker/jupyterlab
+          file: docker/jupyterlab/Dockerfile
+          builder: ${{ steps.buildx.outputs.name }}
+          push: true
+          tags: |
+            esiil/${{ steps.repo_name.outputs.repo_name }}_jupyterlab:latest
+     
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

docker/jupyterlab/Dockerfile

@@ -0,0 +1,136 @@
+FROM jupyter/r-notebook:hub-4.0.1 
+
+USER root
+
+# Set up package manager
+RUN apt-get install -y apt-transport-https && \
+    apt-get clean && apt-get update && apt-get install -y software-properties-common && \
+    add-apt-repository multiverse && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install some base software
+RUN apt-get update --yes && \
+    apt-get install --yes \
+    fonts-dejavu \
+    unixodbc \
+    unixodbc-dev \
+    r-base \
+    r-cran-rodbc && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Add sudo to jovyan user
+RUN apt update && \
+    apt install -y sudo && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# This is where we can control which root permissions the jovyan user will have
+ARG PRIV_CMDS='/bin/ch*,/bin/cat,/bin/gunzip,/bin/tar,/bin/mkdir,/bin/ps,/bin/mv,/bin/cp,/usr/bin/apt*,/usr/bin/pip*,/bin/yum,/opt,/opt/conda/bin/*,/usr/bin/*'
+
+RUN usermod -aG sudo jovyan && \
+    echo "$LOCAL_USER ALL=NOPASSWD: $PRIV_CMDS" >> /etc/sudoers
+RUN addgroup jovyan
+RUN usermod -aG jovyan jovyan
+
+# Install RStudio
+RUN apt-get update && apt-get install --yes gdebi-core && \
+    wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.09.1-494-amd64.deb && \
+    gdebi -n rstudio-server-2023.09.1-494-amd64.deb && \
+    rm rstudio-server-2023.09.1-494-amd64.deb && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install Geospatial libraries
+RUN apt-get update && \
+    apt install -y \
+    gdal-bin \
+    lbzip2 \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgsl0-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libhdf4-alt-dev \
+    libhdf5-dev \
+    libjq-dev \
+    libpq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    libsqlite3-dev \
+    libudunits2-dev \
+    lsb-release \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    libfmt-dev \
+    unixodbc-dev && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Fix RStudio / Conda openssl version mismatch
+RUN wget https://www.openssl.org/source/openssl-3.2.0.tar.gz && \
+    tar xfz openssl-3.2.0.tar.gz && \
+    mkdir openssl-build && cd openssl-build && \
+    ../openssl-3.2.0/Configure --libdir=/lib/x86_64-linux-gnu/ && \
+    make && \
+    make install
+
+# Update permissions for /opt/conda
+RUN mkdir /usr/local/bin/start-notebook.d && \
+    chown -R jovyan:users /opt/conda/share /usr/local/share /usr/local/bin/start-notebook.d 
+
+USER jovyan
+
+# Install jupyterlab and rstudio dependencies
+RUN conda install -c conda-forge \ 
+    jupyter_client \ 
+    jupyter_core \ 
+    jupyterlab_server \ 
+    jupyter_server \
+    r-rgl \
+    r-htmlwidgets \
+    r-htmltools && \ 
+    jupyter lab clean
+
+# reinstall R packages. Here is where you add any new R packages you would like to install 
+RUN mamba install --quiet --yes \
+    r-base \
+    r-tidyverse \
+    r-terra \
+    r-future \
+    r-future.apply \
+    r-furrr \
+    && \ 
+    mamba clean --all -f -y
+
+# Install Jupyter Lab Proxy extensions (cards in Launcher)
+RUN pip install jupyter-rsession-proxy jupyter-server-proxy jupyter-shiny-proxy jupyterlab-git 
+
+# Install Mamba Gator package manager
+RUN rm -f ~/.jupyter/lab/workspaces/default* && \
+    mamba install -y -c conda-forge mamba_gator
+
+# Install and configure jupyter lab 
+COPY jupyter_notebook_config.json /opt/conda/etc/jupyter/jupyter_notebook_config.json
+
+# Rebuild the Jupyter Lab with new tools
+RUN jupyter lab build
+
+# Build Conda environment. Any packages you would like to install with conda need to be added to the environment.yml file in this Dockerfiles directory
+RUN conda update -y conda && \
+    conda config --remove channels conda-forge && \
+    conda config --add channels conda-forge
+WORKDIR /home/jovyan
+COPY environment.yml /home/jovyan/ 
+RUN mamba env create -f /home/jovyan/environment.yml
+RUN . /opt/conda/etc/profile.d/conda.sh && conda deactivate && conda activate custom && python -m ipykernel install --name custom && pip install jupyter_contrib_nbextensions
+
+# Install R packages from CRAN and GitHub
+RUN R -e "remotes::install_github('tomroh/ecoregions')"
+RUN R -e "install.packages('mblm', repos='http://cran.rstudio.com/')"
+
+# Set any required environment variables 
+ENV PROJ_LIB=/opt/conda/envs/custom/share/proj
+RUN echo "PROJ_LIB=/opt/conda/envs/custom/share/proj" > /home/jovyan/.Renviron

docker/jupyterlab/environment.yml

@@ -0,0 +1,40 @@
+name: custom
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.10
+
+  - pip:
+      - affine==2.4.0
+      - aiosignal==1.3.1
+      - appdirs==1.4.4
+      - attrs==23.1.0
+      - certifi==2023.7.22
+      - charset-normalizer==3.1.0
+      - click==8.1.3
+      - click-plugins==1.1.1
+      - cligj==0.7.2
+
+  # Core scientific python
+  - numpy
+  - matplotlib
+  - rioxarray
+  - geopandas
+  - gdal
+
+  # Jupyter Lab Environment & Kernel
+  - papermill
+  - autopep8
+  - jupyterlab
+  - notebook
+  - ipython
+  - nbclean
+  - nbresuse
+  - jupyterlab-geojson
+  - nb_conda_kernels
+  - ipykernel
+
+  # openssh because openssl bin path is in conda now for Rstudio issue
+  - openssh  

docker/jupyterlab/jupyter_notebook_config.json

@@ -0,0 +1,11 @@
+{
+    "NotebookApp": {
+      "allow_origin" : "*",
+        "token":"",
+        "password":"",
+      "nbserver_extensions": {
+        "jupyterlab": true,
+        "mamba_gator": true
+      }
+    }
+  }