Merge pull request #6 from carbonplan/repo2docker_tmp

add dockerfile and build.yaml

.github/workflows/build.yaml

@@ -0,0 +1,47 @@
+
+
+name: Build and push container image
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test-build:
+    runs-on: ubuntu-latest
+
+    steps:
+
+
+    # For biggish images, github actions runs out of disk space.
+    # So we cleanup some unwanted things in the disk image, and reclaim that space for our docker use
+    # https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150
+    # and https://github.com/easimon/maximize-build-space/blob/b4d02c14493a9653fe7af06cc89ca5298071c66e/action.yml#L104
+    # This gives us a total of about 52G of free space, which should be enough for now
+    - name: cleanup disk space
+      run: |
+        sudo rm -rf /usr/local/lib/android /usr/share/dotnet /opt/ghc
+        df -h
+
+    - name: Set Environment Variables
+      run: |
+
+        echo "DATE_TAG=$(TZ='America/Seattle' date +'%Y.%m.%d')" >> "$GITHUB_ENV"
+
+    - name: Checkout files in repo
+      uses: actions/checkout@main
+
+    - name: Build and push the image to quay.io ${{ matrix.environment }}
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        # Make sure username & password/token pair matches your registry credentials
+        DOCKER_USERNAME: ${{ secrets.QUAY_USERNAME }}
+        DOCKER_PASSWORD: ${{ secrets.QUAY_PASSWORD }}
+        DOCKER_REGISTRY: "quay.io"
+        ADDITIONAL_TAG: ${{ env.DATE_TAG }}
+        # Disable pushing a 'latest' tag, as this often just causes confusion
+        # LATEST_TAG_OFF: true
+
+        IMAGE_NAME: "carbonplan/aglime-swap-cdr"

Dockerfile

@@ -0,0 +1,62 @@
+# FROM quay.io/nebari/nebari-jupyterlab:2024.3.2
+# Trying to build off a sort minimal jupyter image. This gives us the ability to run notebooks.
+# Is this something the average crunchtope user would want?
+
+# FROM quay.io/jupyter/minimal-notebook
+# this fails on the coiled deployment b/c distribued is missing:
+
+FROM quay.io/jupyter/scipy-notebook
+
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    gfortran \
+    gcc \
+    g++ \
+    # git \ # should be covered by base
+    make \
+    # python3 \ # should be covered by base
+    # python3-pip \ # should be covered by base
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+ENV PETSC_DIR=/opt/petsc-3.15.5
+ENV PETSC_ARCH=linux-gnu-opt
+ENV PATH=$PATH:/opt/crunch/source
+
+WORKDIR /opt
+RUN wget https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.15.5.tar.gz \
+    && tar -xzf petsc-3.15.5.tar.gz \
+    && cd petsc-3.15.5 \
+    && ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --with-mpi=0 --with-debugging=0 --with-shared-libraries=0 --with-x=0 PETSC_ARCH=linux-gnu-opt \
+    && make PETSC_DIR=/opt/petsc-3.15.5 PETSC_ARCH=linux-gnu-opt all \
+    && rm /opt/petsc-3.15.5.tar.gz \
+    && make PETSC_DIR=/opt/petsc-3.15.5 PETSC_ARCH=linux-gnu-opt check
+
+# Clone and build CrunchFlow
+WORKDIR /opt
+RUN git clone https://bitbucket.org/crunchflow/crunchtope-dev.git \
+    && mkdir -p /opt/crunch \
+    && mv crunchtope-dev/source /opt/crunch/ \
+    && cd /opt/crunch/source \
+    && make
+
+# Clean up
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Set up permissions for the default Jupyter user
+RUN mkdir -p /home/jovyan/work && \
+    chown -R 1000:100 /home/jovyan && \
+    chmod -R 775 /home/jovyan
+
+# Set working directory
+WORKDIR /home/jovyan/work
+
+# Ensure the PATH is updated for all users
+ENV PATH=$PATH:/opt/crunch/source
+
+# Switch back to the default Jupyter user
+USER 1000